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Conserved domains on  [gi|20150826]
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Protein Classification

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List of domain hits

Name Accession Description Interval E-value
IgC_beta2m cd05770
Class I major histocompatibility complex (MHC) beta2-microglobulin. IgC_beta2m: ...
4-96 9.65e-57

Class I major histocompatibility complex (MHC) beta2-microglobulin. IgC_beta2m: Immunoglobulin-like domain in beta2-Microglobulin (beta2m). Beta2m is the non-covalently bound light chain of the human class I major histocompatibility complex (MHC-I). Beta2m is structured as a beta-sandwich domain composed of two facing beta-sheets (four stranded and three stranded), that is typical of the C-type immunoglobulin superfamily. This structure is stabilized by an intramolecular disulfide bridge connecting two Cys residues in the facing beta -sheets. In vivo, MHC-I continuously exposes beta2m on the cell surface, where it may be released to plasmatic fluids, transported to the kidneys, degraded and then excreted.


:

Pssm-ID: 143247  Cd Length: 93  Bit Score: 169.97  E-value: 9.65e-57
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20150826  4 TPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVK 83
Cdd:cd05770  1 TPKVQVYSRFPAENGKPNVLNCYVTGFHPPDIEIRLLKNGVKIPKVEQSDLSFSKDWTFYLLKSTEFTPTKGDEYACRVR 80
                       90
               ....*....|...
gi 20150826 84 HDSMAEPKTVYWD 96
Cdd:cd05770 81 HNSMSEPKKYKWD 93
 
Name Accession Description Interval E-value
IgC_beta2m cd05770
Class I major histocompatibility complex (MHC) beta2-microglobulin. IgC_beta2m: ...
4-96 9.65e-57

Class I major histocompatibility complex (MHC) beta2-microglobulin. IgC_beta2m: Immunoglobulin-like domain in beta2-Microglobulin (beta2m). Beta2m is the non-covalently bound light chain of the human class I major histocompatibility complex (MHC-I). Beta2m is structured as a beta-sandwich domain composed of two facing beta-sheets (four stranded and three stranded), that is typical of the C-type immunoglobulin superfamily. This structure is stabilized by an intramolecular disulfide bridge connecting two Cys residues in the facing beta -sheets. In vivo, MHC-I continuously exposes beta2m on the cell surface, where it may be released to plasmatic fluids, transported to the kidneys, degraded and then excreted.


Pssm-ID: 143247  Cd Length: 93  Bit Score: 169.97  E-value: 9.65e-57
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20150826  4 TPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVK 83
Cdd:cd05770  1 TPKVQVYSRFPAENGKPNVLNCYVTGFHPPDIEIRLLKNGVKIPKVEQSDLSFSKDWTFYLLKSTEFTPTKGDEYACRVR 80
                       90
               ....*....|...
gi 20150826 84 HDSMAEPKTVYWD 96
Cdd:cd05770 81 HNSMSEPKKYKWD 93
C1-set pfam07654
Immunoglobulin C1-set domain.
7-87 1.86e-31

Immunoglobulin C1-set domain.


Pssm-ID: 369453  Cd Length: 85  Bit Score: 105.41  E-value: 1.86e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20150826    7 IQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPK-VEMSDMSFSKDWSFYILAHTEFTPT---ETDTYACRV 82
Cdd:pfam07654  1 VYVFPPSPEELGKPNTLTCLVTGFYPPDITVTWLKNGQEVTEgVTTTPPSPNSDWTYQLSSYLTVTPSdweSGDTYTCRV 80

                 ....*
gi 20150826   83 KHDSM 87
Cdd:pfam07654 81 EHEGL 85
IGc1 smart00407
Immunoglobulin C-Type;
20-90 2.22e-22

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 82.36  E-value: 2.22e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 20150826    20 PNILNCYVTQFHPPHIEIQMLKNGKKIP-KVEMSDMSFSKDWSFYILAHTEF---TPTETDTYACRVKHDSMAEP 90
Cdd:smart00407  1 KATLVCLVSGFYPPDITVTWLRNGQEVTeGVSTTDPLKNSDGTYFLSSYLTVpasTWESGDVYTCQVTHEGLKEP 75
 
Name Accession Description Interval E-value
IgC_beta2m cd05770
Class I major histocompatibility complex (MHC) beta2-microglobulin. IgC_beta2m: ...
4-96 9.65e-57

Class I major histocompatibility complex (MHC) beta2-microglobulin. IgC_beta2m: Immunoglobulin-like domain in beta2-Microglobulin (beta2m). Beta2m is the non-covalently bound light chain of the human class I major histocompatibility complex (MHC-I). Beta2m is structured as a beta-sandwich domain composed of two facing beta-sheets (four stranded and three stranded), that is typical of the C-type immunoglobulin superfamily. This structure is stabilized by an intramolecular disulfide bridge connecting two Cys residues in the facing beta -sheets. In vivo, MHC-I continuously exposes beta2m on the cell surface, where it may be released to plasmatic fluids, transported to the kidneys, degraded and then excreted.


Pssm-ID: 143247  Cd Length: 93  Bit Score: 169.97  E-value: 9.65e-57
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20150826  4 TPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVK 83
Cdd:cd05770  1 TPKVQVYSRFPAENGKPNVLNCYVTGFHPPDIEIRLLKNGVKIPKVEQSDLSFSKDWTFYLLKSTEFTPTKGDEYACRVR 80
                       90
               ....*....|...
gi 20150826 84 HDSMAEPKTVYWD 96
Cdd:cd05770 81 HNSMSEPKKYKWD 93
C1-set pfam07654
Immunoglobulin C1-set domain.
7-87 1.86e-31

Immunoglobulin C1-set domain.


Pssm-ID: 369453  Cd Length: 85  Bit Score: 105.41  E-value: 1.86e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20150826    7 IQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPK-VEMSDMSFSKDWSFYILAHTEFTPT---ETDTYACRV 82
Cdd:pfam07654  1 VYVFPPSPEELGKPNTLTCLVTGFYPPDITVTWLKNGQEVTEgVTTTPPSPNSDWTYQLSSYLTVTPSdweSGDTYTCRV 80

                 ....*
gi 20150826   83 KHDSM 87
Cdd:pfam07654 81 EHEGL 85
IgC_MHC_II_alpha cd05767
Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain. ...
4-96 7.94e-24

Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain. IgC_MHC_II_alpha: Immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II alpha chain. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. In both humans and in mice these molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), for example on B-lymphocytes, monocytes, and macrophages. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from protelytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 143244  Cd Length: 94  Bit Score: 86.63  E-value: 7.94e-24
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20150826  4 TPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPK-VEMSDMSFSKDWSFYILAHTEFTPTETDTYACRV 82
Cdd:cd05767  1 PPEVTVFSLKPVELGEPNTLICFVDNFFPPVLNVTWLKNGVPVTDgVSETRYYPRQDLSFQKFSYLNFTPEEGDIYSCIV 80
                       90
               ....*....|....
gi 20150826 83 KHDSMAEPKTVYWD 96
Cdd:cd05767 81 EHWGLETPATRYWE 94
IGc1 smart00407
Immunoglobulin C-Type;
20-90 2.22e-22

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 82.36  E-value: 2.22e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 20150826    20 PNILNCYVTQFHPPHIEIQMLKNGKKIP-KVEMSDMSFSKDWSFYILAHTEF---TPTETDTYACRVKHDSMAEP 90
Cdd:smart00407  1 KATLVCLVSGFYPPDITVTWLRNGQEVTeGVSTTDPLKNSDGTYFLSSYLTVpasTWESGDVYTCQVTHEGLKEP 75
IgC_MHC_II_beta cd05766
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain. ...
5-96 1.49e-19

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain. IgC_MHC_II_beta: Immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II beta chain. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. In both humans and in mice these molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), for example on B-lymphocytes, monocytes, and macrophages. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from protelytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 143243  Cd Length: 94  Bit Score: 75.90  E-value: 1.49e-19
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20150826  5 PQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPK-VEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVK 83
Cdd:cd05766  1 PSVKISPSQTGSLSHPHLLVCHVWGFYPPEITVKWFKNGQEETEgVVSTELIPNGDWTYQILVMLETTPSRGDTYTCVVE 80
                       90
               ....*....|...
gi 20150826 84 HDSMAEPKTVYWD 96
Cdd:cd05766 81 HSSLQEPLTVDWR 93
IgC_MHC_I_alpha3 cd07698
Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain. ...
5-96 8.80e-14

Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain. IgC_MHC_I_alpha3; Immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class I alpha chain. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta2 microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 143322  Cd Length: 93  Bit Score: 61.15  E-value: 8.80e-14
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20150826  5 PQIQVYSRHPPENGKPniLNCYVTQFHPPHIEIQMLKNGK-KIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVK 83
Cdd:cd07698  3 PEVRVTRKRAPDGSLT--LSCHATGFYPRDIEVTWLRDGEdSVDDVESGEILPNGDGTYQLWVTLEVPPEDKARYSCRVE 80
                       90
               ....*....|...
gi 20150826 84 HDSMAEPKTVYWD 96
Cdd:cd07698 81 HSGLKEPLIVPWE 93
IgC cd00098
Immunoglobulin Constant (IgC) domain. Members of the IgC family are components of ...
8-96 7.93e-13

Immunoglobulin Constant (IgC) domain. Members of the IgC family are components of immunoglobulin, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and Major Histocompatibility Complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IgV) and one or more IgC domains. These names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. The IgV domain is responsible for antigen binding, and the IgC domain is involved in oligomerization and molecular interactions.


Pssm-ID: 319274  Cd Length: 95  Bit Score: 58.61  E-value: 7.93e-13
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20150826  8 QVYSRHPPEN-GKPNILNCYVTQFHPPHIEIQMLKNGKKIP-KVEMSDMSFSKDWSFYILAHTEFTPTETD---TYACRV 82
Cdd:cd00098  2 TLLPPSPEEKlGGTVTLVCLVSGFYPKDITVTWLKNGKEVTsGVSTTPPTKNSDGTFSVTSYLTVPPSDWDegtTYTCEV 81
                       90
               ....*....|....
gi 20150826 83 KHDSMAEPKTVYWD 96
Cdd:cd00098 82 SHESLSQPVSKSLN 95
IgC_CH3_IgAGD_CH4_IgAEM cd05768
CH4 domain (fourth constant Ig domain of the heavy chain) in immunoglobulin. ...
8-86 2.31e-05

CH4 domain (fourth constant Ig domain of the heavy chain) in immunoglobulin. IgC_CH3_IgAGD_CH4_IgAEM: Contains the third and fourth immunoglobulin constant domain (IgC) of alpha, delta, gamma and alpha, epsilon, and mu heavy chains, respectively. This domain is found on the Fc fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma and mu, all consisting of a variable domain (VH) and three (in alpha, delta and gamma) or four (in epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns.


Pssm-ID: 319312  Cd Length: 100  Bit Score: 39.60  E-value: 2.31e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20150826   8 QVYSRHPPE---NGKPNILNCYVTQFHPPHIEIQMLKNGKKIPK---------VEMSDMSFSkdwSFYILAHTEFTPTET 75
Cdd:cd05768   2 SVYLLPPPEeelSLNTVTLTCLVKGFSPEDIFVRWLQNGQPLPEedyktttpvKEESDGSFF---VYSKLTVTASDWKSG 78
                        90
                ....*....|.
gi 20150826  76 DTYACRVKHDS 86
Cdd:cd05768  79 DVFSCVVGHEA 89
IgC_Tapasin_R cd05771
Tapasin-R immunoglobulin-like domain. IgC_Tapasin_R: Immunoglobulin-like domain on Tapasin-R. ...
1-93 1.24e-03

Tapasin-R immunoglobulin-like domain. IgC_Tapasin_R: Immunoglobulin-like domain on Tapasin-R. Tapasin is a V-C1 (variable-constant) immunoglobulin superfamily molecule present in the endoplasmic reticulum (ER), where it links MHC class I molecules to the transporter associated with antigen processing (TAP). Tapasin-R is a tapasin-related protein that contains similar structural motifs to Tapasin, with some marked differences, especially in the V domain, transmembrane and cytoplasmic regions. The majority of Tapasin-R is located within the ER; however, there may be some expression of Tapasin-R at the cell surface. Tapasin-R lacks an obvious ER retention signal.


Pssm-ID: 319313  Cd Length: 138  Bit Score: 35.58  E-value: 1.24e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20150826   1 IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEI--QMLKNGKKIPKVEMSDMSFS-----KDWSFYILAHTEFTPT 73
Cdd:cd05771  35 VSEPPRVRLSLEKTVSIEEPQTLICHIAGYYPLDVQVewTREPPGDSPPRVSVSNVSFSshrqhADGTYSLSSALTLEPG 114
                        90       100
                ....*....|....*....|...
gi 20150826  74 ET---DTYACRVKHDSMAEPKTV 93
Cdd:cd05771 115 TPhpgATYTCRVTHVALETPVSV 137
IgC_CH2_IgE cd05847
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin E (IgE). ...
23-84 2.76e-03

CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin E (IgE). IgC_CH2_IgE: The second constant domain of the heavy chain of immunoglobulin E (IgE). The basic structure of immunoglobulin (Ig) molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) and three (in alpha, delta, and gamma) or four (in epsilon and mu) constant domains (CH1 to CH4). The different classes of antibodies vary in their heavy chains; the IgE class has the epsilon type. This domain (Cepsilon2) of IgE is in place of the flexible hinge region found in IgG.


Pssm-ID: 143255  Cd Length: 94  Bit Score: 33.92  E-value: 2.76e-03
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 20150826 23 LNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYiLAHTEFTPTETD-----TYACRVKH 84
Cdd:cd05847 19 LLCLISGYTPGTIEVEWLVDGQVATLVAASTAPQKEEGSTF-STTSELNVTQEDwksgkTYTCKVTH 84
IgC1_CH1_IgD cd16092
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin delta chain; member ...
12-94 7.54e-03

CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin delta chain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the first immunoglobulin constant-1 set domain of delta chains. It belongs to a family composed of the first immunoglobulin constant-1 set domain of alpha, delta, epsilon, gamma, and mu heavy chains. This domain is found on the Fab antigen-binding fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. This group belongs to the C1-set of IgSF domains, which are classical Ig-like domains resembling the antibody constant domain. C1-set domains are found almost exclusively in molecules involved in the immune system, such as in immunoglobulin light and heavy chains, in the major histocompatibility complex (MHC) class I and II complex molecules, and in various T-cell receptors.


Pssm-ID: 319341  Cd Length: 96  Bit Score: 32.89  E-value: 7.54e-03
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20150826 12 RHPPENgKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMsfSKDWSFYILAHTEFTPTE---TDTYACRVKHDSMA 88
Cdd:cd16092 12 RHPKDN-SPVVLACLITGYHPTSVTVTWYMGTQSQPQRTFPEI--QRRDSYYMTSSQLSTPLQqwrQGEYKCVVQHTASK 88

               ....*.
gi 20150826 89 EPKTVY 94
Cdd:cd16092 89 SKKEIF 94
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.19
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
  • Marchler-Bauer A et al. (2015), "CDD: NCBI's conserved domain database.", Nucleic Acids Res.43(D)222-6.
  • Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.
  • Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
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