1I50,1I3Q,1I6H


Conserved Protein Domain Family
RNAP_II_Rpb1_C

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cd02584: RNAP_II_Rpb1_C 
Click on image for an interactive view with Cn3D
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain
RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.
Statistics
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PSSM-Id: 132720
View PSSM: cd02584
Aligned: 37 rows
Threshold Bit Score: 474.001
Threshold Setting Gi: 161899215
Created: 9-Jun-2005
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
  next features
Conserved site includes 13 residues -Click on image for an interactive view with Cn3D
Feature 1:Rpb1 - Rpb2 interaction site [polypeptide binding site]
Evidence:
  • Comment:The two largest subunits, Rpb1 and Rpb2, form distinct masses with a deep cleft between them. Each of the small subunits occurs in a single copy, arrayed around the periphery.
  • Structure:1I50; Interface between Rpb1 (1I50_A) and Rpb2 (1I50_B) subunits in Saccharomyces cerevisiae RNAP II; defined using 3.5A contacts
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                     #  #                                                
1I50_A       1035 YRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVaSKKVTSGVPRLKEILNVAKNMKTP 1114
gi 51702033  1020 HRLNTEAFNWVVEVIDAKILKAKITPNEMVGTLAAQSVGEPATQMTLNTFHLAGV-ASTVTMGVPRLKEIFNVTKNLKTP 1098
gi 4001824   1020 YKLSLEAYNWILKEIKFKILKSIISPNEMVGTLAAQSVGEPATQMTLNTFHLAGV-SANITMGVPRLKEIINVAKNIKTP 1098
gi 4092885    998 YRISTLGVEWIANEIKKKFVRGIISTNEMVGTLAAQSIGEPATQMTLNTFHYAGV-AQAITQGVPRLKEIINVAKNIRTP 1076
gi 12642618   951 ERLSKDAFNWILGEIKSRFDQALVNPGEMVGSIGAQSMGEPATQMTLNTFHFAGVsAKNVTLGVPRLKEIINVAKNIKTP 1030
gi 160331837 1036 YKFSKVAFLWVLNEICTQYRKSIASPGEMVGTISAQSIGQPATQMTLNTFHYAGVsAKNVTLGVPRLKEIINVLQTVKTP 1115
gi 162606578 1029 FNLNQHALNWIVNEICLSIRKSLIQPGEMVGTISAQSIGQPATQMTLNTFHFAGVsAKNVTLGVPRLKEIIDIQKNIKSP 1108
gi 1143740   1055 YRLNEQAFKYILGSIKDRFYRSIVAPGEMVGTIAGQSIGEPSTQMTLNTFHFAGIsAHDVTLGVPRLNELMNLAKHIRTP 1134
gi 48249473  1050 HHLSKESFDDLMDRIKNIYERSFINPGEMVGSIAAQSIGAPATQMTLNTFHHAGIsSASVTEGVPRLKELLNVSKTPKTP 1129
gi 118348890 1086 HKLSMEVFDKLTKEIFDKFKKAISHPGETIGAISAQSVGEPTTQMTLNTFHFAGVsDRNVTLGVPRLQEILDASKNVKTP 1165
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
1I50_A       1115 SLTVYLEpgh-----------------aaDQEQAKLIRSAIEHTTLk----SVTIASEIYYDPDPRstVIPEDEEIIQLH 1173
gi 51702033  1099 SMKIYLDreh-----------------gkSIEAAKTIQNEIECLTVk----DLCLFSEIYYDPEITgtEISDDKDFVEAY 1157
gi 4001824   1099 CMKIYLKdpf-----------------nkTLEMAKKIQSELEFSDIk----SLCEFSEIYYDPVIEdtSIKEDKDFVQEY 1157
gi 4092885   1077 SHKIYLKpg-------------------sTIEQAKKVASEIEYINIe----MVCSEIKIIYDPKVDttIINEDRDFVEAY 1133
gi 12642618  1031 SMKIFLKdkd-----------------kqDERIATIIGGRIEHTTLc----HVVKSSAIYYDPDPErtIVREDEELIRLY 1089
gi 160331837 1116 SLTIYFRkef-----------------ssSLSKIKQFQQTLEFITLk----SMIKKKTVFYDPDPYktILKNDQIILENY 1174
gi 162606578 1109 SLTIFLHkkc-----------------snDPRKVKKIQESIESVRLn----RISNYFEIIYDPDFFfsISKCNRILVKNY 1167
gi 1143740   1135 SVTVEFErdv-----------------akDEEIVKAVRAQIESASFk----KFVIKAEIYYDPNPEetIIEPDTKWINTR 1193
gi 48249473  1130 SMNVYLTndt----------------resMVDLDKELNKTIPYTKLk----DLIDNVEIWFDPDIAnsVIEEDREFINDF 1189
gi 118348890 1166 EMTVFFEnglrkkifrkdmmsnydaesfkREYDEIVSQERQEILRLkqeieYQTISYYINQTRIVY--KSKDDEDFQQQD 1243
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
1I50_A       1174 FSLLDEeaeqsfdqqSPWLLRLELDRAAMNDKDLTMGQVg--ERIKQTFKNDLFVIWSEDNde----kLIIRCRVVRpks 1247
gi 51702033  1158 FEFPDEdvdf--sclSPFLMRLVVDRAKLVGRGINLEYVa--MFIRKELGGGAHVICSDENav----nMVVRVRTTKs-- 1227
gi 4001824   1158 FDFPDEhldf--skmPKFIIRLKIDRIKLVSKNLKLENIv--KSLHEAFPNIFHIIRSDENsq----nLIIRIRCISsln 1229
gi 4092885   1134 FEFPDEyvsl--dtlNPWLLRLVVARDRLISNNLDFEFIa--QKIKKVFHQDIFLLHSDANae----eLVIRIRVLGms- 1204
gi 12642618  1090 NEVRLFeter--rrtSPWVLRFELDNDKVQFKDLSMQLIe--QKINDIFRDQIDVVKSDENae----kLVLRLRVNDied 1161
gi 160331837 1175 FEIPDWasei--sciGTWTTKIGLEKDEFIDKKLSTIQIv-eKMKKKIKPLPLFIVNSDENsq----nLFFRLKLIWpni 1247
gi 162606578 1168 MEIPDEdinf--lqaSSWILKLKLLTEEFVEKGLFSNYIi-eTIKKKIKPIPFLIIASDENsg----sIEFLVRFIWp-- 1238
gi 1143740   1194 IRYGGVedre-lqdlAPWVLRFEINREEMIASNIESISDi-vQKIKGMYGDKFFVIGDDDAr-----iIRMQARLKDeqa 1266
gi 48249473  1190 IEVEEIkpe----dyCKWTIRLVFGYNKMVSMGVDSDSDilrVKIKELFKDALVIPSDSNNivngtvkIVVHIRFRVgsi 1265
gi 118348890 1244 NIFDDDnisd--dleDPIVLIIYFDTQKTTIDTFELLNAk-iRKIADDSKKWGNLIVEKKQfe----kGQIHVKFDStq- 1315
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                     #   #                                               
1I50_A       1248 ldaete-----------aeedhmlkKIENTMLENITLRGven-------------ieRVVMMKYDRKVps---------- 1293
gi 51702033  1228 -------------------------EDESLNFYTTALNSll--------------rlQLGGYKNVKKVy----------- 1257
gi 4001824   1230 -----------------------nnVEYYNLQYKNILNL------------------KIMGYNKIKKVf----------- 1257
gi 4092885   1205 -----------------------anEEFYRRLLNTILGI------------------HLKGITNIRRI------------ 1231
gi 12642618  1162 deedr-------------tvcmylkGFQDELFNDLALKGl-----------------HEISKVTFTKYndeif------- 1204
gi 160331837 1248 dwtknskktvknpnfnffnferkylNRTTYFLSNINLKSygts----------kikkAFIRKSSQIIFes---------- 1307
gi 162606578 1239 -------------------------EFINNYNSEKIEKLfsrsn--------antffEYIKRANQKVSenlflepnyfkk 1285
gi 1143740   1267 efam---------------dvkflrETEQQMYKSFTLKGipg------------isrVKINSAAEKMFlnp--------- 1310
gi 48249473  1266 -----------------------seCSNIDHLTDEVDKSveavayykskldellrtvVISGIEGITKViipqkpkn---- 1318
gi 118348890 1316 -----------------------lgQGQQNPDSQMNAYSslllfe------sefkdaYIGGIQKIQKVyptqkkefrpwv 1366
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
1I50_A       1294 ----------------------------------ptGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVL 1339
gi 51702033  1258 -----------------------------------iSEDKDRKEWYLQTDGICLSQILGNPAVNSRLTISNDLVEIAETL 1302
gi 4001824   1258 -----------------------------------iSEDKDKDEWYLQTDGVCIREIFSHPNVEGHLVTSNDLNEIVEVL 1302
gi 4092885   1232 ------------------------------------YLLREREEWILQTDGKNLKQLLLVEDILANKVYCNDLLEVYEVL 1275
gi 12642618  1205 -------------------------------dvetgECKQDKECWLIETDGVALQKVLGLEGINYKKTVSNDIIEILRVL 1253
gi 160331837 1308 ----------------------------------isGSIKNNEEYVLDTEGVDLRYILNYSGIDYTRCSSNDILEIYKIL 1353
gi 162606578 1286 ikhyfynynlkpygsqkltklyprridiiepepnqsGKLKNNFEFVLETEGVDLRFVMNYNGIDYSRCTTNDLLESLKVL 1365
gi 1143740   1311 ----------------------------------etHGFDKEKVSCLYTEGTAFREILSLDHVDTVHTITNDIYQVCDVL 1356
gi 48249473  1319 ----------------------------aivvdpetKMLRDQLQWVVFTEGSNMAGLAECDNVDFYKTVTNNVYETFLYL 1370
gi 118348890 1367 en---------------------eciceapkpgaafFTERKPQEHIFNTSGSNLKEVLKVDKVDATRTYSNDIQEIITIL 1425
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                #        
1I50_A       1340 GIEAGRAALYKEVYNVIAsdGSYVNYRHMALLVDVMTTQGgLTSVTRHGFNRSN-TGALMRCSFEETVEILFEAGASAEL 1418
gi 51702033  1303 GIEAARESILRELTIVIDgnGSYVNYRHMSLLADVMTMRGyLCGITRHGVNKVG-AGALKRSSFEETVEILLDAALVSEK 1381
gi 4001824   1303 GIEAARETILNELTLVIDgnGSYVNHRHISLLADVMTMKGyLTGITRHGVNKVG-FGCTKRASFEETVDILLDAALVAEK 1381
gi 4092885   1276 GIEAVRECILRELRNVIEaeGSYVNFRHLYLLCDVMTLKG-LRGITRHGANRAA-TGALKRCSFEETVEILLEASCFAER 1353
gi 12642618  1254 GIEAVRMSLINELRFVLSsyGIYVNYRHLSTLCDVMTQRGiLTAITRHGINRVD-SSPLRKCSFEETVEILLEAAVFAET 1332
gi 160331837 1354 GIEAVRKILIQELRNLISfdGSYVNSRHLSLLVDVMTHKGkLMSITRHGINRTD-IGPIAKCSFEETIEVLYQAAAFGVC 1432
gi 162606578 1366 GIEATRKILIQELRNLISfdGSYVNYRHLCTLVDLITFRGsLMSINRHGINKCN-SGPIAKSTFEETVDIFYESAVFGLN 1444
gi 1143740   1357 GIEAARHSLSYEMMLIMEkaGAALNRRHLDLLADTMTQYGvLYPVSRHGINKTP-TGTLMRASYEMTNDVFFDAAVFSEI 1435
gi 48249473  1371 GIEAGRTQLEAELIKTLS--GSYVNFRHLALMADVMTFTGrIQPFNRMGLSRGR-AGVITRASFEQTLEQFRRAAAFSES 1447
gi 118348890 1426 GIEAGRRSIVNQIRVVIEpyGIYINYRHLAILAEWMTVRGrLTPINRNGINRIPgLSCLRKSSFEETVDILNTAAIFFEK 1505
                         490       500
                  ....*....|....*....|....*...
Feature 1          ###     ## # #    #        
1I50_A       1419 DDCRGVSENVILGQMAPIGTGAFDVMID 1446
gi 51702033  1382 NICRGITENIMMGQLAPMGTGNIEIMLD 1409
gi 4001824   1382 YVTKGYTENIMMGHLAPLGTGIGNLLLD 1409
gi 4092885   1354 NYCRGVTENIMLGQLAPIGTGNTICILD 1381
gi 12642618  1333 DPLKGITENIIMGQLAPFGTGCFEITID 1360
gi 160331837 1433 DNLKGVSGSILVGQVSSLGTGKIDLFLC 1460
gi 162606578 1445 DNLRGVSAQIMTGMVPKIGTGKIDLFVN 1472
gi 1143740   1436 DYMRDVSSNIIAGKPSRAGTGIVEVLIN 1463
gi 48249473  1448 DILNGISQNILMGQRTVAGTGAFTVLLD 1475
gi 118348890 1506 DDLKGVTENIIFGQNCDIGTGCFDLLVD 1533

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