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5SVA: Mediator-RNA Polymerase II Pre-Initiation Complex

PDB ID:	5SVA Download
MMDB ID:	181865
PDB Deposition Date:	2016/8/5
Updated in MMDB:	2019/12
Experimental Method:	electron microscopy
Resolution:	15.3 Å
Source Organism:	Saccharomyces cerevisiae
Similar Structures:

Biological Unit for 5SVA: 40-meric; determined by author

Molecular Components in 5SVA
Label	Count	Molecule
Proteins (38 molecules)
A	1	DNA-directed RNA Polymerase II Subunit Rpb1 (Gene symbol: RPO21)
B	1	DNA-directed RNA Polymerase II Subunit Rpb2 (Gene symbol: RPB2)
C	1	DNA-directed RNA Polymerase II Subunit Rpb3 (Gene symbol: RPB3)
D	1	DNA-directed RNA Polymerase II Subunit Rpb4 (Gene symbol: RPB4)
E	1	DNA-directed RNA Polymerases I, II, and III Subunit Rpabc1 (Gene symbol: RPB5)
F	1	DNA-directed RNA Polymerases I, II, and III Subunit Rpabc2 (Gene symbol: RPO26)
G	1	DNA-directed RNA Polymerase II Subunit Rpb7 (Gene symbol: RPB7)
H	1	DNA-directed RNA Polymerases I, II, and III Subunit Rpabc3 (Gene symbol: RPB8)
I	1	DNA-directed RNA Polymerase II Subunit Rpb9 (Gene symbol: RPB9)
J	1	DNA-directed RNA Polymerases I, II, and III Subunit Rpabc5 (Gene symbol: RPB10)
K	1	DNA-directed RNA Polymerase II Subunit Rpb11 (Gene symbol: RPB11)
L	1	DNA-directed RNA Polymerases I, II, and III Subunit Rpabc4 (Gene symbol: RPC10)
M	1	Mediator of RNA Polymerase II Transcription Subunit 6 (Gene symbol: MED6)
N	1	Mediator of RNA Polymerase II Transcription Subunit 8 (Gene symbol: MED8)
O	1	Mediator of RNA Polymerase II Transcription Subunit 11 (Gene symbol: MED11)
P	1	Mediator of RNA Polymerase II Transcription Subunit 17 (Gene symbol: SRB4)
Q	1	Mediator of RNA Polymerase II Transcription Subunit 18 (Gene symbol: SRB5)
R	1	Mediator of RNA Polymerase II Transcription Subunit 20 (Gene symbol: SRB2)
S	1	Mediator of RNA Polymerase II Transcription Subunit 22 (Gene symbol: SRB6)
T	1	Mediator of RNA Polymerase II Transcription Subunit 4 (Gene symbol: MED4)
U	1	Mediator of RNA Polymerase II Transcription Subunit 7 (Gene symbol: MED7)
V	1	Mediator of RNA Polymerase II Transcription Subunit 9 (Gene symbol: CSE2)
W	1	Mediator of RNA Polymerase II Transcription Subunit 21 (Gene symbol: SRB7)
X	1	Mediator of RNA Polymerase II Transcription Subunit 31 (Gene symbol: SOH1)
Y	1	DNA Repair Helicase Rad3 (Gene symbol: RAD3)
Z	1	DNA Repair Helicase Rad25 (Gene symbol: SSL2)
a	1	RNA Polymerase II Transcription Factor B Subunit 2 (Gene symbol: TFB2)
b	1	RNA Polymerase II Transcription Factor B Subunit 5 (Gene symbol: TFB5)
c	1	Transcription Initiation Factor IIB (Gene symbol: SUA7)
d	1	Transcription Initiation Factor IIA Large Subunit (Gene symbol: TOA1)
e	1	Transcription Initiation Factor IIA Subunit 2 (Gene symbol: TOA2)
f	1	Transcription Initiation Factor IIF Subunit Alpha (Gene symbol: TFG1)
g	1	Transcription Initiation Factor IIF Subunit Beta (Gene symbol: TFG2)
h	1	Transcription Initiation Factor IIE Subunit Alpha (Gene symbol: TFA1)
i	1	Transcription Initiation Factor IIE Subunit Beta (Gene symbol: TFA2)
j	1	Tata-box-binding Protein (Gene symbol: SPT15)
k	1	DNA-directed RNA Polymerase II Subunit Rpb1 (Gene symbol: RPO21)
n	1	Transcription Initiation Factor Tfiid Subunit 14 (Gene symbol: TAF14)
Nucleotides(2 molecules)
l	1	108bp His4 Promoter Non-template Strand (-92/+16)
m	1	108bp His4 Promoter Template Strand (+16/-92)
Chemicals and Non-standard biopolymers (9 molecules)
1	8	ZINC ION (Link to PubChem not yet available)
2	1	MAGNESIUM ION (Link to PubChem not yet available)

* Click molecule labels to explore molecular sequence information.

Citing MMDB

Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303