5SVA | pdb_00005sva

Mediator-RNA Polymerase II Pre-Initiation Complex

PDB DOI: https://doi.org/10.2210/pdb5SVA/pdb
NAKB: 5SVA
EM Map EMD-8305: EMDB EMDataResource

Classification: TRANSCRIPTION, TRANSFERASE/DNA
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-08-05 Released: 2016-09-28
Deposition Author(s): Robinson, P.J., Bushnell, D.A., Kornberg, R.D.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 15.3 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex.

Robinson, P.J., Trnka, M.J., Bushnell, D.A., Davis, R.E., Mattei, P.J., Burlingame, A.L., Kornberg, R.D.

(2016) Cell 166: 1411-1422.e16

PubMed: 27610567 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.cell.2016.08.050
Primary Citation Related Structures:
5SVA

PubMed Abstract:
A complete, 52-protein, 2.5 million dalton, Mediator-RNA polymerase II pre-initiation complex (Med-PIC) was assembled and analyzed by cryo-electron microscopy and by chemical cross-linking and mass spectrometry. The resulting complete Med-PIC structure reveals two components of functional significance, absent from previous structures, a protein kinase complex and the Mediator-activator interaction region. It thereby shows how the kinase and its target, the C-terminal domain of the polymerase, control Med-PIC interaction and transcription.

Organizational Affiliation

Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.

Macromolecule Content

Total Structure Weight: 1,522.75 kDa
Atom Count: 66,133
Modeled Residue Count: 8,647
Deposited Residue Count: 13,074
Unique protein chains: 38
Unique nucleic acid chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB1	A	1,733	Saccharomyces cerevisiae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for P04050 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P04050 Go to UniProtKB: P04050
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04050
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB2	B	1,224	Saccharomyces cerevisiae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for P08518 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P08518 Go to UniProtKB: P08518
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08518
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB3	C	318	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P16370 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P16370 Go to UniProtKB: P16370
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P16370
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB4	D	221	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P20433 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20433 Go to UniProtKB: P20433
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20433
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC1	E	215	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P20434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20434 Go to UniProtKB: P20434
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20434
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC2	F	155	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P20435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20435 Go to UniProtKB: P20435
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20435
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB7	G	171	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P34087 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P34087 Go to UniProtKB: P34087
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P34087
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC3	H	146	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P20436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20436 Go to UniProtKB: P20436
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20436
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB9	I	122	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P27999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P27999 Go to UniProtKB: P27999
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27999
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC5	J	70	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P22139 Go to UniProtKB: P22139
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22139
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB11	K	120	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P38902 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38902 Go to UniProtKB: P38902
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38902
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC4	L	70	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40422 Go to UniProtKB: P40422
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40422
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 6	M	295	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P38782 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38782 Go to UniProtKB: P38782
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38782
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 8	N	223	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P38304 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38304 Go to UniProtKB: P38304
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38304
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 11	O	115	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q99278 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q99278 Go to UniProtKB: Q99278
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q99278
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 17	P	687	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P32569 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32569 Go to UniProtKB: P32569
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32569
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 18	Q	307	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P32585 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32585 Go to UniProtKB: P32585
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32585
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 20	R	210	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P34162 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P34162 Go to UniProtKB: P34162
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P34162
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 22	S	121	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P32570 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32570 Go to UniProtKB: P32570
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32570
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 4	T	284	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q12343 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12343 Go to UniProtKB: Q12343
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q12343
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 7	U	222	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q08278 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08278 Go to UniProtKB: Q08278
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q08278
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 9	V	149	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P33308 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P33308 Go to UniProtKB: P33308
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P33308
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 21	W	140	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P47822 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P47822 Go to UniProtKB: P47822
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P47822
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 31	X	127	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P38633 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38633 Go to UniProtKB: P38633
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38633
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair helicase RAD3	Y	778	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.6.4.12 (PDB Primary Data), 5.6.2.3 (UniProt)
UniProt
Find proteins for P06839 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P06839 Go to UniProtKB: P06839
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06839
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair helicase RAD25	Z	843	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.6.4.12 (PDB Primary Data), 5.6.2.4 (UniProt)
UniProt
Find proteins for Q00578 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q00578 Go to UniProtKB: Q00578
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q00578
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase II transcription factor B subunit 2	AA [auth a]	513	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q02939 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02939 Go to UniProtKB: Q02939
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q02939
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase II transcription factor B subunit 5	BA [auth b]	72	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q3E7C1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q3E7C1 Go to UniProtKB: Q3E7C1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3E7C1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription initiation factor IIB	CA [auth c]	345	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: SUA7, YPR086W, P9513.4
UniProt
Find proteins for P29055 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P29055 Go to UniProtKB: P29055
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29055
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription initiation factor IIA large subunit	DA [auth d]	286	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: TOA1, YOR194C
UniProt
Find proteins for P32773 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32773 Go to UniProtKB: P32773
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32773
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription initiation factor IIA subunit 2	EA [auth e]	122	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: TOA2, YKL058W
UniProt
Find proteins for P32774 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32774 Go to UniProtKB: P32774
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32774
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription initiation factor IIF subunit alpha	FA [auth f]	735	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P41895 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P41895 Go to UniProtKB: P41895
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41895
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription initiation factor IIF subunit beta	GA [auth g]	400	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.6.4.12
UniProt
Find proteins for P41896 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P41896 Go to UniProtKB: P41896
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41896
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription initiation factor IIE subunit alpha	HA [auth h]	482	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: TFA1, YKL028W
UniProt
Find proteins for P36100 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36100 Go to UniProtKB: P36100
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P36100
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription initiation factor IIE subunit beta	IA [auth i]	328	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: TFA2, YKR062W
UniProt
Find proteins for P36145 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36145 Go to UniProtKB: P36145
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P36145
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
TATA-box-binding protein	JA [auth j]	240	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: SPT15, BTF1, TBP1, YER148W
UniProt
Find proteins for P13393 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P13393 Go to UniProtKB: P13393
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P13393
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB1	KA [auth k]	25	Saccharomyces cerevisiae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for P04050 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P04050 Go to UniProtKB: P04050
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04050
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription initiation factor TFIID subunit 14	NA [auth n]	244	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P35189 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P35189 Go to UniProtKB: P35189
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P35189
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 38
108bp HIS4 Promoter Non-template Strand (-92/+16)	LA [auth l]	108	Saccharomyces cerevisiae
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 39
108bp HIS4 Promoter Template Strand (+16/-92)	MA [auth m]	108	Saccharomyces cerevisiae
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain OA [auth A] SDF format, chain PA [auth A] SDF format, chain RA [auth B] SDF format, chain SA [auth C] SDF format, chain TA [auth I] SDF format, chain UA [auth I] SDF format, chain VA [auth J] SDF format, chain WA [auth L] MOL2 format, chain OA [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain SA [auth C] MOL2 format, chain TA [auth I] MOL2 format, chain UA [auth I] MOL2 format, chain VA [auth J] MOL2 format, chain WA [auth L] mmCIF format, chain OA [auth A] mmCIF format, chain PA [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain SA [auth C] mmCIF format, chain TA [auth I] mmCIF format, chain UA [auth I] mmCIF format, chain VA [auth J] mmCIF format, chain WA [auth L]	OA [auth A] PA [auth A] RA [auth B] SA [auth C] TA [auth I] OA [auth A], PA [auth A], RA [auth B], SA [auth C], TA [auth I], UA [auth I], VA [auth J], WA [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain OA [auth A] Focus chain PA [auth A] Focus chain RA [auth B] Focus chain SA [auth C] Focus chain TA [auth I] Focus chain UA [auth I] Focus chain VA [auth J] Focus chain WA [auth L] Interactions & Density Focus chain OA [auth A] Focus chain PA [auth A] Focus chain RA [auth B] Focus chain SA [auth C] Focus chain TA [auth I] Focus chain UA [auth I] Focus chain VA [auth J] Focus chain WA [auth L]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain QA [auth A] MOL2 format, chain QA [auth A] mmCIF format, chain QA [auth A]	QA [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain QA [auth A] Interactions & Density Focus chain QA [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 15.3 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2016-09-28

Deposition Author(s):

Robinson, P.J.

Bushnell, D.A.

Kornberg, R.D.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI21144
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM49985
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM36659
National Science Foundation (NSF, United States)	United States	1231306
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM103481

Revision History (Full details and data files)

Version 1.0: 2016-09-28
Type: Initial release
Version 1.1: 2017-09-13
Changes: Author supporting evidence
Version 1.2: 2019-11-27
Changes: Author supporting evidence
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

5SVA | pdb_00005sva

Mediator-RNA Polymerase II Pre-Initiation Complex

Literature

Structure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Entity ID: 11

UniProt

Entity Groups

Sequence Annotations

Entity ID: 12

UniProt

Entity Groups

Sequence Annotations

Entity ID: 13

UniProt

Entity Groups

Sequence Annotations

Entity ID: 14

UniProt

Entity Groups

Sequence Annotations

Entity ID: 15

UniProt

Entity Groups

Sequence Annotations

Entity ID: 16

UniProt

Entity Groups

Sequence Annotations

Entity ID: 17

UniProt

Entity Groups

Sequence Annotations

Entity ID: 18

UniProt

Entity Groups

Sequence Annotations

Entity ID: 19

UniProt