Promoter Distortion and Opening in the RNA Polymerase II Cleft.

Dienemann, C.; Schwalb, B.; Schilbach, S.; Cramer, P.

doi:10.2210/pdb6gym/pdb

Macromolecule Content

Total Structure Weight: 1297092.75
Atom Count: 63012
Residue Count: 11347
Unique protein chains: 29
Unique nucleic acid chains: 2

6GYM

Structure of a yeast closed complex with distorted DNA (CCdist)

DOI: 10.2210/pdb6GYM/pdb
EMDataBank: EMD-0092

Classification: TRANSCRIPTION
Organism(s): Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Saccharomyces cerevisiae S288C
Expression System: Trichoplusia ni, Escherichia coli

Deposited: 2018-06-30 Released: 2018-12-05
Deposition Author(s): Dienemann, C., Schwalb, B., Schilbach, S., Cramer, P.
Funding Organization(s): European Research Council; German Research Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 6.7 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Promoter Distortion and Opening in the RNA Polymerase II Cleft.

Dienemann, C., Schwalb, B., Schilbach, S., Cramer, P.

(2019) Mol. Cell 73: 97-106.e4

PubMed: 30472190 Search on PubMed
Primary Citation of Related Structures:
6GYL, 6GYK

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
General transcription and DNA repair factor IIH helicase subunit XPD,General transcription and DNA repair factor IIH helicase subunit XPD,DNA repair helicase RAD3,DNA repair helicase RAD3,General transcription and DNA repair factor IIH helicase subunit XPD	0	778	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: RAD3 (REM1) EC: 3.6.4.12
Find proteins for P06839 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: P06839
Protein Feature View Full Protein Feature View for P06839

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
General transcription and DNA repair factor IIH subunit TFB1,General transcription and DNA repair factor IIH subunit TFB1,RNA polymerase II transcription factor B subunit 1,General transcription and DNA repair factor IIH subunit TFB1,RNA polymerase II transcription factor B subunit 1,General transcription and DNA repair factor IIH subunit TFB1,General transcription and DNA repair factor IIH subunit TFB1,General transcription and DNA repair factor IIH subunit TFB1,RNA polymerase II transcription factor B subunit 1,General transcription and DNA repair factor IIH subunit TFB1,RNA polymerase II transcription factor B subunit 1,General transcription and DNA repair factor IIH subunit TFB1,General transcription and DNA repair factor IIH subunit TFB1	1	641	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: TFB1
Find proteins for P32776 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: P32776
Protein Feature View Full Protein Feature View for P32776

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
General transcription and DNA repair factor IIH subunit TFB2,General transcription and DNA repair factor IIH subunit TFB2,General transcription and DNA repair factor IIH subunit TFB2,General transcription and DNA repair factor IIH subunit TFB2,General transcription and DNA repair factor IIH subunit TFB2,General transcription and DNA repair factor IIH subunit TFB2,General transcription and DNA repair factor IIH subunit TFB2	2	462	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: TFB2
Find proteins for Q02939 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: Q02939
Protein Feature View Full Protein Feature View for Q02939

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
RNA polymerase II transcription factor B subunit 3	3	321	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: TFB3 (RIG2)
Find proteins for Q03290 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: Q03290
Protein Feature View Full Protein Feature View for Q03290

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
General transcription and DNA repair factor IIH subunit TFB4,General transcription and DNA repair factor IIH subunit TFB4,RNA polymerase II transcription factor B subunit 4,General transcription and DNA repair factor IIH subunit TFB4,General transcription and DNA repair factor IIH subunit TFB4	4	338	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: TFB4
Find proteins for Q12004 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: Q12004
Protein Feature View Full Protein Feature View for Q12004

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details
General transcription and DNA repair factor IIH subunit TFB5	5	72	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: TFB5
Find proteins for Q3E7C1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: Q3E7C1
Protein Feature View Full Protein Feature View for Q3E7C1

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details
General transcription and DNA repair factor IIH subunit SSL1,General transcription and DNA repair factor IIH subunit SSL1,General transcription and DNA repair factor IIH subunit SSL1,General transcription and DNA repair factor IIH subunit SSL1,General transcription and DNA repair factor IIH subunit SSL1,General transcription and DNA repair factor IIH subunit SSL1,General transcription and DNA repair factor IIH subunit SSL1	6	461	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: SSL1
Find proteins for Q04673 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: Q04673
Protein Feature View Full Protein Feature View for Q04673

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details
General transcription and DNA repair factor IIH helicase subunit XPB,General transcription and DNA repair factor IIH helicase subunit XPB,DNA repair helicase RAD25,General transcription and DNA repair factor IIH helicase subunit XPB,DNA repair helicase RAD25,General transcription and DNA repair factor IIH helicase subunit XPB,General transcription and DNA repair factor IIH helicase subunit XPB,DNA repair helicase RAD25,General transcription and DNA repair factor IIH helicase subunit XPB,DNA repair helicase RAD25,General transcription and DNA repair factor IIH helicase subunit XPB,General transcription and DNA repair factor IIH helicase subunit XPB,DNA repair helicase RAD25,General transcription and DNA repair factor IIH helicase subunit XPB,DNA repair helicase RAD25,General transcription and DNA repair factor IIH helicase subunit XPB,General transcription and DNA repair factor IIH helicase subunit XPB	7	843	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: SSL2 (LOM3, RAD25, UVS112) EC: 3.6.4.12
Find proteins for Q00578 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: Q00578
Protein Feature View Full Protein Feature View for Q00578

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerase II subunit RPB1	A	1733	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: RPO21 (RPB1, RPB220, SUA8) EC: 2.7.7.6
Find proteins for P04050 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: P04050
Protein Feature View Full Protein Feature View for P04050

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerase II subunit RPB2	B	1224	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: RPB2 (RPB150, RPO22) EC: 2.7.7.6
Find proteins for P08518 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: P08518
Protein Feature View Full Protein Feature View for P08518

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerase II subunit RPB3	C	318	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: RPB3
Find proteins for P16370 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: P16370
Protein Feature View Full Protein Feature View for P16370

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerase II subunit RPB4	D	221	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: RPB4
Find proteins for P20433 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: P20433
Protein Feature View Full Protein Feature View for P20433

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerases I, II, and III subunit RPABC1	E	215	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: RPB5 (RPA7, RPC9)
Find proteins for P20434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: P20434
Protein Feature View Full Protein Feature View for P20434

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerases I, II, and III subunit RPABC2	F	155	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: RPO26 (RPB6)
Find proteins for P20435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: P20435
Protein Feature View Full Protein Feature View for P20435

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerase II subunit RPB7	G	171	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: RPB7
Find proteins for P34087 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: P34087
Protein Feature View Full Protein Feature View for P34087

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerases I, II, and III subunit RPABC3	H	146	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: RPB8
Find proteins for P20436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: P20436
Protein Feature View Full Protein Feature View for P20436

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerase II subunit RPB9	I	122	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: RPB9
Find proteins for P27999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: P27999
Protein Feature View Full Protein Feature View for P27999

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerases I, II, and III subunit RPABC5	J	70	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: RPB10
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: P22139
Protein Feature View Full Protein Feature View for P22139

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerase II subunit RPB11	K	120	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: RPB11
Find proteins for P38902 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: P38902
Protein Feature View Full Protein Feature View for P38902

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerases I, II, and III subunit RPABC4	L	70	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: RPC10 (RPB12)
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: P40422
Protein Feature View Full Protein Feature View for P40422

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details
Transcription initiation factor IIB	M	345	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: SUA7
Find proteins for P29055 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: P29055
Protein Feature View Full Protein Feature View for P29055

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details
TATA-box-binding protein	O	240	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: SPT15 (BTF1, TBP1)
Find proteins for P13393 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: P13393
Protein Feature View Full Protein Feature View for P13393

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details
Transcription initiation factor IIF subunit alpha	Q	735	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: TFG1 (SSU71)
Find proteins for P41895 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: P41895
Protein Feature View Full Protein Feature View for P41895

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details
Transcription initiation factor IIF subunit beta	R	400	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: TFG2
Find proteins for P41896 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: P41896
Protein Feature View Full Protein Feature View for P41896

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details
Transcription initiation factor IIA large subunit,Transcription initiation factor IIA large subunit	U	171	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: TOA1
Find proteins for P32773 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: P32773
Protein Feature View Full Protein Feature View for P32773

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details
Transcription initiation factor IIA subunit 2	V	122	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: TOA2
Find proteins for P32774 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: P32774
Protein Feature View Full Protein Feature View for P32774

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details
Transcription initiation factor IIE subunit alpha,Transcription initiation factor IIE subunit alpha,Transcription initiation factor IIE subunit alpha,Transcription initiation factor IIE subunit alpha,Transcription initiation factor IIE subunit alpha	W	332	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: TFA1
Find proteins for P36100 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: P36100
Protein Feature View Full Protein Feature View for P36100

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details
Transcription initiation factor IIE subunit beta	X	328	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: TFA2
Find proteins for P36145 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: P36145
Protein Feature View Full Protein Feature View for P36145

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details
Unknown protein	Z	43	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 30
Molecule	Chains	Length	Organism
non-template DNA (HIS4)	N	75	Saccharomyces cerevisiae S288C

Entity ID: 31
Molecule	Chains	Length	Organism
Template DNA (HIS4)	T	75	Saccharomyces cerevisiae S288C

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
SF4 Query on SF4 Download SDF File Download CCD File	0	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-VKOJMFJBAC		Ligand Interaction
ZN Query on ZN Download SDF File Download CCD File	3, 4, 6, A, B, C, I, J, L, M, W	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction
MG Query on MG Download SDF File Download CCD File	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
UNK Query on UNK	0, 1, 2, 4, 6, 7, W, Z	L-PEPTIDE LINKING	C₄ H₉ N O₂		--
MSE Query on MSE	0	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 6.7 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History & Funding Information

Deposition Data

Deposited Date: 2018-06-30
Released Date: 2018-12-05
Deposition Author(s): Dienemann, C., Schwalb, B., Schilbach, S., Cramer, P.

Funding Organization	Location	Grant Number
European Research Council	Germany	693023
German Research Foundation	Germany	SFB860

Revision History

Version 1.0: 2018-12-05
Type: Initial release
Version 1.1: 2019-01-16
Type: Data collection, Database references

Prepare Data

Validate Data

Deposit Data

Deposition Help & Resources

148268 Biological Macromolecular Structures Enabling Breakthroughs in Research and Education

6GYM

Structure of a yeast closed complex with distorted DNA (CCdist)

Promoter Distortion and Opening in the RNA Polymerase II Cleft.

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Experimental Data

Structure Validation

Deposition Data

Revision History