Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 29-mer - ABCDEFGHIJKLMNOPQRSTUVWXYZabc 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

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
• EMDataResource: 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 

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Experimental Data Snapshot

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

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 
• DOI: 10.1016/j.molcel.2018.10.014
• Primary Citation of Related Structures:  
  6GYL, 6GYK


• PubMed Abstract: 
  

Transcription initiation requires opening of promoter DNA in the RNA polymerase II (Pol II) pre-initiation complex (PIC), but it remains unclear how this is achieved. Here we report the cryo-electron microscopic (cryo-EM) structure of a yeast PIC that contains underwound, distorted promoter DNA in the closed Pol II cleft. The DNA duplex axis is offset at the upstream edge of the initially melted DNA region (IMR) where DNA opening begins. Unstable IMRs are found in a subset of yeast promoters that we show can still initiate transcription after depletion of the transcription factor (TF) IIH (TFIIH) translocase Ssl2 (XPB in human) from the nucleus in vivo. PIC-induced DNA distortions may thus prime the IMR for melting and may explain how unstable IMRs that are predicted in promoters of Pol I and Pol III can open spontaneously. These results suggest that DNA distortion in the polymerase cleft is a general mechanism that contributes to promoter opening.

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Organizational Affiliation: 

Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany.,Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany. Electronic address: [e-mail].

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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
SF4	0	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC
ZN	3, 4, 6, A, B, C, I, J, L, M, W	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

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.

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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