Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 20-mer - A2BCDE1FGHIJKLMNOP Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 20-mer - A8B1CDEFGHIJKLM 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 732.09 kDa 
• Atom Count: 43988 
• Residue Count: 5002 
• Unique protein chains: 16
• Unique nucleic acid chains: 3

6I84

Structure of transcribing RNA polymerase II-nucleosome complex

• DOI: 10.2210/pdb6I84/pdb
• EMDataResource: EMD-4429

• Classification: TRANSCRIPTION
• Organism(s): Xenopus laevis, synthetic construct, Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-11-19 Released: 2019-01-02 
• Deposition Author(s): Farnung, L., Vos, S.M., Cramer, P.
• Funding Organization(s): European Research Council, European Molecular Biology Organization, German Research Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of transcribing RNA polymerase II-nucleosome complex.

Farnung, L., Vos, S.M., Cramer, P.

(2018) Nat Commun 9: 5432-5432

• PubMed: 30575770 
• DOI: 10.1038/s41467-018-07870-y
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Transcription of eukaryotic protein-coding genes requires passage of RNA polymerase II (Pol II) through nucleosomes, but it is unclear how this is achieved. Here we report the cryo-EM structure of transcribing Saccharomyces cerevisiae Pol II engaged with a downstream nucleosome core particle at an overall resolution of 4.4 Å. Pol II and the nucleosome are observed in a defined relative orientation that is not predicted. Pol II contacts both sides of the nucleosome dyad using its clamp head and lobe domains. Structural comparisons reveal that the elongation factors TFIIS, DSIF, NELF, SPT6, and PAF1 complex can be accommodated on the Pol II surface in the presence of the oriented nucleosome. Our results provide a starting point for analysing the mechanisms of chromatin transcription.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Histone H3.2	M, S	136	Xenopus laevis	Mutation(s): 0
Find proteins for P84233 (Xenopus laevis) Explore P84233  Go to UniProtKB:  P84233

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Histone H2A type 1	Q, V	130	Xenopus laevis	Mutation(s): 0
Find proteins for P06897 (Xenopus laevis) Explore P06897  Go to UniProtKB:  P06897

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details
Histone H2B 1.1	R, W	123	Xenopus laevis	Mutation(s): 0
Find proteins for P02281 (Xenopus laevis) Explore P02281  Go to UniProtKB:  P02281

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerase II subunit RPB1	A	1733	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: RPO21, RPB1, RPB220, SUA8, YDL140C, D2150 EC: 2.7.7.6
Find proteins for P04050 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P04050  Go to UniProtKB:  P04050

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerase II subunit RPB2	B	1224	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: RPB2, RPB150, RPO22, YOR151C EC: 2.7.7.6
Find proteins for P08518 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P08518  Go to UniProtKB:  P08518

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerase II subunit RPB3	C	348	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: RPB3, YIL021W
Find proteins for P16370 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P16370  Go to UniProtKB:  P16370

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerase II subunit RPB4	D	221	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: RPB4, YJL140W, J0654
Find proteins for P20433 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20433  Go to UniProtKB:  P20433

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerase II subunit RPB9	I	122	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: RPB9, YGL070C
Find proteins for P27999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P27999  Go to UniProtKB:  P27999

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerases I, II, and III subunit RPABC5	J	70	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: RPB10, YOR210W
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P22139  Go to UniProtKB:  P22139

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerase II subunit RPB11	K	120	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: RPB11, YOL005C
Find proteins for P38902 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38902  Go to UniProtKB:  P38902

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerases I, II, and III subunit RPABC4	L	70	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: RPC10, RPB12, YHR143W-A, YHR143BW
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40422  Go to UniProtKB:  P40422

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerases I, II, and III subunit RPABC1	E	215	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: RPB5, RPA7, RPC9, YBR154C, YBR1204
Find proteins for P20434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20434  Go to UniProtKB:  P20434

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerases I, II, and III subunit RPABC2	F	155	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: RPO26, RPB6, YPR187W, P9677.8
Find proteins for P20435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20435  Go to UniProtKB:  P20435

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerase II subunit RPB7	G	171	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: RPB7, YDR404C, D9509.22
Find proteins for P34087 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P34087  Go to UniProtKB:  P34087

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerases I, II, and III subunit RPABC3	H	146	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: RPB8, YOR224C, YOR50-14
Find proteins for P20436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20436  Go to UniProtKB:  P20436

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
Histone H4	O, U	103	Xenopus laevis	Mutation(s): 0
Find proteins for P62799 (Xenopus laevis) Explore P62799  Go to UniProtKB:  P62799

Entity ID: 4
Molecule	Chains	Length	Organism
DNA (158-MER)	N	160	synthetic construct

Entity ID: 19
Molecule	Chains	Length	Organism
RNA	P	10	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism
DNA (170-MER)	T	169	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	A, B, C, I, J, L	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-11-19 
• Released Date: 2019-01-02 
Deposition Author(s): Farnung, L., Vos, S.M., Cramer, P.

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Funding Organization	Location	Grant Number
European Research Council	Germany	Transregulon (693023)
European Molecular Biology Organization	Germany	ALTF-725-2014
German Research Foundation	Germany	SFB1064
German Research Foundation	Germany	SFB860

Revision History 

• Version 1.0: 2019-01-02
  Type: Initial release
  
• Version 1.1: 2019-08-21
  Changes: Data collection, Experimental preparation
• Version 1.2: 2019-12-18
  Changes: Other