Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 20-mer - A2B2C2D2EFGHIJKLMNOP Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 20-mer -A8BCDEFGHIJKLM 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 732091.00 
• Atom Count: 43988 
• Residue Count: 5918 
• Unique protein chains: 16
• Unique nucleic acid chains: 3

6I84

Structure of transcribing RNA polymerase II-nucleosome complex

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

• Classification: TRANSCRIPTION
• Organism(s): synthetic construct, Xenopus laevis, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
• Expression System: Escherichia coli


• 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: 4.4 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 

Macromolecules

Find similar proteins by: Sequence  |  Structure

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) 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) Go to UniProtKB:  P06897

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) Go to UniProtKB:  P62799

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) Go to UniProtKB:  P02281

Entity ID: 7
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: 8
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: 9
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerase II subunit RPB3	C	348	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: 10
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: 11
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: 12
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: 13
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: 14
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: 15
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: 16
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: 17
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: 18
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: 3
Molecule	Chains	Length	Organism
DNA (170-MER)	T	169	synthetic construct

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
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: 4.4 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Software Package:

Software Name	Purpose
PHENIX	refinement

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