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 -A6B2CDEFGHIJKLMN 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: authors reported there is no experimental evidence

Macromolecule Content

• Total Structure Weight: 773323.25 
• Atom Count: 43983 
• Residue Count: 6023 
• Unique protein chains: 16
• Unique nucleic acid chains: 5

6A5U

RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA, tilt conformation

• DOI: 10.2210/pdb6A5U/pdb
• EMDataBank: EMD-6985

• Classification: TRANSCRIPTION/RNA/DNA
• Organism(s): Komagataella phaffii (strain GS115 / ATCC 20864), synthetic construct, Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1), Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2018-06-25 Released: 2018-10-03 
• Deposition Author(s): Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S., Kurumizaka, H.
• Funding Organization(s): Japan Society for the Promotion of Science; Japan Agency for Medical Research and Development (AMED); Japan Science and Technology; RIKEN Dynamic Structural Biology project 

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 7.6 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of the nucleosome transition during RNA polymerase II passage.

Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S.I., Kurumizaka, H.

(2018) Science 362: 595-598

• PubMed: 30287617 
• Primary Citation of Related Structures:  
  6A5V, 6A5T, 6A5R, 6A5P, 6A5O, 6A5L

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerase subunit	A	1743	Komagataella phaffii (strain GS115 / ATCC 20864)	Mutation(s): 0  EC: 2.7.7.6
Find proteins for C4R4Y0 (Komagataella phaffii (strain GS115 / ATCC 20864)) Go to UniProtKB:  C4R4Y0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerase subunit beta	B	1227	Komagataella phaffii (strain GS115 / ATCC 20864)	Mutation(s): 0  EC: 2.7.7.6
Find proteins for C4QZQ7 (Komagataella phaffii (strain GS115 / ATCC 20864)) Go to UniProtKB:  C4QZQ7

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
RNA polymerase II third largest subunit B44, part of central core	C	304	Komagataella phaffii (strain GS115 / ATCC 20864)	Mutation(s): 0
Find proteins for C4R7L2 (Komagataella phaffii (strain GS115 / ATCC 20864)) Go to UniProtKB:  C4R7L2

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
RNA polymerase II subunit B32	D	186	Komagataella phaffii (strain GS115 / ATCC 20864)	Mutation(s): 0
Find proteins for C4R2U9 (Komagataella phaffii (strain GS115 / ATCC 20864)) Go to UniProtKB:  C4R2U9

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III	E	214	Komagataella phaffii (strain GS115 / ATCC 20864)	Mutation(s): 0
Find proteins for C4R3P8 (Komagataella phaffii (strain GS115 / ATCC 20864)) Go to UniProtKB:  C4R3P8

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details
RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III	F	155	Komagataella phaffii (strain GS115 / ATCC 20864)	Mutation(s): 0
Find proteins for C4R1V1 (Komagataella phaffii (strain GS115 / ATCC 20864)) Go to UniProtKB:  C4R1V1

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details
RNA polymerase II subunit	G	171	Komagataella phaffii (strain GS115 / ATCC 20864)	Mutation(s): 0
Find proteins for C4R9A1 (Komagataella phaffii (strain GS115 / ATCC 20864)) Go to UniProtKB:  C4R9A1

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerases I, II, and III subunit RPABC3	H	145	Komagataella phaffii (strain GS115 / ATCC 20864)	Mutation(s): 0
Find proteins for C4R273 (Komagataella phaffii (strain GS115 / ATCC 20864)) Go to UniProtKB:  C4R273

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerase subunit	I	115	Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1)	Mutation(s): 0  Gene Names: RPB9
Find proteins for F2QPE6 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1)) Go to UniProtKB:  F2QPE6

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details
RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III	J	72	Komagataella phaffii (strain GS115 / ATCC 20864)	Mutation(s): 0
Find proteins for C4R009 (Komagataella phaffii (strain GS115 / ATCC 20864)) Go to UniProtKB:  C4R009

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details
RNA polymerase II subunit B12.5	K	118	Komagataella phaffii (strain GS115 / ATCC 20864)	Mutation(s): 0
Find proteins for C4R3Z5 (Komagataella phaffii (strain GS115 / ATCC 20864)) Go to UniProtKB:  C4R3Z5

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details
RNA polymerase subunit ABC10-alpha	L	72	Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1)	Mutation(s): 0  Gene Names: RPC10
Find proteins for F2QMI1 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1)) Go to UniProtKB:  F2QMI1

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details
Histone H3.3	a, e	139	Homo sapiens	Mutation(s): 0  Gene Names: H3F3A, H3F3B (H3.3A, H3F3, H3.3B)
Find proteins for P84243 (Homo sapiens) Go to Gene View: H3F3A H3F3B Go to UniProtKB:  P84243

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details
Histone H4	b, f	106	Homo sapiens	Mutation(s): 0  Gene Names: HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4A, HIST2H4B, HIST4H4 (H4/A, H4FA, H4/I, H4FI, H4/G, H4FG, H4/B, H4FB, H4/J, H4FJ, H4/C, H4FC, H4/H, H4FH, H4/M, H4FM, H4/E, H4FE, H4/D, H4FD, H4/K, H4FK, H4/N, H4F2, H4FN, HIST2H4, H4/O, H4FO)
Find proteins for P62805 (Homo sapiens) Go to Gene View: HIST1H4A HIST1H4B HIST1H4C HIST1H4D HIST1H4E HIST1H4F HIST1H4H HIST1H4I HIST1H4J HIST1H4K HIST1H4L HIST2H4A HIST2H4B HIST4H4 Go to UniProtKB:  P62805

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details
Histone H2A, Histone H2A type 1-B/E	c, g	133	Homo sapiens	Mutation(s): 0  Gene Names: HIST1H2AB, HIST1H2AE (H2AFM, H2AFA)
Find proteins for P04908 (Homo sapiens) Go to Gene View: HIST1H2AB HIST1H2AE Go to UniProtKB:  P04908

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details
Histone H2B, Histone H2B type 1-J	d, h	129	Homo sapiens	Mutation(s): 0  Gene Names: HIST1H2BJ (H2BFR)
Find proteins for P06899 (Homo sapiens) Go to Gene View: HIST1H2BJ Go to UniProtKB:  P06899

Entity ID: 13
Molecule	Chains	Length	Organism
RNA (5'-R(P*GP*GP*UP*GP*UP*CP*UP*UP*GP*GP*G)-3')	P	11	synthetic construct

Entity ID: 14
Molecule	Chains	Length	Organism
DNA (198-MER)	T	198	synthetic construct

Entity ID: 15
Molecule	Chains	Length	Organism
DNA (198-MER)	N	198	synthetic construct

Entity ID: 20
Molecule	Chains	Length	Organism
DNA (40-MER)	0	40	synthetic construct

Entity ID: 21
Molecule	Chains	Length	Organism
DNA (40-MER)	1	40	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: 7.6 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-06-25 
• Released Date: 2018-10-03 
• Deposition Author(s): Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S., Kurumizaka, H.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	JP25116002
Japan Society for the Promotion of Science	Japan	JP15H04344
Japan Agency for Medical Research and Development (AMED)	Japan	JP18am0101076
Japan Agency for Medical Research and Development (AMED)	Japan	JP18am0101082
Japan Science and Technology	Japan	JPMJCR16G1
RIKEN Dynamic Structural Biology project	Japan	--

Revision History 

• Version 1.0: 2018-10-03
  Type: Initial release
• Version 1.1: 2018-10-24
  Type: Data collection, Database references
• Version 1.2: 2018-11-14
  Type: Data collection, Database references