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 - A6B2C1DEFGHIJKLMN 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 773.32 kDa 
• Atom Count: 43983 
• Residue Count: 5004 
• 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
• EMDataResource: EMD-6985

• Classification: TRANSCRIPTION/RNA/DNA
• Organism(s): Komagataella phaffii GS115, Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• 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: 7.60 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 
• DOI: 10.1126/science.aau9904
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Genomic DNA forms chromatin, in which the nucleosome is the repeating unit. The mechanism by which RNA polymerase II (RNAPII) transcribes the nucleosomal DNA remains unclear. Here we report the cryo-electron microscopy structures of RNAPII-nucleosome complexes in which RNAPII pauses at the superhelical locations SHL(-6), SHL(-5), SHL(-2), and SHL(-1) of the nucleosome. RNAPII pauses at the major histone-DNA contact sites, and the nucleosome interactions with the RNAPII subunits stabilize the pause. These structures reveal snapshots of nucleosomal transcription, in which RNAPII gradually tears DNA from the histone surface while preserving the histone octamer. The nucleosomes in the SHL(-1) complexes are bound to a "foreign" DNA segment, which might explain the histone transfer mechanism. These results provide the foundations for understanding chromatin transcription and epigenetic regulation.

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Organizational Affiliation: 

Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerase subunit	A	1743	Komagataella phaffii GS115	Mutation(s): 0  Gene Names: PAS_chr3_0568 EC: 2.7.7.6
Find proteins for C4R4Y0 (Komagataella phaffii (strain GS115 / ATCC 20864)) Explore C4R4Y0  Go to UniProtKB:  C4R4Y0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerase subunit beta	B	1227	Komagataella phaffii GS115	Mutation(s): 0  Gene Names: PAS_chr2-1_0125 EC: 2.7.7.6
Find proteins for C4QZQ7 (Komagataella phaffii (strain GS115 / ATCC 20864)) Explore C4QZQ7  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 GS115	Mutation(s): 0  Gene Names: PAS_chr4_0344
Find proteins for C4R7L2 (Komagataella phaffii (strain GS115 / ATCC 20864)) Explore C4R7L2  Go to UniProtKB:  C4R7L2

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerases I, II, and III subunit RPABC3	H	145	Komagataella phaffii GS115	Mutation(s): 0  Gene Names: PAS_chr2-2_0309
Find proteins for C4R273 (Komagataella phaffii (strain GS115 / ATCC 20864)) Explore C4R273  Go to UniProtKB:  C4R273

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details
RNA polymerase II subunit B12.5	K	118	Komagataella phaffii GS115	Mutation(s): 0  Gene Names: PAS_chr3_0244
Find proteins for C4R3Z5 (Komagataella phaffii (strain GS115 / ATCC 20864)) Explore C4R3Z5  Go to UniProtKB:  C4R3Z5

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details
RNA polymerase subunit ABC10-alpha	L	72	Komagataella phaffii GS115	Mutation(s): 0
Find proteins for F2QMI1 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1)) Explore F2QMI1  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, H3.3A, H3F3, PP781, H3F3B, H3.3B, H3-3A, H3-3B
Find proteins for P84243 (Homo sapiens) Explore P84243  Go to UniProtKB:  P84243
NIH Common Fund Data Resources
PHAROS  P84243 GTEx  ENSG00000163041

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 GS115	Mutation(s): 0  Gene Names: PAS_chr2-1_0223
Find proteins for C4R009 (Komagataella phaffii (strain GS115 / ATCC 20864)) Explore C4R009  Go to UniProtKB:  C4R009

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details
Histone H4	b, f	106	Homo sapiens	Mutation(s): 0  Gene Names:  HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4, H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4-16
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
NIH Common Fund Data Resources
PHAROS  P62805 GTEx  ENSG00000274618GTEx  ENSG00000197238GTEx  ENSG00000197837GTEx  ENSG00000158406GTEx  ENSG00000278705GTEx  ENSG00000197061GTEx  ENSG00000270882GTEx  ENSG00000270276GTEx  ENSG00000273542GTEx  ENSG00000277157GTEx  ENSG00000276966GTEx  ENSG00000276180GTEx  ENSG00000278637GTEx  ENSG00000275126

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, H2AFM, HIST1H2AE, H2AFA, H2AC4, H2AC8
Find proteins for P04908 (Homo sapiens) Explore P04908  Go to UniProtKB:  P04908
NIH Common Fund Data Resources
PHAROS  P04908 GTEx  ENSG00000277075GTEx  ENSG00000278463

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, H2BC11
Find proteins for P06899 (Homo sapiens) Explore P06899  Go to UniProtKB:  P06899
NIH Common Fund Data Resources
PHAROS  P06899 GTEx  ENSG00000124635

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
RNA polymerase II subunit B32	D	186	Komagataella phaffii GS115	Mutation(s): 0  Gene Names: PAS_chr2-2_0104
Find proteins for C4R2U9 (Komagataella phaffii (strain GS115 / ATCC 20864)) Explore C4R2U9  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 GS115	Mutation(s): 0  Gene Names: PAS_chr3_0157
Find proteins for C4R3P8 (Komagataella phaffii (strain GS115 / ATCC 20864)) Explore C4R3P8  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 GS115	Mutation(s): 0  Gene Names: PAS_chr2-2_0434
Find proteins for C4R1V1 (Komagataella phaffii (strain GS115 / ATCC 20864)) Explore C4R1V1  Go to UniProtKB:  C4R1V1

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details
RNA polymerase II subunit	G	171	Komagataella phaffii GS115	Mutation(s): 0  Gene Names: PAS_chr4_0906
Find proteins for C4R9A1 (Komagataella phaffii (strain GS115 / ATCC 20864)) Explore C4R9A1  Go to UniProtKB:  C4R9A1

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerase subunit	I	115	Komagataella phaffii GS115	Mutation(s): 0
Find proteins for F2QPE6 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1)) Explore F2QPE6  Go to UniProtKB:  F2QPE6

Entity ID: 21
Molecule	Chains	Length	Organism
DNA (40-MER)	1	40	synthetic construct

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

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: 7.60 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
  Changes: Data collection, Database references
• Version 1.2: 2018-11-14
  Changes: Data collection, Database references
• Version 1.3: 2019-11-06
  Changes: Data collection, Other