9UXW | pdb_00009uxw

RNA polymerase II elongation complex stalled at SHL(-0.5) in the hexasome of the overlapping dinucleosome

PDB DOI: https://doi.org/10.2210/pdb9UXW/pdb
EM Map EMD-64603: EMDB EMDataResource

Classification: TRANSCRIPTION
Organism(s): Komagataella phaffii GS115, synthetic construct, Homo sapiens
Expression System: Escherichia coli, Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-05-14 Released: 2026-07-01
Deposition Author(s): Chen, Z., Ho, C., Tanaka, H., Kujirai, T., Ogasawara, M., Ehara, H., Sekine, S., Takizawa, Y., Kurumizaka, H.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology, Japan Agency for Medical Research and Development (AMED)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.74 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural basis of asymmetric transcription through a composite nucleosome formed by a hexasome and an octasome

Chen, Z., Ho, C., Tanaka, H., Kujirai, T., Ogasawara, M., Ehara, H., Sekine, S., Takizawa, Y., Kurumizaka, H.

To be published.

Macromolecule Content

Total Structure Weight: 867.38 kDa
Atom Count: 51,489
Modeled Residue Count: 5,672
Deposited Residue Count: 6,810
Unique protein chains: 16
Unique nucleic acid chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit	A	1,743	Komagataella phaffii GS115	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for C4R4Y0 (Komagataella phaffii (strain GS115 / ATCC 20864)) Explore C4R4Y0 Go to UniProtKB: C4R4Y0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C4R4Y0
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	B	1,227	Komagataella phaffii GS115	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for C4QZQ7 (Komagataella phaffii (strain GS115 / ATCC 20864)) Explore C4QZQ7 Go to UniProtKB: C4QZQ7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C4QZQ7
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase II third largest subunit B44, part of central core	C	304	Komagataella phaffii GS115	Mutation(s): 0
UniProt
Find proteins for C4R7L2 (Komagataella phaffii (strain GS115 / ATCC 20864)) Explore C4R7L2 Go to UniProtKB: C4R7L2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C4R7L2
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase II subunit B32	D	186	Komagataella phaffii GS115	Mutation(s): 0
UniProt
Find proteins for C4R2U9 (Komagataella phaffii (strain GS115 / ATCC 20864)) Explore C4R2U9 Go to UniProtKB: C4R2U9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C4R2U9
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III	E	214	Komagataella phaffii GS115	Mutation(s): 0
UniProt
Find proteins for C4R3P8 (Komagataella phaffii (strain GS115 / ATCC 20864)) Explore C4R3P8 Go to UniProtKB: C4R3P8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C4R3P8
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III	F	155	Komagataella phaffii GS115	Mutation(s): 0
UniProt
Find proteins for C4R1V1 (Komagataella phaffii (strain GS115 / ATCC 20864)) Explore C4R1V1 Go to UniProtKB: C4R1V1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C4R1V1
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase II subunit	G	171	Komagataella phaffii GS115	Mutation(s): 0
UniProt
Find proteins for C4R9A1 (Komagataella phaffii (strain GS115 / ATCC 20864)) Explore C4R9A1 Go to UniProtKB: C4R9A1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C4R9A1
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC3	H	145	Komagataella phaffii GS115	Mutation(s): 0
UniProt
Find proteins for C4R273 (Komagataella phaffii (strain GS115 / ATCC 20864)) Explore C4R273 Go to UniProtKB: C4R273
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C4R273
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit	I	115	Komagataella phaffii GS115	Mutation(s): 0
UniProt
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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F2QPE6
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III	J	72	Komagataella phaffii GS115	Mutation(s): 0
UniProt
Find proteins for C4R009 (Komagataella phaffii (strain GS115 / ATCC 20864)) Explore C4R009 Go to UniProtKB: C4R009
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C4R009
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase II subunit B12.5	K	118	Komagataella phaffii GS115	Mutation(s): 0
UniProt
Find proteins for C4R3Z5 (Komagataella phaffii (strain GS115 / ATCC 20864)) Explore C4R3Z5 Go to UniProtKB: C4R3Z5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C4R3Z5
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase subunit ABC10-alpha	L	72	Komagataella phaffii GS115	Mutation(s): 0
UniProt
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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F2QMI1
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.3	O [auth a], S [auth e], W [auth k], Y [auth m]	139	Homo sapiens	Mutation(s): 0 Gene Names: H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B
UniProt & NIH Common Fund Data Resources
Find proteins for P84243 (Homo sapiens) Explore P84243 Go to UniProtKB: P84243
PHAROS: P84243 GTEx: ENSG00000132475 ENSG00000163041
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P84243
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Reference Sequence

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	P [auth b], T [auth f], X [auth l], Z [auth n]	106	Homo sapiens	Mutation(s): 0 Gene Names: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G... H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4C16, H4-16, HIST4H4
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805 Go to UniProtKB: P62805
PHAROS: P62805 GTEx: ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62805
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Reference Sequence

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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1-B/E	AA [auth o], Q [auth c], U [auth g]	133	Homo sapiens	Mutation(s): 0 Gene Names: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE
UniProt & NIH Common Fund Data Resources
Find proteins for P04908 (Homo sapiens) Explore P04908 Go to UniProtKB: P04908
PHAROS: P04908 GTEx: ENSG00000277075 ENSG00000278463
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04908
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Reference Sequence

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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-J	BA [auth p], R [auth d], V [auth h]	129	Homo sapiens	Mutation(s): 0 Gene Names: H2BC11, H2BFR, HIST1H2BJ
UniProt & NIH Common Fund Data Resources
Find proteins for P06899 (Homo sapiens) Explore P06899 Go to UniProtKB: P06899
PHAROS: P06899 GTEx: ENSG00000124635
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06899
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 13
RNA (5'-R(PGPUPCPGPCPUPCPUPUPCPCPUPCPC)-3')	M [auth P]	14	synthetic construct
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 14
DNA (254-MER)	N [auth T]	254	synthetic construct
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 19
DNA (254-MER)	CA [auth N]	254	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain LA [auth L] SDF format, chain KA [auth J] SDF format, chain JA [auth I] SDF format, chain IA [auth I] SDF format, chain HA [auth C] SDF format, chain GA [auth B] SDF format, chain EA [auth A] SDF format, chain DA [auth A] MOL2 format, chain LA [auth L] MOL2 format, chain KA [auth J] MOL2 format, chain JA [auth I] MOL2 format, chain IA [auth I] MOL2 format, chain HA [auth C] MOL2 format, chain GA [auth B] MOL2 format, chain EA [auth A] MOL2 format, chain DA [auth A] mmCIF format, chain LA [auth L] mmCIF format, chain KA [auth J] mmCIF format, chain JA [auth I] mmCIF format, chain IA [auth I] mmCIF format, chain HA [auth C] mmCIF format, chain GA [auth B] mmCIF format, chain EA [auth A] mmCIF format, chain DA [auth A]	DA [auth A] EA [auth A] GA [auth B] HA [auth C] IA [auth I] DA [auth A], EA [auth A], GA [auth B], HA [auth C], IA [auth I], JA [auth I], KA [auth J], LA [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain DA [auth A] Focus chain EA [auth A] Focus chain GA [auth B] Focus chain HA [auth C] Focus chain IA [auth I] Focus chain JA [auth I] Focus chain KA [auth J] Focus chain LA [auth L] Interactions & Density Focus chain DA [auth A] Focus chain EA [auth A] Focus chain GA [auth B] Focus chain HA [auth C] Focus chain IA [auth I] Focus chain JA [auth I] Focus chain KA [auth J] Focus chain LA [auth L]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain FA [auth A] MOL2 format, chain FA [auth A] mmCIF format, chain FA [auth A]	FA [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain FA [auth A] Interactions & Density Focus chain FA [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.74 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286
RECONSTRUCTION	cryoSPARC	v4

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-07-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP20H05690
Japan Society for the Promotion of Science (JSPS)	Japan	JP25K18403
Japan Society for the Promotion of Science (JSPS)	Japan	JP24H02319
Japan Society for the Promotion of Science (JSPS)	Japan	JP24H00062
Japan Society for the Promotion of Science (JSPS)	Japan	JP20H03201
Japan Society for the Promotion of Science (JSPS)	Japan	JP23K17392
Japan Society for the Promotion of Science (JSPS)	Japan	JP24H02328
Japan Society for the Promotion of Science (JSPS)	Japan	JP23H05475
Japan Society for the Promotion of Science (JSPS)	Japan	JP20H05906
Japan Science and Technology	Japan	JPMJER1901
Japan Science and Technology	Japan	JPMJCR24T3
Japan Agency for Medical Research and Development (AMED)	Japan	JP25ama121009
Japan Agency for Medical Research and Development (AMED)	Japan	JP25ama121002

Revision History (Full details and data files)

Version 1.0: 2026-07-01
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

9UXW | pdb_00009uxw

RNA polymerase II elongation complex stalled at SHL(-0.5) in the hexasome of the overlapping dinucleosome

Literature

Structural basis of asymmetric transcription through a composite nucleosome formed by a hexasome and an octasome

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Entity ID: 11

UniProt

Entity Groups

Sequence Annotations

Entity ID: 12

UniProt

Entity Groups

Sequence Annotations

Entity ID: 15

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 16

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 17

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 18

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 13

Sequence Annotations

Entity ID: 14

Sequence Annotations

Entity ID: 19

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation