8XSO | pdb_00008xso

RNA polymerase II elongation complex transcribing genomic DNA extracted from human nuclei

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 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

Multiple structures of RNA polymerase II isolated from human nuclei by ChIP-CryoEM analysis

Kujirai, T., Kato, J., Yamamoto, K., Hirai, S., Fujii, T., Maehara, K., Harada, A., Negishi, L., Ogasawara, M., Yamaguchi, Y., Ohkawa, Y., Takizawa, Y., Kurumizaka, H.

To be published.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11,970Homo sapiensMutation(s): 0 
EC: 2.7.7.6 (PDB Primary Data), 2.7.7.48 (PDB Primary Data), 3.1.13 (UniProt)
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PHAROS:  P24928
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UniProt GroupP24928
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB21,174Homo sapiensMutation(s): 0 
EC: 2.7.7.6 (PDB Primary Data), 3.1.13 (UniProt), 2.7.7.48 (UniProt)
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Find proteins for P30876 (Homo sapiens)
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PHAROS:  P30876
GTEx:  ENSG00000047315 
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UniProt GroupP30876
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3292Homo sapiensMutation(s): 0 
Gene Names: POLR2C, A-152E5.7
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PHAROS:  P19387
GTEx:  ENSG00000102978 
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UniProt GroupP19387
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4142Homo sapiensMutation(s): 0 
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PHAROS:  O15514
GTEx:  ENSG00000144231 
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UniProt GroupO15514
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1210Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000099817 
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UniProt GroupP19388
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2127Homo sapiensMutation(s): 0 
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PHAROS:  P61218
GTEx:  ENSG00000100142 
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UniProt GroupP61218
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7172Homo sapiensMutation(s): 0 
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PHAROS:  P62487
GTEx:  ENSG00000168002 
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UniProt GroupP62487
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3150Homo sapiensMutation(s): 0 
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PHAROS:  P52434
GTEx:  ENSG00000163882 
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UniProt GroupP52434
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9125Homo sapiensMutation(s): 0 
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PHAROS:  P36954
GTEx:  ENSG00000105258 
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UniProt GroupP36954
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC567Homo sapiensMutation(s): 0 
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PHAROS:  P62875
GTEx:  ENSG00000177700 
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UniProt GroupP62875
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11-a117Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000005075 
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UniProt GroupP52435
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC458Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147669 
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UniProt GroupP53803
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Entity ID: 13
MoleculeChains LengthOrganismImage
DNAM [auth N]37Homo sapiens
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Entity ID: 14
MoleculeChains LengthOrganismImage
RNAN [auth P]11Homo sapiens
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Entity ID: 15
MoleculeChains LengthOrganismImage
DNAO [auth T]37Homo sapiens
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
P [auth A]
Q [auth A]
S [auth B]
T [auth C]
U [auth I]
P [auth A],
Q [auth A],
S [auth B],
T [auth C],
U [auth I],
V [auth I],
W [auth J],
X [auth L]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
R [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP20H03201
Japan Society for the Promotion of Science (JSPS)JapanJP20H05690
Japan Society for the Promotion of Science (JSPS)JapanJP22K15033
Japan Society for the Promotion of Science (JSPS)JapanJP23K17392
Japan Society for the Promotion of Science (JSPS)JapanJP22KJ0858
Japan Society for the Promotion of Science (JSPS)JapanJP22K06098
Japan Society for the Promotion of Science (JSPS)JapanJP20H00449
Japan Society for the Promotion of Science (JSPS)JapanJP23H05475
Japan Science and TechnologyJapanJPMJER1901
Japan Agency for Medical Research and Development (AMED)JapanJP22ama121009

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-07
    Type: Initial release