8H0V

RNA polymerase II transcribing a chromatosome (type I)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structural basis of RNA polymerase II transcription on the chromatosome containing linker histone H1.

Hirano, R.Ehara, H.Kujirai, T.Uejima, T.Takizawa, Y.Sekine, S.I.Kurumizaka, H.

(2022) Nat Commun 13: 7287-7287

  • DOI: https://doi.org/10.1038/s41467-022-35003-z
  • Primary Citation of Related Structures:  
    8H0V, 8H0W

  • PubMed Abstract: 

    In chromatin, linker histone H1 binds to nucleosomes, forming chromatosomes, and changes the transcription status. However, the mechanism by which RNA polymerase II (RNAPII) transcribes the DNA in the chromatosome has remained enigmatic. Here we report the cryo-electron microscopy (cryo-EM) structures of transcribing RNAPII-chromatosome complexes (forms I and II), in which RNAPII is paused at the entry linker DNA region of the chromatosome due to H1 binding. In the form I complex, the H1 bound to the nucleosome restricts the linker DNA orientation, and the exit linker DNA is captured by the RNAPII DNA binding cleft. In the form II complex, the RNAPII progresses a few bases ahead by releasing the exit linker DNA from the RNAPII cleft, and directly clashes with the H1 bound to the nucleosome. The transcription elongation factor Spt4/5 masks the RNAPII DNA binding region, and drastically reduces the H1-mediated RNAPII pausing.


  • Organizational Affiliation

    Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan. kurumizaka@iqb.u-tokyo.ac.jp.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit1,743Komagataella phaffiiMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for C4R4Y0 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,227Komagataella phaffiiMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for C4QZQ7 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II third largest subunit B44, part of central core304Komagataella phaffiiMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit B32186Komagataella phaffiiMutation(s): 0 
UniProt
Find proteins for C4R2U9 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1214Komagataella phaffiiMutation(s): 0 
UniProt
Find proteins for C4R3P8 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III155Komagataella phaffiiMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit171Komagataella phaffiiMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3145Komagataella phaffiiMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit115Komagataella phaffiiMutation(s): 0 
UniProt
Find proteins for F2QPE6 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III72Komagataella phaffiiMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit B12.5118Komagataella phaffiiMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase subunit ABC10-alpha72Komagataella phaffiiMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1P [auth a],
T [auth e]
139Homo sapiensMutation(s): 0 
Gene Names: H3C1
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4Q [auth b],
U [auth f]
106Homo sapiensMutation(s): 0 
Gene Names: H4C1
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1-B/ER [auth c],
V [auth g]
133Homo sapiensMutation(s): 0 
Gene Names: H2AC4H2AFMHIST1H2ABH2AC8H2AFAHIST1H2AE
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-JS [auth d],
W [auth h]
129Homo sapiensMutation(s): 0 
Gene Names: H2BC11H2BFRHIST1H2BJ
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PHAROS:  P06899
GTEx:  ENSG00000124635 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H1.2X [auth u]219Homo sapiensMutation(s): 0 
Gene Names: H1-2H1F2HIST1H1C
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GTEx:  ENSG00000187837 
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Entity ID: 13
MoleculeChains LengthOrganismImage
RNA (5'-R(P*AP*GP*CP*AP*AP*UP*AP*GP*GP*AP*GP*CP*UP*U)-3')M [auth P]14synthetic construct
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Entity ID: 14
MoleculeChains LengthOrganismImage
DNA (261-MER)N [auth T]261synthetic construct
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Entity ID: 15
MoleculeChains LengthOrganismImage
DNA (261-MER)O [auth N]261synthetic construct
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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 
BA [auth B]
CA [auth C]
DA [auth I]
EA [auth I]
FA [auth J]
BA [auth B],
CA [auth C],
DA [auth I],
EA [auth I],
FA [auth J],
GA [auth L],
Y [auth A],
Z [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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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)JapanJP18H05534
Japan Society for the Promotion of Science (JSPS)JapanJP20H00449
Japan Society for the Promotion of Science (JSPS)JapanJP20H05690
Japan Agency for Medical Research and Development (AMED)JapanJP22ama121009
Japan Science and TechnologyJapanJPMJER1901

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-07
    Type: Initial release