7XT7

RNA polymerase II elongation complex transcribing a nucleosome (EC49B)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 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 nucleosome disassembly and reassembly by RNAPII elongation complex with FACT.

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

(2022) Science 377: eabp9466-eabp9466

  • DOI: https://doi.org/10.1126/science.abp9466
  • Primary Citation of Related Structures:  
    7XN7, 7XSE, 7XSX, 7XSZ, 7XT7, 7XTD, 7XTI

  • PubMed Abstract: 

    During gene transcription, RNA polymerase II (RNAPII) traverses nucleosomes in chromatin, but the mechanism has remained elusive. Using cryo-electron microscopy, we obtained structures of the RNAPII elongation complex (EC) passing through a nucleosome in the presence of the transcription elongation factors Spt6, Spn1, Elf1, Spt4/5, and Paf1C and the histone chaperone FACT (facilitates chromatin transcription). The structures show snapshots of EC progression on DNA mediating downstream nucleosome disassembly, followed by its reassembly upstream of the EC, which is facilitated by FACT. FACT dynamically adapts to successively occurring subnucleosome intermediates, forming an interface with the EC. Spt6, Spt4/5, and Paf1C form a "cradle" at the EC DNA-exit site and support the upstream nucleosome reassembly. These structures explain the mechanism by which the EC traverses nucleosomes while maintaining the chromatin structure and epigenetic information.


  • Organizational Affiliation

    Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.


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
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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 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit B32186Komagataella phaffiiMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1214Komagataella phaffiiMutation(s): 0 
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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 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit171Komagataella phaffiiMutation(s): 0 
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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 
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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 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit B12.5118Komagataella phaffiiMutation(s): 0 
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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: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor 1 homolog113Komagataella phaffiiMutation(s): 0 
Gene Names: PAS_c121_0006
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT4Q [auth V]108Komagataella phaffiiMutation(s): 0 
Gene Names: PAS_chr2-1_0350
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT5R [auth W]911Komagataella phaffiiMutation(s): 0 
Gene Names: PAS_chr3_1136
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor Spt6S [auth m]1,503Komagataella phaffiiMutation(s): 0 
Gene Names: PAS_chr4_0308
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase IIT [auth n]417Komagataella phaffiiMutation(s): 0 
Gene Names: PAS_chr4_0349
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Component of the Paf1p complexU [auth q]1,084Komagataella phaffiiMutation(s): 0 
Gene Names: PAS_chr3_1035
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
RNAPII-associated chromatin remodeling Paf1 complex subunitV [auth r]544Komagataella phaffiiMutation(s): 0 
Gene Names: RTF1PP7435_Chr1-1405
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Leo1W [auth u]459Komagataella phaffiiMutation(s): 0 
Gene Names: PAS_chr3_1154
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
RNAP II-associated proteinX [auth v]396Komagataella phaffiiMutation(s): 0 
Gene Names: PAS_chr4_0902
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4pY [auth x]395Komagataella phaffiiMutation(s): 0 
Gene Names: PAS_chr2-1_0674
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.3DA [auth e],
Z [auth a]
139Homo sapiensMutation(s): 0 
Gene Names: H3F3AH3.3AH3F3PP781H3F3BH3.3B
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4AA [auth b],
EA [auth f]
106Homo sapiensMutation(s): 0 
Gene Names: 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1-B/EBA [auth c],
FA [auth g]
133Homo sapiensMutation(s): 0 
Gene Names: H2AC4H2AFMHIST1H2ABH2AC8H2AFAHIST1H2AE
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-JCA [auth d],
GA [auth h]
129Homo sapiensMutation(s): 0 
Gene Names: H2BC11H2BFRHIST1H2BJ
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PHAROS:  P06899
GTEx:  ENSG00000124635 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
FACT complex subunitHA [auth j]1,008Komagataella phaffiiMutation(s): 0 
Gene Names: SPT16PP7435_Chr1-1329
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
FACT complex subunit POB3IA [auth k]531Komagataella phaffiiMutation(s): 0 
Gene Names: POB3PP7435_Chr1-0311
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Entity ID: 14
MoleculeChains LengthOrganismImage
DNA (198-MER)198synthetic construct
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Entity ID: 15
MoleculeChains LengthOrganismImage
RNA (5'-R(P*GP*AP*CP*CP*CP*GP*GP*GP*UP*GP*UP*CP*UP*UP*CP*CP*CP*CP*A)-3')O [auth P]19synthetic construct
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Entity ID: 16
MoleculeChains LengthOrganismImage
DNA (198-MER)P [auth T]198synthetic 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 
JA [auth A]
KA [auth A]
MA [auth B]
NA [auth C]
OA [auth I]
JA [auth A],
KA [auth A],
MA [auth B],
NA [auth C],
OA [auth I],
PA [auth I],
QA [auth J],
RA [auth L],
SA [auth M],
TA [auth V]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 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)JapanJP20H05690
Japan Society for the Promotion of Science (JSPS)JapanJP20H00449
Japan Society for the Promotion of Science (JSPS)JapanJP18H05534
Japan Agency for Medical Research and Development (AMED)JapanJP20am0101082
Japan Agency for Medical Research and Development (AMED)JapanJP21am0101076
Japan Science and TechnologyJapanJPMJER1901

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-12
    Type: Initial release