7UND

Pol II-DSIF-SPT6-PAF1c-TFIIS-nucleosome complex (stalled at +38)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of nucleosome retention during transcription elongation.

Filipovski, M.Soffers, J.H.M.Vos, S.M.Farnung, L.

(2022) Science 376: 1313-1316

  • DOI: https://doi.org/10.1126/science.abo3851
  • Primary Citation of Related Structures:  
    7UNC, 7UND

  • PubMed Abstract: 

    In eukaryotes, RNA polymerase (Pol) II transcribes chromatin and must move past nucleosomes, often resulting in nucleosome displacement. How Pol II unwraps the DNA from nucleosomes to allow transcription and how DNA rewraps to retain nucleosomes has been unclear. Here, we report the 3.0-angstrom cryo-electron microscopy structure of a mammalian Pol II-DSIF-SPT6-PAF1c-TFIIS-nucleosome complex stalled 54 base pairs within the nucleosome. The structure provides a mechanistic basis for nucleosome retention during transcription elongation where upstream DNA emerging from the Pol II cleft has rewrapped the proximal side of the nucleosome. The structure uncovers a direct role for Pol II and transcription elongation factors in nucleosome retention and explains how nucleosomes are retained to prevent the disruption of chromatin structure across actively transcribed genes.


  • Organizational Affiliation

    Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit1,984Sus scrofaMutation(s): 0 
EC: 2.7.7.6
UniProt
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UniProt GroupA0A7M4DUC2
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,251Sus scrofaMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for A0A4X1TVZ5 (Sus scrofa)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3275Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RPOL4c domain-containing protein184Sus scrofaMutation(s): 0 
UniProt
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UniProt GroupA0A8D1GCS3
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit E210Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2127Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7172Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
RPB8150Sus scrofaMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
RPB9125Sus scrofaMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
RPB1067Sus scrofaMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
RPB11117Sus scrofaMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit K58Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT61,729Homo sapiensMutation(s): 0 
Gene Names: SUPT6HKIAA0162SPT6H
UniProt & NIH Common Fund Data Resources
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PHAROS:  Q7KZ85
GTEx:  ENSG00000109111 
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UniProt GroupQ7KZ85
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor A protein 1304Homo sapiensMutation(s): 0 
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PHAROS:  P23193
GTEx:  ENSG00000187735 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase-associated protein CTR9 homolog1,179Homo sapiensMutation(s): 0 
Gene Names: CTR9KIAA0155SH2BP1
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PHAROS:  Q6PD62
GTEx:  ENSG00000198730 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase-associated protein RTF1 homolog713Homo sapiensMutation(s): 0 
Gene Names: RTF1KIAA0252
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PHAROS:  Q92541
GTEx:  ENSG00000137815 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase-associated protein LEO1T [auth U]666Homo sapiensMutation(s): 0 
Gene Names: LEO1RDL
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PHAROS:  Q8WVC0
GTEx:  ENSG00000166477 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II-associated factor 1 homologU [auth V]531Homo sapiensMutation(s): 0 
Gene Names: PAF1PD2
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GTEx:  ENSG00000006712 
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UniProt GroupQ8N7H5
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
WDR61V [auth W]305Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000140395 
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UniProt GroupQ9GZS3
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
ParafibrominW [auth X]531Homo sapiensMutation(s): 0 
Gene Names: CDC73C1orf28HRPT2
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Find proteins for Q6P1J9 (Homo sapiens)
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PHAROS:  Q6P1J9
GTEx:  ENSG00000134371 
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UniProt GroupQ6P1J9
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT4X [auth Y]117Homo sapiensMutation(s): 0 
Gene Names: SUPT4H1SPT4HSUPT4H
UniProt & NIH Common Fund Data Resources
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PHAROS:  P63272
GTEx:  ENSG00000213246 
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UniProt GroupP63272
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT5Y [auth Z]1,087Homo sapiensMutation(s): 0 
Gene Names: SUPT5HSPT5SPT5H
UniProt & NIH Common Fund Data Resources
Find proteins for O00267 (Homo sapiens)
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PHAROS:  O00267
GTEx:  ENSG00000196235 
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UniProt GroupO00267
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2DA [auth e],
Z [auth a]
136Xenopus laevisMutation(s): 1 
UniProt
Find proteins for P84233 (Xenopus laevis)
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UniProt GroupP84233
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4AA [auth b],
EA [auth f]
103Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2ABA [auth c],
FA [auth g]
130Xenopus laevisMutation(s): 0 
Gene Names: hist1h2ajLOC494591XELAEV_18003602mg
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B 1.1CA [auth d],
GA [auth h]
123Xenopus laevisMutation(s): 1 
UniProt
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UniProt GroupP02281
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Entity ID: 14
MoleculeChains LengthOrganismImage
Non-template DNA209synthetic construct
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Entity ID: 16
MoleculeChains LengthOrganismImage
RNA18synthetic construct
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Entity ID: 19
MoleculeChains LengthOrganismImage
Template DNAS [auth T]215synthetic construct
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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HA [auth A]
IA [auth A]
KA [auth B]
LA [auth C]
MA [auth I]
HA [auth A],
IA [auth A],
KA [auth B],
LA [auth C],
MA [auth I],
NA [auth I],
OA [auth J],
PA [auth R],
QA [auth Y]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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JA [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTCoot0.9.7
MODEL REFINEMENTISOLDE1.3
MODEL REFINEMENTPHENIX1.20.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited StatesNA

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-19
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Data collection, Refinement description, Structure summary