8SN4

Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 2)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mechanisms of RNF168 nucleosome recognition and ubiquitylation.

Hu, Q.Zhao, D.Cui, G.Bhandari, J.Thompson, J.R.Botuyan, M.V.Mer, G.

(2024) Mol Cell 84: 839-853.e12

  • DOI: https://doi.org/10.1016/j.molcel.2023.12.036
  • Primary Citation of Related Structures:  
    8SMW, 8SMX, 8SMY, 8SMZ, 8SN0, 8SN1, 8SN2, 8SN3, 8SN4, 8SN5, 8SN6, 8SN7, 8SN8, 8SN9, 8SNA, 8TXV, 8TXW, 8TXX, 8U13, 8U14, 8UPF, 8UQ8, 8UQ9, 8UQA, 8UQB, 8UQC, 8UQD, 8UQE

  • PubMed Abstract: 

    RNF168 plays a central role in the DNA damage response (DDR) by ubiquitylating histone H2A at K13 and K15. These modifications direct BRCA1-BARD1 and 53BP1 foci formation in chromatin, essential for cell-cycle-dependent DNA double-strand break (DSB) repair pathway selection. The mechanism by which RNF168 catalyzes the targeted accumulation of H2A ubiquitin conjugates to form repair foci around DSBs remains unclear. Here, using cryoelectron microscopy (cryo-EM), nuclear magnetic resonance (NMR) spectroscopy, and functional assays, we provide a molecular description of the reaction cycle and dynamics of RNF168 as it modifies the nucleosome and recognizes its ubiquitylation products. We demonstrate an interaction of a canonical ubiquitin-binding domain within full-length RNF168, which not only engages ubiquitin but also the nucleosome surface, clarifying how such site-specific ubiquitin recognition propels a signal amplification loop. Beyond offering mechanistic insights into a key DDR protein, our study aids in understanding site specificity in both generating and interpreting chromatin ubiquitylation.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1
A, E
140Homo sapiensMutation(s): 0 
Gene Names: 
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UniProt GroupP68431
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
107Homo sapiensMutation(s): 0 
Gene Names: 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1-B/E
C, G
119Homo sapiensMutation(s): 2 
Gene Names: H2AC4H2AFMHIST1H2ABH2AC8H2AFAHIST1H2AE
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PHAROS:  P04908
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-J
D, H
128Homo sapiensMutation(s): 0 
Gene Names: H2BC11H2BFRHIST1H2BJ
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GTEx:  ENSG00000124635 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RNF168103Homo sapiensMutation(s): 0 
Gene Names: RNF168
EC: 2.3.2.27
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Find proteins for Q8IYW5 (Homo sapiens)
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GTEx:  ENSG00000163961 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 D3151Homo sapiensMutation(s): 4 
Gene Names: UBE2D3UBC5CUBCH5C
EC: 2.3.2.23 (PDB Primary Data), 2.3.2.24 (PDB Primary Data)
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GTEx:  ENSG00000109332 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Polyubiquitin-B81Homo sapiensMutation(s): 0 
Gene Names: UBB
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GTEx:  ENSG00000170315 
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (147-MER)147Homo sapiens
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (147-MER)147Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18.2-3874
RECONSTRUCTIONRELION3.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM136262
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01 CA132878

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-17
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Database references
  • Version 1.2: 2024-03-20
    Changes: Database references