5KGF

Structural model of 53BP1 bound to a ubiquitylated and methylated nucleosome, at 4.5 A resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.54 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The structural basis of modified nucleosome recognition by 53BP1.

Wilson, M.D.Benlekbir, S.Fradet-Turcotte, A.Sherker, A.Julien, J.P.McEwan, A.Noordermeer, S.M.Sicheri, F.Rubinstein, J.L.Durocher, D.

(2016) Nature 536: 100-103

  • DOI: 10.1038/nature18951

  • PubMed Abstract: 
  • DNA double-strand breaks (DSBs) elicit a histone modification cascade that controls DNA repair. This pathway involves the sequential ubiquitination of histones H1 and H2A by the E3 ubiquitin ligases RNF8 and RNF168, respectively. RNF168 ubiquitinates ...

    DNA double-strand breaks (DSBs) elicit a histone modification cascade that controls DNA repair. This pathway involves the sequential ubiquitination of histones H1 and H2A by the E3 ubiquitin ligases RNF8 and RNF168, respectively. RNF168 ubiquitinates H2A on lysine 13 and lysine 15 (refs 7, 8) (yielding H2AK13ub and H2AK15ub, respectively), an event that triggers the recruitment of 53BP1 (also known as TP53BP1) to chromatin flanking DSBs. 53BP1 binds specifically to H2AK15ub-containing nucleosomes through a peptide segment termed the ubiquitination-dependent recruitment motif (UDR), which requires the simultaneous engagement of histone H4 lysine 20 dimethylation (H4K20me2) by its tandem Tudor domain. How 53BP1 interacts with these two histone marks in the nucleosomal context, how it recognizes ubiquitin, and how it discriminates between H2AK13ub and H2AK15ub is unknown. Here we present the electron cryomicroscopy (cryo-EM) structure of a dimerized human 53BP1 fragment bound to a H4K20me2-containing and H2AK15ub-containing nucleosome core particle (NCP-ubme) at 4.5 Å resolution. The structure reveals that H4K20me2 and H2AK15ub recognition involves intimate contacts with multiple nucleosomal elements including the acidic patch. Ubiquitin recognition by 53BP1 is unusual and involves the sandwiching of the UDR segment between ubiquitin and the NCP surface. The selectivity for H2AK15ub is imparted by two arginine fingers in the H2A amino-terminal tail, which straddle the nucleosomal DNA and serve to position ubiquitin over the NCP-bound UDR segment. The structure of the complex between NCP-ubme and 53BP1 reveals the basis of 53BP1 recruitment to DSB sites and illuminates how combinations of histone marks and nucleosomal elements cooperate to produce highly specific chromatin responses, such as those elicited following chromosome breaks.



Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3.2
A, E
136Xenopus laevis
Find proteins for P84233 (Xenopus laevis)
Go to UniProtKB:  P84233
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
103Xenopus laevis
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1
C, G
130Homo sapiensMutations: K14R, T17S, K37R
Gene Names: HIST1H2AG, HIST1H2AI, HIST1H2AK, HIST1H2AL, HIST1H2AM (H2AFP, H2AFC, H2AFD, H2AFI, H2AFN)
Find proteins for P0C0S8 (Homo sapiens)
Go to UniProtKB:  P0C0S8
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B type 1-C/E/F/G/I
D, H
126Homo sapiensGene Names: HIST1H2BC, HIST1H2BE, HIST1H2BF, HIST1H2BG, HIST1H2BI (H2BFL, H2BFH, H2BFG, H2BFA, H2BFK)
Find proteins for P62807 (Homo sapiens)
Go to UniProtKB:  P62807
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Tumor suppressor p53-binding protein 1
L, K
21Homo sapiensGene Names: TP53BP1
Find proteins for Q12888 (Homo sapiens)
Go to Gene View: TP53BP1
Go to UniProtKB:  Q12888
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
O, M
76Homo sapiensGene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (145-MER)I145synthetic construct
Entity ID: 6
MoleculeChainsLengthOrganism
DNA (145-MER)J145synthetic construct
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M2L
Query on M2L
B, F
L-PEPTIDE LINKINGC7 H16 N2 O2 SLYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.54 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
Canadian Institutes of Health ResearchCanadaFDN143343
Canadian Institutes of Health ResearchCanadaMOP81294
Canadian Institutes of Health ResearchCanadaFDN143277

Revision History 

  • Version 1.0: 2016-07-27
    Type: Initial release
  • Version 1.1: 2016-08-10
    Type: Database references
  • Version 1.2: 2016-08-17
    Type: Database references
  • Version 1.3: 2017-09-13
    Type: Author supporting evidence, Data collection, Database references