Biological Assembly 1  

 3D View: Structure

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 12-mer - A2B2C2D2E2F2 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Hetero 12-mer -A6B2C2D2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 221341.95 
• Atom Count: 13782 
• Residue Count: 1474 
• Unique protein chains: 6
• Unique nucleic acid chains: 2

5KGF

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

• DOI: 10.2210/pdb5KGF/pdb
• EMDataBank: EMD-8246

• Classification: STRUCTURAL PROTEIN/DNA
• Organism(s): synthetic construct, Xenopus laevis, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 3 


• Deposited: 2016-06-13 Released: 2016-07-27 
• Deposition Author(s): Wilson, M.D., Benlekbir, S., Sicheri, F., Rubinstein, J.L., Durocher, D.
• Funding Organization(s): Canadian Institutes of Health Research 

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Experimental Data Snapshot

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

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

• PubMed: 27462807 
• 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 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
Molecule	Chains	Sequence Length	Organism	Details
Histone H3.2	A, E	136	Xenopus laevis	Mutation(s): 0
Find proteins for P84233 (Xenopus laevis) Go to UniProtKB:  P84233

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Histone H4	B, F	103	Xenopus laevis	Mutation(s): 0
Find proteins for P62799 (Xenopus laevis) Go to UniProtKB:  P62799

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Histone H2A type 1	C, G	130	Homo sapiens	Mutation(s): 3  Gene Names: HIST1H2AG, HIST1H2AI, HIST1H2AK, HIST1H2AL, HIST1H2AM (H2AFP, H2AFC, H2AFD, H2AFI, H2AFN)
Find proteins for P0C0S8 (Homo sapiens) Go to Gene View: HIST1H2AG HIST1H2AI HIST1H2AK HIST1H2AL HIST1H2AM Go to UniProtKB:  P0C0S8

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Histone H2B type 1-C/E/F/G/I	D, H	126	Homo sapiens	Mutation(s): 0  Gene Names: HIST1H2BC, HIST1H2BE, HIST1H2BF, HIST1H2BG, HIST1H2BI (H2BFL, H2BFH, H2BFG, H2BFA, H2BFK)
Find proteins for P62807 (Homo sapiens) Go to Gene View: HIST1H2BC HIST1H2BE HIST1H2BF HIST1H2BG HIST1H2BI Go to UniProtKB:  P62807

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details
Tumor suppressor p53-binding protein 1	L, K	21	Homo sapiens	Mutation(s): 0  Gene Names: TP53BP1
Find proteins for Q12888 (Homo sapiens) Go to Gene View: TP53BP1 Go to UniProtKB:  Q12888

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details
Ubiquitin	O, M	76	Homo sapiens	Mutation(s): 0  Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens) Go to Gene View: UBB Go to UniProtKB:  P0CG47

Entity ID: 5
Molecule	Chains	Length	Organism
DNA (145-MER)	I	145	synthetic construct

Entity ID: 6
Molecule	Chains	Length	Organism
DNA (145-MER)	J	145	synthetic construct

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
M2L	B, F	L-PEPTIDE LINKING	C7 H16 N2 O2 S		LYS

Experimental Data & Validation

Experimental Data

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

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-06-13 
• Released Date: 2016-07-27 
• Deposition Author(s): Wilson, M.D., Benlekbir, S., Sicheri, F., Rubinstein, J.L., Durocher, D.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research	Canada	FDN143343
Canadian Institutes of Health Research	Canada	MOP81294
Canadian Institutes of Health Research	Canada	FDN143277

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
• Version 1.4: 2018-07-18
  Type: Data collection