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

Literature

Macromolecules
Sequence Display for 5KGF

Classification: STRUCTURAL PROTEIN / DNA

Total Structure Weight: 221341.95


Macromolecule Entities
Molecule Chains Length Organism Details
Histone H3.2 A, E 136 Xenopus laevis Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Histone H4 B, F 103 Xenopus laevis Details: cysteine alkylation at position 20
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Histone H2A type 1 C, G 130 Homo sapiens Mutation: K13R, T16S, K36R
Details: Isopeptide amide crosslink between K15 of H2A and G76 of ubiquitin
Gene Name(s): HIST1H2AG Gene View H2AFP HIST1H2AI Gene View H2AFC HIST1H2AK Gene View H2AFD HIST1H2AL Gene View H2AFI HIST1H2AM Gene View H2AFN
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Histone H2B type 1-C/E/F/G/I D, H 126 Homo sapiens Gene Name(s): HIST1H2BC Gene View H2BFL HIST1H2BE Gene View H2BFH HIST1H2BF Gene View H2BFG HIST1H2BG Gene View H2BFA HIST1H2BI Gene View H2BFK
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Tumor suppressor p53-binding protein 1 K, L 21 Homo sapiens Details: full protein not modeled
Gene Name(s): TP53BP1 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Ubiquitin M, O 76 Homo sapiens Gene Name(s): UBB Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (145-MER) I 145 Synthetic construct
DNA (145-MER) J 145 Synthetic construct

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

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.54 Å
  • Reconstruction Method: Single Particle

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

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.

Revision History

  • 2016-08-10
    Type: Database references
  • 2016-08-17
    Type: Database references
  • 2017-09-13
    Type: Author supporting evidence, Data collection, Database references