2AZM Cell Cycle date Sep 12, 2005
title Crystal Structure Of The Mdc1 Brct Repeat In Complex With The Histone Tail Of Gamma-H2ax
authors J.A.Clapperton, M.Stucki, D.Mohammad, M.B.Yaffe, S.P.Jackson, S.J.Smerdon
compound source
Molecule: Mediator Of Dna Damage Checkpoint Protein 1
Chain: A, B
Fragment: Brct Repeat
Synonym: Nuclear Factor With Brct Domains 1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mdc1
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex4t1

Molecule: Gamma-H2ax Histone
Chain: C, D
Synonym: Histone H2afx
Engineered: Yes

Synthetic: Yes
Other_details: Gamma H2ax Synthetic Peptide
symmetry Space Group: P 21 21 21
R_factor 0.191 R_Free 0.248
crystal
cell
length a length b length c angle alpha angle beta angle gamma
67.437 75.609 114.849 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.41 Å
ligand MSE, SEP enzyme
Primary referenceMDC1 directly binds phosphorylated histone H2AX to regulate cellular responses to DNA double-strand breaks., Stucki M, Clapperton JA, Mohammad D, Yaffe MB, Smerdon SJ, Jackson SP, Cell. 2005 Dec 29;123(7):1213-26. PMID:16377563
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (74 Kb) [Save to disk]
  • Biological Unit Coordinates (2azm.pdb1.gz) 36 Kb
  • Biological Unit Coordinates (2azm.pdb2.gz) 36 Kb
  • LPC: Ligand-Protein Contacts for 2AZM
  • CSU: Contacts of Structural Units for 2AZM
  • Likely Quarternary Molecular Structure file(s) for 2AZM
  • Structure Factors (388 Kb)
  • Retrieve 2AZM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2AZM from S2C, [Save to disk]
  • Re-refined 2azm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2AZM in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 2AZM
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2AZM, from MSDmotif at EBI
  • Fold representative 2azm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2azm_D] [2azm] [2azm_C] [2azm_A] [2azm_B]
  • SWISS-PROT database: [Q14676]
  • Domain organization of [MDC1_HUMAN] by SWISSPFAM
  • Domain found in 2AZM: [BRCT ] by SMART
  • Other resources with information on 2AZM
  • Community annotation for 2AZM at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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