Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 25.02 kDa 
• Atom Count: 1719 
• Residue Count: 207 
• Unique protein chains: 1

3UNM

Crystal Structure of The Human MDC1 FHA Domain

• DOI: 10.2210/pdb3UNM/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-11-16 Released: 2012-01-25 
• Deposition Author(s): Luo, S., Ye, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.274 
• R-Value Work: 0.234 
• R-Value Observed: 0.236 

Literature

Structural mechanism of the phosphorylation-dependent dimerization of the MDC1 forkhead-associated domain

Liu, J., Luo, S., Zhao, H., Liao, J., Li, J., Yang, C., Xu, B., Stern, D.F., Xu, X., Ye, K.

(2012) Nucleic Acids Res 40: 3898-3912

• PubMed: 22234877 
• DOI: 10.1093/nar/gkr1296
• Structures With Same Primary Citation


• PubMed Abstract: 
  

MDC1 is a key mediator of the DNA-damage response in mammals with several phosphorylation-dependent protein interaction domains. The function of its N-terminal forkhead-associated (FHA) domain remains elusive. Here, we show with structural, biochemical and cellular data that the FHA domain mediates phosphorylation-dependent dimerization of MDC1 in response to DNA damage. Crystal structures of the FHA domain reveal a face-to-face dimer with pseudo-dyad symmetry. We found that the FHA domain recognizes phosphothreonine 4 (pT4) at the N-terminus of MDC1 and determined its crystal structure in complex with a pT4 peptide. Biochemical analysis further revealed that in the dimer, the FHA domain binds in trans to pT4 from the other subunit, which greatly stabilizes the otherwise unstable dimer. We show that T4 is phosphorylated primarily by ATM upon DNA damage. MDC1 mutants with the FHA domain deleted or impaired in its ability to dimerize formed fewer foci at DNA-damage sites, but the localization defect was largely rescued by an artificial dimerization module, suggesting that dimerization is the primary function of the MDC1 FHA domain. Our results suggest a novel mechanism for the regulation of MDC1 function through T4 phosphorylation and FHA-mediated dimerization.

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Organizational Affiliation: 

Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing 100048, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Mediator of DNA damage checkpoint protein 1	A, B	113	Homo sapiens	Mutation(s): 0  Gene Names: MDC1, KIAA0170, NFBD1
Find proteins for Q14676 (Homo sapiens) Explore Q14676  Go to UniProtKB:  Q14676
NIH Common Fund Data Resources
PHAROS  Q14676 GTEx  ENSG00000137337

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.274 
• R-Value Work: 0.234 
• R-Value Observed: 0.236 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.651	α = 90
b = 56.053	β = 97.53
c = 64.92	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-11-16 
• Released Date: 2012-01-25 
Deposition Author(s): Luo, S., Ye, K.

Revision History 

• Version 1.0: 2012-01-25
  Type: Initial release
  
• Version 1.1: 2014-03-12
  Changes: Database references