3VA4

Crystal structure of the mammalian MDC1 FHA domain complexed with CHK2 pThr68 peptide

• PDB DOI: https://doi.org/10.2210/pdb3VA4/pdb

• Classification: CELL CYCLE
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-12-28 Released: 2012-02-01 
• Deposition Author(s): Wu, H.H., Wu, P.Y., Huang, K.F., Kao, Y.Y., Tsai, M.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.205 
• R-Value Work: 0.159 
• R-Value Observed: 0.162 

Literature

Structural Delineation of MDC1-FHA Domain Binding with CHK2-pThr68.

Wu, H.H., Wu, P.Y., Huang, K.F., Kao, Y.Y., Tsai, M.D.

(2012) Biochemistry 

• PubMed: 22211259 
• DOI: https://doi.org/10.1021/bi201709w
• Primary Citation of Related Structures:  
  3VA1, 3VA4


• PubMed Abstract: 
  

  Mammalian MDC1 interacts with CHK2 in the regulation of DNA damage-induced S-phase checkpoint and apoptosis, which is directed by the association of MDC1-FHA and CHK2-pThr68. However, different ligand specificities of MDC1-FHA have been reported, and no structure is available. Here we report the crystal structures of MDC1-FHA and its complex with a CHK2 peptide containing pThr68. Unlike other FHA domains, MDC1-FHA exists as an intrinsic dimer in solution and in crystals. Structural and binding analyses support pThr+3 ligand specificity and provide structural insight into MDC1-CHK2 interaction.

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Organizational Affiliation: 

Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei 115, Taiwan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 30.53 kDa 
• Atom Count: 1,935 
• Modelled Residue Count: 227 
• Deposited Residue Count: 275 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of DNA damage checkpoint protein 1	A, C [auth B]	132	Mus musculus	Mutation(s): 0  Gene Names: MDC1
UniProt & NIH Common Fund Data Resources
Find proteins for Q5PSV9 (Mus musculus) Explore Q5PSV9  Go to UniProtKB:  Q5PSV9
IMPC:  MGI:3525201

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase Chk2	B [auth C]	11	Homo sapiens	Mutation(s): 0  EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O96017 (Homo sapiens) Explore O96017  Go to UniProtKB:  O96017
PHAROS:  O96017 GTEx:  ENSG00000183765

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	B [auth C]	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.205 
• R-Value Work: 0.159 
• R-Value Observed: 0.162 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.508	α = 90
b = 70.224	β = 90
c = 101.335	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SHELXS	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-01 
Deposition Author(s): Wu, H.H., Wu, P.Y., Huang, K.F., Kao, Y.Y., Tsai, M.D.

Revision History  

• Version 1.0: 2012-02-01
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary