4E45 | pdb_00004e45

Crystal structure of the hMHF1/hMHF2 Histone-Fold Tetramer in Complex with Fanconi Anemia Associated Helicase hFANCM

• PDB DOI: https://doi.org/10.2210/pdb4E45/pdb

• Classification: DNA BINDING PROTEIN/HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-03-12 Released: 2013-03-20 
• Deposition Author(s): Fox III, D., Zhao, Y., Yang, W., Weidong, W.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.245 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Crystal Structures Reveal that FANCM remodels the MHF Tetramer in favor of binding Branched DNA

Fox III, D., Yan, Z., Ling, C., Zhao, Y., Lee, D.Y., Yang, W., Weidong, W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B2C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A4B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - A2B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B2C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A4B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - A2B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B2C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A4B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - A2B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 182.34 kDa 
• Atom Count: 11,040 
• Modeled Residue Count: 1,334 
• Deposited Residue Count: 1,581 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Centromere protein S	A, C, F, H, K, M	112	Homo sapiens	Mutation(s): 0  Gene Names: APITD1, CENPS, FAAP16, MHF1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N2Z9 (Homo sapiens) Explore Q8N2Z9  Go to UniProtKB:  Q8N2Z9
PHAROS:  Q8N2Z9 GTEx:  ENSG00000175279

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Centromere protein X	B, D, G, I, L, N	83	Homo sapiens	Mutation(s): 0  Gene Names: STRA13, CENPX, FAAP10, MHF2
UniProt & NIH Common Fund Data Resources
Find proteins for A8MT69 (Homo sapiens) Explore A8MT69  Go to UniProtKB:  A8MT69
PHAROS:  A8MT69 GTEx:  ENSG00000169689

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fanconi anemia group M protein	E, J, O	137	Homo sapiens	Mutation(s): 0  Gene Names: FANCM, KIAA1596 EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IYD8 (Homo sapiens) Explore Q8IYD8  Go to UniProtKB:  Q8IYD8
PHAROS:  Q8IYD8 GTEx:  ENSG00000187790

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	P [auth B], R [auth H]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	Q [auth D], S [auth J], T [auth N]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.245 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.98	α = 90
b = 69.97	β = 91.6
c = 116.05	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-20 
Deposition Author(s): Fox III, D., Zhao, Y., Yang, W., Weidong, W.

Revision History  

• Version 1.0: 2013-03-20
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description