24PV | pdb_000024pv

The crystal structure of the chicken MHF1-MHF2(L77C) disulfide-crosslinked complex

PDB DOI: https://doi.org/10.2210/pdb24PV/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Gallus gallus
Expression System: Escherichia coli B
Mutation(s): Yes

Deposited: 2026-03-16 Released: 2026-09-23
Deposition Author(s): Ito, S., Nishino, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 4.00 Å
R-Value Free:
0.338 (Depositor), 0.340 (DCC)
R-Value Work:
0.253 (Depositor), 0.295 (DCC)
R-Value Observed:
0.262 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Disulfide engineering of the FANCM-MHF complex reveals constraints on crosslink design in symmetric oligomers.

Ito, S., Nishino, T.

(2026) Protein Sci 35: e70761-e70761

PubMed: 42606197 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/pro.70761
Primary Citation Related Structures:
24PU, 24PV

PubMed Abstract:
The Fanconi anemia complementation group M protein (FANCM)-MHF complex is required for branched DNA recognition in the Fanconi anemia pathway, but structural analysis of the intact complex has been hindered by dissociation of FANCM from the FANCM-associated histone fold (MHF) heterotetramer under crystallization conditions. Here, we used structure-guided disulfide engineering to stabilize the FANCM-MHF interface and test whether local geometry is sufficient to predict crosslinking specificity in a symmetric oligomeric assembly. Using endogenous FANCM Cys759 as an anchor, we designed two MHF2 variants, Q74C and L77C. Both supported oxidation-dependent crosslinking in the context of the FANCM-MHF complex, but with distinct outcomes. Q74C formed the intended FANCM-MHF2 disulfide, enabled crystallization of the intact heteropentamer, and preserved DNA-binding behavior under the tested conditions. In contrast, L77C favored a competing MHF2-MHF2 disulfide and yielded only the MHF heterotetramer after FANCM dissociation. Structural analysis further showed distinct crosslinking states for the two MHF tetramers in the asymmetric unit, consistent with local conformational heterogeneity at the MHF dimer-dimer interface. These results show that geometric plausibility alone does not predict crosslinking specificity in symmetric oligomers. Instead, symmetry-related competing pathways can redirect the reaction toward an alternative assembly state. This study provides a practical route to stabilizing FANCM-MHF and reveals a key design constraint for engineered disulfides in symmetric multimeric assemblies.

Organizational Affiliation

Faculty of Advanced Engineering, Tokyo University of Science, Tokyo, Japan.

Macromolecule Content

Total Structure Weight: 85.31 kDa
Atom Count: 5,467
Modeled Residue Count: 686
Deposited Residue Count: 756
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Centromere protein S	A, C, E, G	108	Gallus gallus	Mutation(s): 3 Gene Names: CENPS, APITD1
UniProt
Find proteins for E1BSW7 (Gallus gallus) Explore E1BSW7 Go to UniProtKB: E1BSW7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E1BSW7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Centromere protein X	B, D, F, H	81	Gallus gallus	Mutation(s): 1 Gene Names: CENPX, STRA13
UniProt
Find proteins for P0DJH7 (Gallus gallus) Explore P0DJH7 Go to UniProtKB: P0DJH7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DJH7
Sequence Annotations Expand
Reference Sequence