4e45

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

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Centromere protein S

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Centromere protein X × 2 （A8MT69） Fanconi anemia group M protein × 1 （Q8IYD8） GLYCEROL × 1 ZINC ION × 1 water × 5	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Centromere protein X × 2 （A8MT69） Fanconi anemia group M protein × 1 （Q8IYD8） GLYCEROL × 1 ZINC ION × 1 water × 5	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 5	Centromere protein X × 2 （A8MT69） Fanconi anemia group M protein × 1 （Q8IYD8） ZINC ION × 1 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CENPS_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–112； UniProt 1–110 Author chain C； PDBConstruct 3–112； UniProt 1–110 Author chain F； PDBConstruct 3–112； UniProt 1–110 Author chain H； PDBConstruct 3–112； UniProt 1–110 Author chain K； PDBConstruct 3–112； UniProt 1–110 Author chain M； PDBConstruct 3–112； UniProt 1–110

Centromere protein X

Homo sapiens

UniProt A8MT69

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Centromere protein S × 2 （Q8N2Z9） Fanconi anemia group M protein × 1 （Q8IYD8） GLYCEROL × 1 ZINC ION × 1 water × 5	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Centromere protein S × 2 （Q8N2Z9） Fanconi anemia group M protein × 1 （Q8IYD8） GLYCEROL × 1 ZINC ION × 1 water × 5	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 5	Centromere protein S × 2 （Q8N2Z9） Fanconi anemia group M protein × 1 （Q8IYD8） ZINC ION × 1 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CENPX_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–83； UniProt 1–81 Author chain D； PDBConstruct 3–83； UniProt 1–81 Author chain G； PDBConstruct 3–83； UniProt 1–81 Author chain I； PDBConstruct 3–83； UniProt 1–81 Author chain L； PDBConstruct 3–83； UniProt 1–81 Author chain N； PDBConstruct 3–83； UniProt 1–81

Fanconi anemia group M protein

Homo sapiens

UniProt Q8IYD8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Centromere protein S × 2 （Q8N2Z9） Centromere protein X × 2 （A8MT69） GLYCEROL × 1 ZINC ION × 1 water × 5	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Centromere protein S × 2 （Q8N2Z9） Centromere protein X × 2 （A8MT69） GLYCEROL × 1 ZINC ION × 1 water × 5	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 5	Centromere protein S × 2 （Q8N2Z9） Centromere protein X × 2 （A8MT69） ZINC ION × 1 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FANCM_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 4–137； UniProt 667–800 Author chain J； PDBConstruct 4–137； UniProt 667–800 Author chain O； PDBConstruct 4–137； UniProt 667–800

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4e45
Deposition date deposition_date	2012-03-12
Structure title title	Crystal structure of the hMHF1/hMHF2 Histone-Fold Tetramer in Complex with Fanconi Anemia Associated Helicase hFANCM
Keywords keywords	Histone-Fold, Pentamer, Fanconi Anemia, Helicase, FANCM, MHF, DNA BINDING PROTEIN-HYDROLASE complex; DNA BINDING PROTEIN/HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

4e45__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4e45__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4e45__assembly_2__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	23.90 Å
Rg (electron density)	22.69 Å
Total Rg	23.51 Å
Atom count	3526
Residues	449
Excluded volume	62721 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4e45__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4e45__assembly_2__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4e45__assembly_3__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Centromere protein S
Molecular weight formula_weight	13042.7 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,F,H,K,M
Atom count atom_count	11040

GSMEEEAETEEQQRFSYQQRLKAAVHYTVGCLCEEVALDKEMQFSKQTIAAISELTFRQCENFAKDLEMFARHAKRTTINTEDVKLLARRSNSLLKYITDKSEEIAQINLER

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Centromere protein X
Molecular weight formula_weight	9116.5 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,G,I,L,N

GSMEGAGAGSGFRKELVSRLLHLHFKDDKTKVSGDALQLMVELLKVFVVEAAVRGVRQAQAEDALRVDVDQLEKVLPQLLLDF

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Fanconi anemia group M protein
Molecular weight formula_weight	16333.2 kDa
EC 编号 ec_number	3.6.4.13
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,J,O

GAMDPMRQSSLKKDWFLSEEEFKLWNRLYRLRDSDEIKEITLPQVQFSSLQNEENKPAQESTTGIHQLSLSEWRLWQDHPLPTHQVDHSDRCRHFIGLMQMIEGMRHEEGECSYELEVESYLQMEDVTSTFIAPRNE

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	546

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6. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

Domain ID domain_id	4e45A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	4e45B01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	4980 —

Domain ID domain_id	4e45B02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	130 — GTP Cyclohydrolase I; Chain A, domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	4e45C00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	4e45D01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	4980 —

Domain ID domain_id	4e45D02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	130 — GTP Cyclohydrolase I; Chain A, domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	4e45F00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	4e45G01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	4980 —

Domain ID domain_id	4e45G02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	130 — GTP Cyclohydrolase I; Chain A, domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	4e45H00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	4e45I01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	4980 —

Domain ID domain_id	4e45I02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	130 — GTP Cyclohydrolase I; Chain A, domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	4e45K00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	4e45L01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	4980 —

Domain ID domain_id	4e45L02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	130 — GTP Cyclohydrolase I; Chain A, domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	4e45M00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	4e45N01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	4980 —

Domain ID domain_id	4e45N02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	130 — GTP Cyclohydrolase I; Chain A, domain 1
Homologous superfamily homologous superfamily	30 —

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Unit-cell length a length_a	110.980 Å
Unit-cell length b length_b	69.970 Å
Unit-cell length c length_c	116.050 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.60 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	49.510 Å
R factor r_factor	0.2040
R_work r_work	0.2020
R_free r_free	0.2450

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Centromere protein S

State in the Current Structure

Other States of the Same Protein in the Database

Centromere protein X

State in the Current Structure

Other States of the Same Protein in the Database

Fanconi anemia group M protein

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4e45__assembly_2__model_1

4e45__assembly_2__model_1 | I(q)

4e45__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

7. Citations (1)

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Centromere protein S

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Centromere protein X

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Fanconi anemia group M protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4e45__assembly_2__model_1

4e45__assembly_2__model_1 | I(q)

4e45__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

7. Citations (1)