SAXSdb — 4ndy

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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–DNA	Heteromer	Protein 4 DNA 2	DNA (26-MER) × 1 DNA (26-MER) × 1 Centromere protein X × 2 （A8MT69）	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 4 DNA 4	DNA (26-MER) × 2 DNA (26-MER) × 2 Centromere protein X × 2 （A8MT69）	Consistent with all polymers
3	Protein–DNA	Heteromer	Protein 4 DNA 2	DNA (26-MER) × 1 DNA (26-MER) × 1 Centromere protein X × 2 （A8MT69）	Consistent with all polymers
4	Protein heterocomplex	Heteromer	Protein 4	Centromere protein X × 2 （A8MT69）	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 4	Centromere protein X × 2 （A8MT69）	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	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–92； UniProt 14–105 Author chain C； PDBConstruct 1–92； UniProt 14–105 Author chain G； PDBConstruct 1–92； UniProt 14–105 Author chain I； PDBConstruct 1–92； UniProt 14–105 Author chain J； PDBConstruct 1–92； UniProt 14–105 Author chain K； PDBConstruct 1–92； UniProt 14–105 Author chain Q； PDBConstruct 1–92； UniProt 14–105 Author chain R； PDBConstruct 1–92； UniProt 14–105 Author chain S； PDBConstruct 1–92； UniProt 14–105 Author chain T； PDBConstruct 1–92； UniProt 14–105

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–DNA	Heteromer	Protein 4 DNA 2	DNA (26-MER) × 1 DNA (26-MER) × 1 Centromere protein S × 2 （Q8N2Z9）	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 4 DNA 4	DNA (26-MER) × 2 DNA (26-MER) × 2 Centromere protein S × 2 （Q8N2Z9）	Consistent with all polymers
3	Protein–DNA	Heteromer	Protein 4 DNA 2	DNA (26-MER) × 1 DNA (26-MER) × 1 Centromere protein S × 2 （Q8N2Z9）	Consistent with all polymers
4	Protein heterocomplex	Heteromer	Protein 4	Centromere protein S × 2 （Q8N2Z9）	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 4	Centromere protein S × 2 （Q8N2Z9）	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	4
Chains and sequence ranges	Author chain B； PDBConstruct 1–74； UniProt 8–81 Author chain D； PDBConstruct 1–74； UniProt 8–81 Author chain H； PDBConstruct 1–74； UniProt 8–81 Author chain L； PDBConstruct 1–74； UniProt 8–81 Author chain M； PDBConstruct 1–74； UniProt 8–81 Author chain N； PDBConstruct 1–74； UniProt 8–81 Author chain U； PDBConstruct 1–74； UniProt 8–81 Author chain V； PDBConstruct 1–74； UniProt 8–81 Author chain W； PDBConstruct 1–74； UniProt 8–81 Author chain X； PDBConstruct 1–74； UniProt 8–81

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	4ndy
Deposition date deposition_date	2013-10-28
Structure title title	Human MHF1-MHF2 DNA complex
Keywords keywords	;Histone Fold, DNA repair, genome maintenance, centromere construction, Fanconi Anemia, FancM, nucleus, DNA Binding Protein-DNA complex ;; DNA Binding Protein/DNA
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.

4ndy__assembly_1__model_1

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

Download this curve (.dat)

4ndy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4ndy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.32 Å
Rg (electron density)	32.81 Å
Total Rg	33.35 Å
Atom count	3833
Residues	398
Excluded volume	65482 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4ndy__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4ndy__assembly_2__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4ndy__assembly_3__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4ndy__assembly_4__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`4ndy__assembly_5__model_1`	tetrameric （4）	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 (4)

Entity 1 Entity 1 polymer

Description description	DNA (26-MER)
Molecular weight formula_weight	8098.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,O
Atom count atom_count	15914

AAAAAAAAAAAAAAAAAAAAAAAAAA

Entity 2 Entity 2 polymer

Description description	DNA (26-MER)
Molecular weight formula_weight	7864.1 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F,P

TTTTTTTTTTTTTTTTTTTTTTTTTT

Entity 3 Entity 3 polymer

Description description	Centromere protein S
Molecular weight formula_weight	12091.9 kDa
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,G,A,I,J,K,Q,R,S,T

SYQQRLKAAVHYTVGCLCEEVALDKAMQFSKQTIAAISELTFRQCENFAKDLEMFARHAKRTTINTEDVKLLARRSNSLLKYITDKSEEIAQANLERKAQKKKKS

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 polymer

Description description	Centromere protein X
Molecular weight formula_weight	8398.8 kDa
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,H,B,L,M,N,U,V,W,X

SGFRKELVSRLLHLHFKDDKTKVSGDALQLMVELLKVFVVEAAVRGVRQAQAEDALRVDVDQLEKVLPQLLLDF

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

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Unit-cell length a length_a	250.098 Å
Unit-cell length b length_b	250.098 Å
Unit-cell length c length_c	65.561 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	30

Space group space_group	P 3
Space-group number int_tables_number	143
Crystal system crystal_system	—

Resolution resolution	6.999 Å
Low-resolution limit resolution_low	108.300 Å
R factor r_factor	0.2440
R_work r_work	0.2419
R_free r_free	0.2791

Human MHF1-MHF2 DNA complex

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4ndy__assembly_1__model_1

4ndy__assembly_1__model_1 | I(q)

4ndy__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

7. Citations (1)

Human MHF1-MHF2 DNA complex

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4ndy__assembly_1__model_1

4ndy__assembly_1__model_1 | I(q)

4ndy__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

7. Citations (1)