SAXSdb — 3vza

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

Uncharacterized protein

Gallus gallus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Spc24 protein × 1 Centromere protein T × 1 （F1NPG5） water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Spc24 protein × 1 Centromere protein T × 1 （F1NPG5） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	E1C4Y2_CHICK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–105； UniProt 132–234 Author chain B； PDBConstruct 3–105； UniProt 132–234

Centromere protein T

Gallus gallus

UniProt F1NPG5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Uncharacterized protein × 1 （E1C4Y2） Spc24 protein × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Uncharacterized protein × 1 （E1C4Y2） Spc24 protein × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CENPT_CHICK
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 3–38； UniProt 63–98 Author chain F； PDBConstruct 3–38； UniProt 63–98

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	3vza
Deposition date deposition_date	2012-10-09
Structure title title	Crystal structure of the chicken Spc24-Spc25 globular domain in complex with CENP-T peptide
Keywords keywords	RWD domain, kinetochore component, chromosome segregation, Ndc80 complex, CELL CYCLE; CELL CYCLE
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.

3vza__assembly_1__model_1

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

Download this curve (.dat)

3vza__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3vza__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.85 Å
Rg (electron density)	16.32 Å
Total Rg	17.47 Å
Atom count	1592
Residues	192
Excluded volume	28256 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3vza__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3vza__assembly_2__model_1`	trimeric （3）	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	Uncharacterized protein
Molecular weight formula_weight	12466.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	3532

GYKERVERLCKSKELFEERLGLEIRRIHNEQLQFIFRHIDHKDPDKPYMFTLSINEQGDYEVTSCTPPLDCISEFQLKVRETNNFSAFIANIRKAFTALSFKQST

Source Source

Source organism organism	Gallus gallus
Common name common_name	chicken
NCBI taxonomy ID ncbi_taxonomy_id	9031
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Spc24 protein
Molecular weight formula_weight	8455.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,C

GDEREDDGVPSAAYVTQLYYKISRIDWDYEVEPARIKGIHYGPDIAQPINMDSSHHSRCFISDYLWSLVPTAW

Source Source

Source organism organism	Gallus gallus
Common name common_name	chicken
NCBI taxonomy ID ncbi_taxonomy_id	9031
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Centromere protein T
Molecular weight formula_weight	4421.0 kDa
Mutation mutation	T72D, S88D
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F

GRNAFSELDSADPRVMLRRIIQNQPQVDPLALQTVQLEP

Source Source

Source organism organism	Gallus gallus
Common name common_name	chicken
NCBI taxonomy ID ncbi_taxonomy_id	9031
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	357

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3vzaA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	457 — Copper Amine Oxidase; Chain A, domain 1
Homologous superfamily homologous superfamily	50 — Chromosome segregation protein Spc25

Domain ID domain_id	3vzaB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	457 — Copper Amine Oxidase; Chain A, domain 1
Homologous superfamily homologous superfamily	50 — Chromosome segregation protein Spc25

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Unit-cell length a length_a	61.321 Å
Unit-cell length b length_b	61.321 Å
Unit-cell length c length_c	111.275 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	6

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	1.898 Å
Low-resolution limit resolution_low	30.409 Å
R factor r_factor	0.1695
R_work r_work	0.1669
R_free r_free	0.2160

Crystal structure of the chicken Spc24-Spc25 globular domain in complex with CENP-T peptide

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

Uncharacterized protein

State in the Current Structure

Other States of the Same Protein in the Database

Centromere protein T

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

3vza__assembly_1__model_1

3vza__assembly_1__model_1 | I(q)

3vza__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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the chicken Spc24-Spc25 globular domain in complex with CENP-T peptide

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

Uncharacterized 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

Centromere protein T

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

3vza__assembly_1__model_1

3vza__assembly_1__model_1 | I(q)

3vza__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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)