SAXSdb — 4geq

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

Kinetochore protein SPC25

Saccharomyces cerevisiae S288c

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Kinetochore protein SPC24 × 1 （Q04477） Kinetochore-associated protein CNN1 × 1 （P43618） GLYCEROL × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Kinetochore protein SPC24 × 1 （Q04477） Kinetochore-associated protein CNN1 × 1 （P43618） GLYCEROL × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPC25_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–90； UniProt 133–221 Author chain C； PDBConstruct 2–90； UniProt 133–221

Kinetochore protein SPC24

Saccharomyces cerevisiae S288c

UniProt Q04477

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Kinetochore protein SPC25 × 1 （P40014） Kinetochore-associated protein CNN1 × 1 （P43618） GLYCEROL × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Kinetochore protein SPC25 × 1 （P40014） Kinetochore-associated protein CNN1 × 1 （P43618） GLYCEROL × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPC24_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–60； UniProt 155–213 Author chain D； PDBConstruct 2–60； UniProt 155–213

Kinetochore-associated protein CNN1

OrganismNot specified

UniProt P43618

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Kinetochore protein SPC25 × 1 （P40014） Kinetochore protein SPC24 × 1 （Q04477） GLYCEROL × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Kinetochore protein SPC25 × 1 （P40014） Kinetochore protein SPC24 × 1 （Q04477） GLYCEROL × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CNN1_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–25； UniProt 60–84 Author chain F； PDBConstruct 1–25； UniProt 60–84

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	4geq
Deposition date deposition_date	2012-08-02
Structure title title	Crystal structure of the Spc24-Spc25/Cnn1 binding interface
Keywords keywords	protein-protein complex, Ndc80-binding motif, RWD domain, kinetochore components, nucleus, 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.

4geq__assembly_1__model_1

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

Download this curve (.dat)

4geq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4geq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.30 Å
Rg (electron density)	15.67 Å
Total Rg	16.79 Å
Atom count	1298
Residues	166
Excluded volume	23121 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4geq__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4geq__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 (5)

Entity 1 Entity 1 polymer

Description description	Kinetochore protein SPC25
Molecular weight formula_weight	9889.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	2750

MNDAAEVALYERLLQLRVLPGASDVHDVRFVFGDDSRCWIEVAMHGDHVIGNSHPALDPKSRATLEHVLTVQGDLAAFLVVARDMLLASL

Source Source

Source organism organism	Saccharomyces cerevisiae S288c
Common name common_name	yeast
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Kinetochore protein SPC24
Molecular weight formula_weight	7903.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MANENILKLKLYRSLGVILDLENDQVLINRKNDGNIDILPLDNNLSDFYKTKYIWERLGKHHHHHH

Source Source

Source organism organism	Saccharomyces cerevisiae S288c
Common name common_name	yeast
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Kinetochore-associated protein CNN1
Molecular weight formula_weight	2848.1 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

NKDPNEVRSFLQDLSQVLARKSQGN

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	150

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4geqA00
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	4geqB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	430 —

Domain ID domain_id	4geqC00
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	4geqD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	430 —

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Unit-cell length a length_a	34.142 Å
Unit-cell length b length_b	61.848 Å
Unit-cell length c length_c	139.056 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.010 Å
Low-resolution limit resolution_low	37.090 Å
R factor r_factor	0.2092
R_work r_work	0.2067
R_free r_free	0.2580

Crystal structure of the Spc24-Spc25/Cnn1 binding interface

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

Kinetochore protein SPC25

State in the Current Structure

Other States of the Same Protein in the Database

Kinetochore protein SPC24

State in the Current Structure

Other States of the Same Protein in the Database

Kinetochore-associated protein CNN1

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

4geq__assembly_1__model_1

4geq__assembly_1__model_1 | I(q)

4geq__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 (5)

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

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of the Spc24-Spc25/Cnn1 binding interface

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

Kinetochore protein SPC25

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Kinetochore protein SPC24

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Kinetochore-associated protein CNN1

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

4geq__assembly_1__model_1

4geq__assembly_1__model_1 | I(q)

4geq__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 (5)

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

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)