SAXSdb — 2ve7

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

KINETOCHORE PROTEIN HEC1, KINETOCHORE PROTEIN SPC25

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	KINETOCHORE PROTEIN NUF2, KINETOCHORE PROTEIN SPC24 × 1 （Q8NBT2,Q9BZD4） GLYCEROL × 1 PHENOL × 1 water × 2	Consistent with protein count
2	Insufficient information	Heteromer	Protein 2	KINETOCHORE PROTEIN NUF2, KINETOCHORE PROTEIN SPC24 × 1 （Q8NBT2,Q9BZD4） GLYCEROL × 1 PHENOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KNTC2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–208； UniProt 80–286 Author chain B； PDBConstruct 2–208； UniProt 80–286

KINETOCHORE PROTEIN HEC1, KINETOCHORE PROTEIN SPC25

HOMO SAPIENS

UniProt Q9HBM1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	KINETOCHORE PROTEIN NUF2, KINETOCHORE PROTEIN SPC24 × 1 （Q8NBT2,Q9BZD4） GLYCEROL × 1 PHENOL × 1 water × 2	Consistent with protein count
2	Insufficient information	Heteromer	Protein 2	KINETOCHORE PROTEIN NUF2, KINETOCHORE PROTEIN SPC24 × 1 （Q8NBT2,Q9BZD4） GLYCEROL × 1 PHENOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPC25_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 209–315； UniProt 118–224 Author chain B； PDBConstruct 209–315； UniProt 118–224

KINETOCHORE PROTEIN NUF2, KINETOCHORE PROTEIN SPC24

HOMO SAPIENS

UniProt Q8NBT2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	KINETOCHORE PROTEIN HEC1, KINETOCHORE PROTEIN SPC25 × 1 （O14777,Q9HBM1） GLYCEROL × 1 PHENOL × 1 water × 2	Consistent with protein count
2	Insufficient information	Heteromer	Protein 2	KINETOCHORE PROTEIN HEC1, KINETOCHORE PROTEIN SPC25 × 1 （O14777,Q9HBM1） GLYCEROL × 1 PHENOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPC24_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 175–250； UniProt 122–197 Author chain D； PDBConstruct 175–250； UniProt 122–197

KINETOCHORE PROTEIN NUF2, KINETOCHORE PROTEIN SPC24

HOMO SAPIENS

UniProt Q9BZD4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	KINETOCHORE PROTEIN HEC1, KINETOCHORE PROTEIN SPC25 × 1 （O14777,Q9HBM1） GLYCEROL × 1 PHENOL × 1 water × 2	Consistent with protein count
2	Insufficient information	Heteromer	Protein 2	KINETOCHORE PROTEIN HEC1, KINETOCHORE PROTEIN SPC25 × 1 （O14777,Q9HBM1） GLYCEROL × 1 PHENOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NUF2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 6–174； UniProt 1–169 Author chain D； PDBConstruct 6–174； UniProt 1–169

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	2ve7
Deposition date deposition_date	2007-10-17
Structure title title	Crystal structure of a bonsai version of the human Ndc80 complex
Keywords keywords	MITOSIS, CENTROMERE, CELL CYCLE, MICROTUBULE, KINETOCHORE, CELL DIVISION, CALPONIN HOMOLOGY; 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.

2ve7__assembly_2__model_1

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

Download this curve (.dat)

2ve7__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ve7__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	51.81 Å
Rg (electron density)	52.88 Å
Total Rg	52.50 Å
Atom count	4443
Residues	545
Excluded volume	79453 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ve7__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2ve7__assembly_2__model_1`	dimeric （2）	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 HEC1, KINETOCHORE PROTEIN SPC25
Molecular weight formula_weight	36351.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	8258

MIKDPRPLNDKAFIQQCIRQLCEFLTENGYAHNVSMKSLQAPSVKDFLKIFTFLYGFLCPSYELPDTKFEEEVPRIFKDLGYPFALSKSSMYTVGAPHTWPHIVAALVWLIDCIKIHTAMKESSPLFDDGQPWGEETEDGIMHNKLFLDYTIKCYESFMSGADSFDEMNAELQSKLKDLFNVDAFKLESLEAKNRALNEQIARLEQERSTANKANAERLKRLQKSADLYKDRLGLEIRKIYGEKLQFIFTNIDPKNPESPFMFSLHLNEARDYEVSDSAPHLEGLAEFQENVRKTNNFSAFLANVRKAFTATVYQ

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	KINETOCHORE PROTEIN NUF2, KINETOCHORE PROTEIN SPC24
Molecular weight formula_weight	28993.4 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GPLGSMETLSFPRYNVAEIVIHIRNKILTGADGKNLTKNDLYPNPKPEVLHMIYMRALQIVYGIRLEHFYMMPVNSGVMYPHLMEGFLPFSNLVTHLDSFLPICRVNDFETADILCPKAKRTSRFLSGIINFIHFREACRETYMEFLWQYKSSADKMQQLNAAHQEALMKLERLEKEVDEDTTVTIPSAVYVAQLYHQVSKIEWEYECEPGMVKGIHHGPSVAQPIHLDSTQLSRKFISDYLWSLVDTEW

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 non-polymer

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

Entity 4 Entity 4 non-polymer

Description description	PHENOL
Molecular weight formula_weight	94.1 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	22

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	2ve7A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	418 — Actin-binding Protein, T-fimbrin; domain 1
Homologous superfamily homologous superfamily	30 — Ncd80 complex, Ncd80 subunit

Domain ID domain_id	2ve7A02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1950 —

Domain ID domain_id	2ve7B01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	418 — Actin-binding Protein, T-fimbrin; domain 1
Homologous superfamily homologous superfamily	30 — Ncd80 complex, Ncd80 subunit

Domain ID domain_id	2ve7C01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	418 — Actin-binding Protein, T-fimbrin; domain 1
Homologous superfamily homologous superfamily	60 — Ncd80 complex, Nuf2 subunit

Domain ID domain_id	2ve7C02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	570 — Ncd80 complex, Spc24 subunit

Domain ID domain_id	2ve7D01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	418 — Actin-binding Protein, T-fimbrin; domain 1
Homologous superfamily homologous superfamily	60 — Ncd80 complex, Nuf2 subunit

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Unit-cell length a length_a	157.653 Å
Unit-cell length b length_b	248.965 Å
Unit-cell length c length_c	58.250 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.880 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2340
R_work r_work	0.2320
R_free r_free	0.2610

Crystal structure of a bonsai version of the human Ndc80 complex

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

KINETOCHORE PROTEIN HEC1, KINETOCHORE PROTEIN SPC25

State in the Current Structure

Other States of the Same Protein in the Database

KINETOCHORE PROTEIN HEC1, KINETOCHORE PROTEIN SPC25

State in the Current Structure

Other States of the Same Protein in the Database

KINETOCHORE PROTEIN NUF2, KINETOCHORE PROTEIN SPC24

State in the Current Structure

Other States of the Same Protein in the Database

KINETOCHORE PROTEIN NUF2, KINETOCHORE PROTEIN SPC24

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

2ve7__assembly_2__model_1

2ve7__assembly_2__model_1 | I(q)

2ve7__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of a bonsai version of the human Ndc80 complex

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

KINETOCHORE PROTEIN HEC1, 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 HEC1, 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 NUF2, 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 PROTEIN NUF2, 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2ve7__assembly_2__model_1

2ve7__assembly_2__model_1 | I(q)

2ve7__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)