SAXSdb — 8v11

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

Kinetochore protein NDC80

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Ipl1/Nuf2 chimera protein × 1 （P33895） Kinetochore protein SPC24 × 1 （Q04477） Kinetochore protein SPC25 × 1 （P40014）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Ipl1/Nuf2 chimera protein × 1 （P33895） Kinetochore protein SPC24 × 1 （Q04477） Kinetochore protein SPC25 × 1 （P40014）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NDC80_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–208； UniProt 114–318 Author chain A； PDBConstruct 209–272； UniProt 621–684 Author chain E； PDBConstruct 4–208； UniProt 114–318 Author chain E； PDBConstruct 209–272； UniProt 621–684

Ipl1/Nuf2 chimera protein

Saccharomyces cerevisiae

UniProt P33895

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Kinetochore protein NDC80 × 1 （P40460） Kinetochore protein SPC24 × 1 （Q04477） Kinetochore protein SPC25 × 1 （P40014）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Kinetochore protein NDC80 × 1 （P40460） Kinetochore protein SPC24 × 1 （Q04477） Kinetochore protein SPC25 × 1 （P40014）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NUF2_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 31–182； UniProt 2–153 Author chain B； PDBConstruct 183–227； UniProt 407–451 Author chain F； PDBConstruct 31–182； UniProt 2–153 Author chain F； PDBConstruct 183–227； UniProt 407–451

Kinetochore protein SPC24

Saccharomyces cerevisiae

UniProt Q04477

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Kinetochore protein NDC80 × 1 （P40460） Ipl1/Nuf2 chimera protein × 1 （P33895） Kinetochore protein SPC25 × 1 （P40014）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Kinetochore protein NDC80 × 1 （P40460） Ipl1/Nuf2 chimera protein × 1 （P33895） Kinetochore protein SPC25 × 1 （P40014）	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	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–48； UniProt 1–48 Author chain C； PDBConstruct 49–99； UniProt 162–212 Author chain G； PDBConstruct 1–48； UniProt 1–48 Author chain G； PDBConstruct 49–99； UniProt 162–212

Kinetochore protein SPC25

Saccharomyces cerevisiae

UniProt P40014

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Kinetochore protein NDC80 × 1 （P40460） Ipl1/Nuf2 chimera protein × 1 （P33895） Kinetochore protein SPC24 × 1 （Q04477）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Kinetochore protein NDC80 × 1 （P40460） Ipl1/Nuf2 chimera protein × 1 （P33895） Kinetochore protein SPC24 × 1 （Q04477）	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	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–31； UniProt 1–31 Author chain D； PDBConstruct 32–114； UniProt 138–220 Author chain H； PDBConstruct 1–31； UniProt 1–31 Author chain H； PDBConstruct 32–114； UniProt 138–220

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	8v11
Deposition date deposition_date	2023-11-19
Structure title title	Structure of a Saccharomyces cerevisiae Ipl1 peptide Bound to dwarf Ndc80 complex
Keywords keywords	Stu2, tension sensing, Ndc80, kinetochore, 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.

8v11__assembly_1__model_1

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

Download this curve (.dat)

8v11__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8v11__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	55.52 Å
Rg (electron density)	56.81 Å
Total Rg	56.43 Å
Atom count	5622
Residues	686
Excluded volume	100330 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8v11__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8v11__assembly_2__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	Kinetochore protein NDC80
Molecular weight formula_weight	32460.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E
Atom count atom_count	11265

SNARDPRPLRDKNFQSAIQEEIYDYLKKNKFDIETNHPISIKFLKQPTQKGFIIIFKWLYLRLDPGYGFTKSIENEIYQILKNLRYPFLESINKSQISAVGGSNWHKFLGMLHWMVRTNIKLDMCLNKVDRSLINQNTQEITILSQPLKTLDEQDQRQERYELMVEKLLIDYFTESYKSFLKLEDNYEPSMQELKLGFEKFVHIINTDVTSTELKLEELKVDLNRKRYKLHQQVIHVIDITSKFKINIQSSLENSENELGNVIEELRNLEFE

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;brewer's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Ipl1/Nuf2 chimera protein
Molecular weight formula_weight	26548.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MTSRINKPWRISHSPNSKIPSPVREKLNRLSRNQDVFPILDLQELVICLQSCDFALATQENISRPTSDYMVTLYKQIIENFMGISVESLLNSSNQETGDGHLQEENENIYLDTLNVLVLNKICFKFFENIGVQDFNMTDLYKPEAQRTQRLLSAVVNYARFREERMFDCNSFILQMESLLGQINKLNDEIKQLQKDFEVEVKEIEAAYSLLSGHINKYMNEMLEYMQ

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;brewer's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Kinetochore protein SPC24
Molecular weight formula_weight	11752.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MSQKDNLLDNPVEFLKEVRESFDIQQDVDAMKRIRHDLDVIKEESEARLKLYRSLGVILDLENDQVLINRKNDGNIDILPLDNNLSDFYKTKYIWERLG

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;brewer's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 polymer

Description description	Kinetochore protein SPC25
Molecular weight formula_weight	12709.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MASIDAFSDLERRMDGFQKDVAQVLARQQNHVALYERLLQLRVLPGASDVHDVRFVFGDDSRCWIEVAMHGDHVIGNSHPALDPKSRATLEHVLTVQGDLAAFLVVARDMLLAS

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;brewer's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli BL21(DE3)

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Unit-cell length a length_a	114.757 Å
Unit-cell length b length_b	114.757 Å
Unit-cell length c length_c	423.841 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	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	tetragonal

Resolution resolution	3.950 Å
Low-resolution limit resolution_low	48.530 Å
R factor r_factor	0.2696
R_work r_work	0.2666
R_free r_free	0.3266

Structure of a Saccharomyces cerevisiae Ipl1 peptide Bound to dwarf Ndc80 complex

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

Kinetochore protein NDC80

State in the Current Structure

Other States of the Same Protein in the Database

Ipl1/Nuf2 chimera protein

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 protein SPC25

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

8v11__assembly_1__model_1

8v11__assembly_1__model_1 | I(q)

8v11__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 polymer

Polymer Polymer

Source Source

7. Citations (1)

Structure of a Saccharomyces cerevisiae Ipl1 peptide Bound to dwarf Ndc80 complex

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

Kinetochore protein NDC80

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ipl1/Nuf2 chimera 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

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 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8v11__assembly_1__model_1

8v11__assembly_1__model_1 | I(q)

8v11__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 polymer

Polymer Polymer

Source Source

7. Citations (1)