SAXSdb — 5td8

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

Kinetochore protein NDC80

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Kinetochore protein NUF2 × 1 （P33895） Kinetochore protein SPC24 × 1 （Q04477） Kinetochore protein SPC25 × 1 （P40014） nanobody × 1 MERCURY (II) ION × 6	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 209–279； UniProt 621–691

Kinetochore protein NUF2

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P33895

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Kinetochore protein NDC80 × 1 （P40460） Kinetochore protein SPC24 × 1 （Q04477） Kinetochore protein SPC25 × 1 （P40014） nanobody × 1 MERCURY (II) ION × 6	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 1–153； UniProt 1–153 Author chain B； PDBConstruct 154–198； UniProt 407–451

Kinetochore protein SPC24

Saccharomyces cerevisiae (strain ATCC 204508 / 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 5	Kinetochore protein NDC80 × 1 （P40460） Kinetochore protein NUF2 × 1 （P33895） Kinetochore protein SPC25 × 1 （P40014） nanobody × 1 MERCURY (II) ION × 6	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 1–62； UniProt 1–62 Author chain C； PDBConstruct 63–114； UniProt 162–213

Kinetochore protein SPC25

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P40014

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Kinetochore protein NDC80 × 1 （P40460） Kinetochore protein NUF2 × 1 （P33895） Kinetochore protein SPC24 × 1 （Q04477） nanobody × 1 MERCURY (II) ION × 6	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 1–45； UniProt 1–45 Author chain D； PDBConstruct 46–129； UniProt 138–221

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	5td8
Deposition date deposition_date	2016-09-17
Structure title title	Crystal structure of an Extended Dwarf Ndc80 Complex
Keywords keywords	RWD, CH, coiled-coil, tetramer, Ndc80, Kinetochore, REPLICATION, NANOBODY; REPLICATION
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.

5td8__assembly_1__model_1

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

Download this curve (.dat)

5td8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5td8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	57.78 Å
Rg (electron density)	59.41 Å
Total Rg	59.21 Å
Atom count	12626
Residues	786
Excluded volume	114660 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5td8__assembly_1__model_1`	pentameric （5）	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 (6)

Entity 1 Entity 1 polymer

Description description	Kinetochore protein NDC80
Molecular weight formula_weight	33256.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	12626

SNARDPRPLRDKNFQSAIQEEIYDYLKKNKFDIETNHPISIKFLKQPTQKGFIIIFKWLYLRLDPGYGFTKSIENEIYQILKNLRYPFLESINKSQISAVGGSNWHKFLGMLHWMVRTNIKLDMCLNKVDRSLINQNTQEITILSQPLKTLDEQDQRQERYELMVEKLLIDYFTESYKSFLKLEDNYEPSMQELKLGFEKFVHIINTDVTSTELKLEELKVDLNRKRYKLHQQVIHVIDITSKFKINIQSSLENSENELGNVIEELRNLEFETEHNVTN

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 polymer

Description description	Kinetochore protein NUF2
Molecular weight formula_weight	23246.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSRNQDVFPILDLQELVICLQSCDFALATQENISRPTSDYMVTLYKQIIENFMGISVESLLNSSNQETGDGHLQEENENIYLDTLNVLVLNKICFKFFENIGVQDFNMTDLYKPEAQRTQRLLSAVVNYARFREERMFDCNSFILQMESLLGQINKLNDEIKQLQKDFEVEVKEIEIEYSLLSGHINKYMNEMLEYMQ

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 3 Entity 3 polymer

Description description	Kinetochore protein SPC24
Molecular weight formula_weight	13469.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MSQKDNLLDNPVEFLKEVRESFDIQQDVDAMKRIRHDLDVIKEESEARISKEHSKVSESNKKLKLYRSLGVILDLENDQVLINRKNDGNIDILPLDNNLSDFYKTKYIWERLGK

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 4 Entity 4 polymer

Description description	Kinetochore protein SPC25
Molecular weight formula_weight	14568.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MASIDAFSDLERRMDGFQKDVAQVLARQQNHARQQLQQFQAEMRQVALYERLLQLRVLPGASDVHDVRFVFGDDSRCWIEVAMHGDHVIGNSHPALDPKSRATLEHVLTVQGDLAAFLVVARDMLLASL

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 5 Entity 5 polymer

Description description	nanobody
Molecular weight formula_weight	15894.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MQVQLVESGGGLVHPGGSLRLSCAASGRTGSRHAVAWFRQAPGKERDFVASINAVGLVRNYADSVLGRFSISRDFAKNEVYLQMNSLEPEDTAVYYCAARYYSGTYSSTYDRDDYDYWGQGTQVTVSSGGGLPETGGLEHHHHHH

Source Source

Source organism organism	Vicugna pacos
NCBI taxonomy ID ncbi_taxonomy_id	30538
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 6 Entity 6 non-polymer

Description description	MERCURY (II) ION
Molecular weight formula_weight	200.6 kDa
Source method src_method	syn
Copy count entity_count	6

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Unit-cell length a length_a	226.825 Å
Unit-cell length b length_b	226.825 Å
Unit-cell length c length_c	237.270 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	I 41 2 2
Space-group number int_tables_number	98
Crystal system crystal_system	—

Resolution resolution	7.531 Å
Low-resolution limit resolution_low	113.413 Å
R factor r_factor	0.3132
R_work r_work	0.3124
R_free r_free	0.3283

Crystal structure of an Extended 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

Kinetochore protein NUF2

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

5td8__assembly_1__model_1

5td8__assembly_1__model_1 | I(q)

5td8__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 (6)

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

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 non-polymer

7. Citations (1)