5tcs

Crystal structure of a Dwarf Ndc80 Tetramer

Method: X-RAY DIFFRACTION Dmax: 170.1 Å Quality: REASONABLE

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

Kinetochore protein NDC80

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P40460

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 114–318 Chain A; UniProt 621–689 Non-standard monomer:Yes (specific site not provided by mmCIF) Kinetochore protein NUF2 × 1 (P33895) Kinetochore protein SPC24 × 1 (Q04477) Kinetochore protein SPC25 × 1 (P40014) MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6;293 K;1.2 magnesium sulfate, 0.1 M ME pH 6.0 Resolution 2.83 Å R-free 0.266

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

7 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

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 209–277; UniProt 621–689

Kinetochore protein NUF2

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P33895

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 2–153 Chain B; UniProt 407–451 Non-standard monomer:Yes (specific site not provided by mmCIF) Kinetochore protein NDC80 × 1 (P40460) Kinetochore protein SPC24 × 1 (Q04477) Kinetochore protein SPC25 × 1 (P40014) MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6;293 K;1.2 magnesium sulfate, 0.1 M ME pH 6.0 Resolution 2.83 Å R-free 0.266

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

7 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NUF2_YEAST
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 19–170; UniProt 2–153 Author chain B; PDBConstruct 171–215; UniProt 407–451

Kinetochore protein SPC24

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q04477

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain C; UniProt 1–48 Chain C; UniProt 162–213 Non-standard monomer:Yes (specific site not provided by mmCIF) Kinetochore protein NDC80 × 1 (P40460) Kinetochore protein NUF2 × 1 (P33895) Kinetochore protein SPC25 × 1 (P40014) MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6;293 K;1.2 magnesium sulfate, 0.1 M ME pH 6.0 Resolution 2.83 Å R-free 0.266

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

9 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

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 49–100; UniProt 162–213

Kinetochore protein SPC25

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P40014

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain D; UniProt 1–31 Chain D; UniProt 138–221 Non-standard monomer:Yes (specific site not provided by mmCIF) Kinetochore protein NDC80 × 1 (P40460) Kinetochore protein NUF2 × 1 (P33895) Kinetochore protein SPC24 × 1 (Q04477) MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6;293 K;1.2 magnesium sulfate, 0.1 M ME pH 6.0 Resolution 2.83 Å R-free 0.266

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

9 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

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 32–115; 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.

SAXS scattering curve SAXS Profile

SAXS profile for 5tcs

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5tcs
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5tcs
Deposition date deposition_date2016-09-15
Structure title titleCrystal structure of a Dwarf Ndc80 Tetramer
Keywords keywordsRWD, CH, coiled-coil, tetramer, Ndc80, Kinetochore, REPLICATION; REPLICATION
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier55.46
Radius of gyration Rg (electron density) rg_electron56.70
Forward intensity I(0) i097599900.00
Molecular weight molecular_weight81325.0 kDa
Excluded volume excluded_volume101410 ų
Envelope volume envelope_volume174570 ų
Hydration-shell volume shell_volume28421 ų
Envelope diameter envelope_diameter181.9
Shell Rg shell_rg51.39
Envelope Rg envelope_rg54.95
Shape Rg shape_rg56.77
Total Rg total_rg56.24
Total atoms total_atoms11319
Residues n_residues671
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax170.1
Rg (real space) rg_real56.39
Rg uncertainty (real space) rg_real_error1.81
I(0) (real space) i0_real9.7600e+07
I(0) uncertainty (real space) i0_real_error1.8450e+06
Rg (reciprocal space) rg_reciprocal54.62
I(0) (reciprocal space) i0_reciprocal97340000.0000
Solution quality estimate total_estimate0.6092
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.4
Skewness Skewness skewness0.428
Kurtosis Kurtosis kurtosis-1.013
Angular range angular_range— – 0.1400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2806000.0000
Real-space data points n_real_points29
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.284; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.065; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id5tcsA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology418 — Actin-binding Protein, T-fimbrin; domain 1
Homologous superfamily homologous superfamily30 — Ncd80 complex, Ncd80 subunit
Domain ID domain_id5tcsD00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology457 — Copper Amine Oxidase; Chain A, domain 1
Homologous superfamily homologous superfamily50 — Chromosome segregation protein Spc25

8. Citations (1)

9. Files and Curves (10)