5td8

Crystal structure of an Extended Dwarf Ndc80 Complex

Method: X-RAY DIFFRACTION Dmax: 179.4 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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 114–318 Chain A; UniProt 621–691 Not recorded Kinetochore protein NUF2 × 1 (P33895) Kinetochore protein SPC24 × 1 (Q04477) Kinetochore protein SPC25 × 1 (P40014) nanobody × 1 HG MERCURY (II) ION × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;16% PEG 4,000, 0.1 M CHES, pH 9.0 Resolution 7.53 Å R-free 0.328

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 209–279; UniProt 621–691

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 1–153 Chain B; UniProt 407–451 Not recorded Kinetochore protein NDC80 × 1 (P40460) Kinetochore protein SPC24 × 1 (Q04477) Kinetochore protein SPC25 × 1 (P40014) nanobody × 1 HG MERCURY (II) ION × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;16% PEG 4,000, 0.1 M CHES, pH 9.0 Resolution 7.53 Å R-free 0.328

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 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 Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain C; UniProt 1–62 Chain C; UniProt 162–213 Not recorded Kinetochore protein NDC80 × 1 (P40460) Kinetochore protein NUF2 × 1 (P33895) Kinetochore protein SPC25 × 1 (P40014) nanobody × 1 HG MERCURY (II) ION × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;16% PEG 4,000, 0.1 M CHES, pH 9.0 Resolution 7.53 Å R-free 0.328

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 1–62; 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 Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain D; UniProt 1–45 Chain D; UniProt 138–221 Not recorded Kinetochore protein NDC80 × 1 (P40460) Kinetochore protein NUF2 × 1 (P33895) Kinetochore protein SPC24 × 1 (Q04477) nanobody × 1 HG MERCURY (II) ION × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;16% PEG 4,000, 0.1 M CHES, pH 9.0 Resolution 7.53 Å R-free 0.328

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 1–45; 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.

SAXS scattering curve SAXS Profile

SAXS profile for 5td8

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5td8
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5td8
Deposition date deposition_date2016-09-17
Structure title titleCrystal structure of an Extended Dwarf Ndc80 Complex
Keywords keywordsRWD, CH, coiled-coil, tetramer, Ndc80, Kinetochore, REPLICATION, NANOBODY; REPLICATION
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier57.78
Radius of gyration Rg (electron density) rg_electron59.41
Forward intensity I(0) i0130598000.00
Molecular weight molecular_weight92496.0 kDa
Excluded volume excluded_volume114660 ų
Envelope volume envelope_volume192860 ų
Hydration-shell volume shell_volume31231 ų
Envelope diameter envelope_diameter192.1
Shell Rg shell_rg48.00
Envelope Rg envelope_rg58.27
Shape Rg shape_rg59.34
Total Rg total_rg59.21
Total atoms total_atoms12626
Residues n_residues786
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 dmax179.4
Rg (real space) rg_real58.87
Rg uncertainty (real space) rg_real_error2.21
I(0) (real space) i0_real1.3060e+08
I(0) uncertainty (real space) i0_real_error2.9420e+06
Rg (reciprocal space) rg_reciprocal56.80
I(0) (reciprocal space) i0_reciprocal130200000.0000
Solution quality estimate total_estimate0.6175
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary26.6
Skewness Skewness skewness0.473
Kurtosis Kurtosis kurtosis-0.833
Angular range angular_range— – 0.1350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3392000.0000
Real-space data points n_real_points28
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.313; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.086; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)