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6xwv

Crystal structure of drosophila melanogaster CENP-C bound to CAL1

Method: X-RAY DIFFRACTION Dmax: 87.9 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Calmodulin

Drosophila melanogaster

UniProt A8WHM0

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 1–1411 Chain B； UniProt 1–1411 Chain C； UniProt 1–1411 Chain D； UniProt 1–1411 Not recorded Ryanodine Receptor 2 × 1 （Q9VEN2） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Calcium acetate, 0.1M Na Cacodylate, pH 6.5, 18% PEG 8000 Resolution 2.27 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.

Other PDB Difference from Current Entry 6XWV Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6XWU Crystal structure of drosophila melanogaster CENP-C cumin domain Deposited 2020-01-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–1411（1411 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；50mM MES pH6.0, 45% PEG 400
Resolution 1.82 Å R-free 0.235

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A8WHM0_DROME
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–1411； UniProt 1–1411 Author chain B； PDBConstruct 1–1411； UniProt 1–1411 Author chain C； PDBConstruct 1–1411； UniProt 1–1411 Author chain D； PDBConstruct 1–1411； UniProt 1–1411

Ryanodine Receptor 2

Drosophila melanogaster

UniProt Q9VEN2

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 E； UniProt 1–979 Not recorded Calmodulin × 4 （A8WHM0） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Calcium acetate, 0.1M Na Cacodylate, pH 6.5, 18% PEG 8000 Resolution 2.27 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.

Other PDB Difference from Current Entry 6XWV Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6XWS Crystal Structure of Drosophila CAL1 1-160 bound to CENP-A/H4 Deposited 2020-01-24 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–47（47 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.2 M lithium sulfate, 0.1 M Tris pH 8.5 and 30% PEG 4000
Resolution 4.36 Å R-free 0.323
6XWT drosophila melanogaster CENP-A/H4 bound to N-terminal CAL1 fragment Deposited 2020-01-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 1–979（979 aa）
Chain F 1–979（979 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.01M Cobalt (II) Chloride hexahydrate, 0.1M MES pH 6.5 and 1.8 M Ammonium Sulphate
Resolution 3.47 Å R-free 0.286

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q9VEN2_DROME
Isoform —
PDB entities 2
Chains and sequence ranges Author chain E； PDBConstruct 1–979； UniProt 1–979

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 6xwv

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6xwv
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6xwv
Deposition date deposition_date2020-01-24
Structure title titleCrystal structure of drosophila melanogaster CENP-C bound to CAL1
Keywords keywordsCentromere, Kinetochore, Cell Division, CELL CYCLE; CELL CYCLE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier28.06 Å
Radius of gyration Rg (electron density) rg_electron27.08 Å
Forward intensity I(0) i058863900.00
Molecular weight molecular_weight59948.0 kDa
Excluded volume excluded_volume75210 ų
Envelope volume envelope_volume95934 ų
Hydration-shell volume shell_volume29810 ų
Envelope diameter envelope_diameter85.5 Å
Shell Rg shell_rg34.21 Å
Envelope Rg envelope_rg26.68 Å
Shape Rg shape_rg27.11 Å
Total Rg total_rg27.80 Å
Total atoms total_atoms4211
Residues n_residues536
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax87.9 Å
Rg (real space) rg_real28.04 Å
Rg uncertainty (real space) rg_real_error0.47 Å
I(0) (real space) i0_real5.8860e+07
I(0) uncertainty (real space) i0_real_error8.7380e+05
Rg (reciprocal space) rg_reciprocal28.05 Å
I(0) (reciprocal space) i0_reciprocal58860000.0000
Solution quality estimate total_estimate0.9051
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks0
Primary peak position r_peak_primary— Å
Skewness Skewness skewness0.270
Kurtosis Kurtosis kurtosis-0.651
Angular range angular_range— – 0.2850 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha17720000.0000
Real-space data points n_real_points58
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.968
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)