9yrp

Full-length human VPS13C in complex with calmodulin from the CryoEM composite map

Method: ELECTRON MICROSCOPY Dmax: 251.9 Å Quality: GOOD

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

Calmodulin-1

OrganismNot specified

UniProt P0DP23

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–149 Not recorded Intermembrane lipid transfer protein VPS13C × 1 (Q709C8) ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions Resolution 4.13 Å

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.

213 other PDB entries and 279 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CALM1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–149; UniProt 1–149

Intermembrane lipid transfer protein VPS13C

Homo sapiens

UniProt Q709C8

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 1–3753 Not recorded Calmodulin-1 × 1 (P0DP23) ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions Resolution 4.13 Å

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.

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

View Construct and Data Evidence
UniProt name VP13C_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–3753; UniProt 1–3753

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 9yrp

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9yrp
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9yrp
Deposition date deposition_date2025-10-16
Structure title titleFull-length human VPS13C in complex with calmodulin from the CryoEM composite map
Keywords keywordsLipid Transport protein; BLTP; lysosomal membrane repair; membrane homeostasis, LIPID TRANSPORT; LIPID TRANSPORT
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier92.41
Radius of gyration Rg (electron density) rg_electron94.25
Forward intensity I(0) i01606990000.00
Molecular weight molecular_weight350880.0 kDa
Excluded volume excluded_volume444620 ų
Envelope volume envelope_volume943270 ų
Hydration-shell volume shell_volume95407 ų
Envelope diameter envelope_diameter296.1
Shell Rg shell_rg66.74
Envelope Rg envelope_rg88.87
Shape Rg shape_rg94.30
Total Rg total_rg93.58
Total atoms total_atoms24677
Residues n_residues3092
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 dmax251.9
Rg (real space) rg_real88.65
Rg uncertainty (real space) rg_real_error1.20
I(0) (real space) i0_real1.5490e+09
I(0) uncertainty (real space) i0_real_error3.2750e+07
Rg (reciprocal space) rg_reciprocal84.88
I(0) (reciprocal space) i0_reciprocal1570000000.0000
Solution quality estimate total_estimate0.8135
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary59.3
Skewness Skewness skewness0.430
Kurtosis Kurtosis kurtosis-0.953
Angular range angular_range— – 0.0850 −1
Current regularization parameter α current_alpha0.8085
Highest regularization parameter α highest_alpha118500000.0000
Real-space data points n_real_points18
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.689; Stabil: 0.909; Sysdev: 1.000; Positv: 1.000; Valcen: 0.785; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

8. Citations (1)

9. Files and Curves (10)