3l8j

Crystal structure of CCM3, a cerebral cavernous malformation protein critical for vascular integrity

Method: X-RAY DIFFRACTION Dmax: 76.6 Å Quality: GOOD

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

Programmed cell death protein 10

Homo sapiens

UniProt Q9BUL8

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 14–212 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;298 K;0.16 M calcium acetate, 0.08 M sodium cacodylate pH 6.5, 20% glycerol, 13.5% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 3.05 Å R-free 0.293

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 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PDC10_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 4–202; UniProt 14–212

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 3l8j

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3l8j
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3l8j
Deposition date deposition_date2009-12-31
Structure title titleCrystal structure of CCM3, a cerebral cavernous malformation protein critical for vascular integrity
Keywords keywordscerebral cavernous malformation, FAT domain, dimerization, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier22.61
Radius of gyration Rg (electron density) rg_electron21.88
Forward intensity I(0) i09206420.00
Molecular weight molecular_weight23161.0 kDa
Excluded volume excluded_volume29390 ų
Envelope volume envelope_volume39895 ų
Hydration-shell volume shell_volume16311 ų
Envelope diameter envelope_diameter78.2
Shell Rg shell_rg26.97
Envelope Rg envelope_rg22.34
Shape Rg shape_rg21.84
Total Rg total_rg22.83
Total atoms total_atoms1630
Residues n_residues200
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 dmax76.6
Rg (real space) rg_real22.73
Rg uncertainty (real space) rg_real_error0.70
I(0) (real space) i0_real9.2060e+06
I(0) uncertainty (real space) i0_real_error1.3590e+05
Rg (reciprocal space) rg_reciprocal22.71
I(0) (reciprocal space) i0_reciprocal9206000.0000
Solution quality estimate total_estimate0.8734
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.1
Skewness Skewness skewness0.435
Kurtosis Kurtosis kurtosis-0.360
Angular range angular_range— – 0.3500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha986800.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.838; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.875; Smooth: 0.961

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id3l8jA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology12 — Lyase 2-enoyl-coa Hydratase; Chain A, domain 2
Homologous superfamily homologous superfamily70
Domain ID domain_id3l8jA02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily330 — Nucleotidyltransferases domain 2

8. Citations (1)

9. Files and Curves (10)