6o3a

Crystal structure of Frizzled 7 CRD in complex with F7.B Fab

Method: X-RAY DIFFRACTION Dmax: 104.3 Å Quality: REASONABLE

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

Frizzled-7

Homo sapiens

UniProt O75084

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 42–179 Not recorded Antibody F7.B Fab, Light chain × 1 Antibody F7.B Fab, Heavy chain × 1 CXS 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID × 1 EDO 1,2-ETHANEDIOL × 6 NA SODIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 10;293 K;0.1 M CAPS, pH 10.5, 20% (w/v) PEG 3350, 0.2 M NaCl Resolution 2.10 Å R-free 0.242

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.

11 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FZD7_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain E; PDBConstruct 1–138; UniProt 42–179

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 6o3a

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6o3a
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6o3a
Deposition date deposition_date2019-02-26
Structure title titleCrystal structure of Frizzled 7 CRD in complex with F7.B Fab
Keywords keywordsReceptor, Wnt, Frizzled, CRD, Antibody, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.00
Radius of gyration Rg (electron density) rg_electron29.71
Forward intensity I(0) i060622300.00
Molecular weight molecular_weight60752.0 kDa
Excluded volume excluded_volume75717 ų
Envelope volume envelope_volume95143 ų
Hydration-shell volume shell_volume28861 ų
Envelope diameter envelope_diameter109.7
Shell Rg shell_rg34.20
Envelope Rg envelope_rg29.87
Shape Rg shape_rg29.65
Total Rg total_rg30.30
Total atoms total_atoms4268
Residues n_residues541
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 dmax104.3
Rg (real space) rg_real31.52
Rg uncertainty (real space) rg_real_error0.39
I(0) (real space) i0_real6.0860e+07
I(0) uncertainty (real space) i0_real_error8.5270e+05
Rg (reciprocal space) rg_reciprocal30.18
I(0) (reciprocal space) i0_reciprocal60620000.0000
Solution quality estimate total_estimate0.6266
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks0
Primary peak position r_peak_primary
Skewness Skewness skewness0.618
Kurtosis Kurtosis kurtosis-0.185
Angular range angular_range— – 0.2650 −1
Current regularization parameter α current_alpha3.5390
Highest regularization parameter α highest_alpha9097000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.782; Stabil: 0.879; Sysdev: 0.000; Positv: 1.000; Valcen: 0.784; Smooth: 0.408

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd6o3aa1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd6o3aa2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd6o3ab_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd6o3ae_
Class classa — All alpha proteins
Fold Fold folda.141 — Frizzled cysteine-rich domain
Superfamily Superfamily superfamilya.141.1 — Frizzled cysteine-rich domain
Family Family familya.141.1.0 — automated matches

CATH v4.4 (3 domains)

Domain ID domain_id6o3aA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6o3aA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6o3aB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)