9cx3

Structure of SH3 domain of Src in complex with beta-arrestin 1

Method: ELECTRON MICROSCOPY Dmax: 108.4 Å Quality: GOOD

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

Proto-oncogene tyrosine-protein kinase Src

Gallus gallus

UniProt P00523

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain C; UniProt 83–141 Mutation:R95C Nanobody 32 × 1 Antibody fragment Fab30, heavy chain × 1 Vasopressin V2 receptor × 1 (P30518) Beta-arrestin-1 × 1 (P29066) Antibody fragment Fab30, light chain × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.47 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.

133 other PDB entries and 236 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SRC_CHICK
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 27–85; UniProt 83–141

Vasopressin V2 receptor

OrganismNot specified

UniProt P30518

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain V; UniProt 343–371 Fragment:UNP residues 343-371 Non-standard monomer:Yes (specific site not provided by mmCIF) Nanobody 32 × 1 Proto-oncogene tyrosine-protein kinase Src × 1 (P00523) Antibody fragment Fab30, heavy chain × 1 Beta-arrestin-1 × 1 (P29066) Antibody fragment Fab30, light chain × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.47 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.

36 other PDB entries and 37 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name V2R_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain V; PDBConstruct 1–29; UniProt 343–371

Beta-arrestin-1

Rattus norvegicus

UniProt P29066

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 2–393 Mutation:C59V, P120C, C125S, C140L, C150V, C242V, C251V, C269S Nanobody 32 × 1 Proto-oncogene tyrosine-protein kinase Src × 1 (P00523) Antibody fragment Fab30, heavy chain × 1 Vasopressin V2 receptor × 1 (P30518) Antibody fragment Fab30, light chain × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.47 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.

16 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ARRB1_RAT
Isoform
PDB entities 5
Chains and sequence ranges Author chain B; PDBConstruct 1–392; UniProt 2–393

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 9cx3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9cx3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9cx3
Deposition date deposition_date2024-07-30
Structure title titleStructure of SH3 domain of Src in complex with beta-arrestin 1
Keywords keywordsGPCR signaling, arrestin, Src, SH3, SIGNALING PROTEIN-IMMUNE SYSTEM complex, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier31.44
Radius of gyration Rg (electron density) rg_electron30.83
Forward intensity I(0) i0102484000.00
Molecular weight molecular_weight79883.0 kDa
Excluded volume excluded_volume99988 ų
Envelope volume envelope_volume131900 ų
Hydration-shell volume shell_volume36527 ų
Envelope diameter envelope_diameter113.7
Shell Rg shell_rg36.87
Envelope Rg envelope_rg30.67
Shape Rg shape_rg30.80
Total Rg total_rg31.47
Total atoms total_atoms5626
Residues n_residues714
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 dmax108.4
Rg (real space) rg_real31.44
Rg uncertainty (real space) rg_real_error1.06
I(0) (real space) i0_real1.0250e+08
I(0) uncertainty (real space) i0_real_error1.6620e+06
Rg (reciprocal space) rg_reciprocal31.44
I(0) (reciprocal space) i0_reciprocal102500000.0000
Solution quality estimate total_estimate0.8782
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary39.0
Skewness Skewness skewness0.336
Kurtosis Kurtosis kurtosis-0.233
Angular range angular_range— – 0.2500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha21440000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.832; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.930

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (2)

9. Files and Curves (10)