6gbu

Crystal structure of the second SH3 domain of FCHSD2 (SH3-2) in complex with the fourth SH3 domain of ITSN1 (SH3d)

Method: X-RAY DIFFRACTION Dmax: 89.2 Å Quality: EXCELLENT

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

F-BAR and double SH3 domains protein 2

Homo sapiens

UniProt O94868

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 × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain A; UniProt 511–573 Chain C; UniProt 511–573 Chain E; UniProt 511–573 Chain G; UniProt 511–573 Not recorded Intersectin-1 × 4 (Q15811) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;291 K;0.5M ammonium sulfate, 10% Glycerol, Tris pH8.5 Resolution 3.44 Å R-free 0.247

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name FCSD2_HUMAN
Isoform O94868-2
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–63; UniProt 511–573 Author chain C; PDBConstruct 1–63; UniProt 511–573 Author chain E; PDBConstruct 1–63; UniProt 511–573 Author chain G; PDBConstruct 1–63; UniProt 511–573

Intersectin-1

Homo sapiens

UniProt Q15811

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 × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain B; UniProt 1069–1133 Chain D; UniProt 1069–1133 Chain F; UniProt 1069–1133 Chain H; UniProt 1069–1133 Not recorded F-BAR and double SH3 domains protein 2 × 4 (O94868) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;291 K;0.5M ammonium sulfate, 10% Glycerol, Tris pH8.5 Resolution 3.44 Å R-free 0.247

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.

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

View Construct and Data Evidence
UniProt name ITSN1_HUMAN
Isoform Q15811-9
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–65; UniProt 1069–1133 Author chain D; PDBConstruct 1–65; UniProt 1069–1133 Author chain F; PDBConstruct 1–65; UniProt 1069–1133 Author chain H; PDBConstruct 1–65; UniProt 1069–1133

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 6gbu

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6gbu
Deposition date deposition_date2018-04-16
Structure title titleCrystal structure of the second SH3 domain of FCHSD2 (SH3-2) in complex with the fourth SH3 domain of ITSN1 (SH3d)
Keywords keywordsSH3-SH3 complex, Endocytosis; ENDOCYTOSIS
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier28.56
Radius of gyration Rg (electron density) rg_electron28.09
Forward intensity I(0) i040227900.00
Molecular weight molecular_weight50390.0 kDa
Excluded volume excluded_volume63511 ų
Envelope volume envelope_volume87582 ų
Hydration-shell volume shell_volume26632 ų
Envelope diameter envelope_diameter95.7
Shell Rg shell_rg34.57
Envelope Rg envelope_rg27.21
Shape Rg shape_rg28.09
Total Rg total_rg28.85
Total atoms total_atoms3581
Residues n_residues473
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 dmax89.2
Rg (real space) rg_real28.51
Rg uncertainty (real space) rg_real_error0.54
I(0) (real space) i0_real4.0230e+07
I(0) uncertainty (real space) i0_real_error6.1740e+05
Rg (reciprocal space) rg_reciprocal28.53
I(0) (reciprocal space) i0_reciprocal40230000.0000
Solution quality estimate total_estimate0.9125
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.1
Skewness Skewness skewness0.222
Kurtosis Kurtosis kurtosis-0.553
Angular range angular_range— – 0.2800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5042000.0000
Real-space data points n_real_points57
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.970; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.958

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id6gbuA00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily40 — SH3 Domains
Domain ID domain_id6gbuB00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily40 — SH3 Domains
Domain ID domain_id6gbuC00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily40 — SH3 Domains
Domain ID domain_id6gbuD00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily40 — SH3 Domains
Domain ID domain_id6gbuE00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily40 — SH3 Domains
Domain ID domain_id6gbuF00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily40 — SH3 Domains
Domain ID domain_id6gbuG00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily40 — SH3 Domains
Domain ID domain_id6gbuH00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily40 — SH3 Domains

8. Citations (1)

9. Files and Curves (10)