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6cpk

Solution structure of SH3 domain from Shank3

Method: SOLUTION NMR Dmax: 41.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

SH3 and multiple ankyrin repeat domains protein 3

Homo sapiens

UniProt Q9BYB0

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 352–411 Not recorded No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6.8；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR sample composition：1 mM [U-99% 13C; U-99% 15N] Shank3 SH3, 20 mM Bis-Tris, 100 mM KCl, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：1 mM [U-99% 13C; U-99% 15N] Shank3 SH3, 20 mM Bis-Tris, 100 mM KCl, 100% D2O | 100% D2O NMR sample composition：1 mM [U-99% 15N] Shank3 SH3, 20 mM Bis-Tris, 100 mM KCl, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：1 mM Shank3 SH3, 20 mM Bis-Tris, 100 mM KCl, 100% D2O | 100% D2O Resolution not provided

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.

Other PDB Difference from Current Entry 6CPK Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7C7I Crystal structure of SHANK3 SPN domain in complex with GTP-bound Rap1b(E30D,K31E) Deposited 2020-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–99（99 aa）
Chain D 1–99（99 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 CA CALCIUM ION × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；14.4% (w/v) PEG 8000, Sodium cacodylate/Hydrochloric acid (pH 6.5), 160 mM Calcium acetate, 20% (v/v) Glycerol
Resolution 2.28 Å R-free 0.246
7C7J Crystal structure of SHANK3 SPN domain in complex with GTP-bound Rap1b(G12V,Q63E) Deposited 2020-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–99（99 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；10% (w/v) PEG 8000, 100 mM Imidazole/Hydrochloric acid (pH 8.0), 200 mM Calcium acetate
Resolution 2.39 Å R-free 0.255
7C7J Crystal structure of SHANK3 SPN domain in complex with GTP-bound Rap1b(G12V,Q63E) Deposited 2020-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–99（99 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；10% (w/v) PEG 8000, 100 mM Imidazole/Hydrochloric acid (pH 8.0), 200 mM Calcium acetate
Resolution 2.39 Å R-free 0.255

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SHAN3_HUMAN
Isoform Q9BYB0-3
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–61； UniProt 352–411

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 6cpk

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6cpk
Deposition date deposition_date2018-03-13
Structure title titleSolution structure of SH3 domain from Shank3
Keywords keywordsPSD, scaffold protein, postsynaptic density, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier11.18 Å
Radius of gyration Rg (electron density) rg_electron10.95 Å
Forward intensity I(0) i0376267000.00
Molecular weight molecular_weight164740.0 kDa
Excluded volume excluded_volume206270 ų
Envelope volume envelope_volume15651 ų
Hydration-shell volume shell_volume10203 ų
Envelope diameter envelope_diameter47.0 Å
Shell Rg shell_rg18.84 Å
Envelope Rg envelope_rg14.30 Å
Shape Rg shape_rg10.85 Å
Total Rg total_rg11.46 Å
Total atoms total_atoms23025
Residues n_residues1525
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax41.8 Å
Rg (real space) rg_real11.17 Å
Rg uncertainty (real space) rg_real_error0.37 Å
I(0) (real space) i0_real3.7630e+08
I(0) uncertainty (real space) i0_real_error4.2800e+06
Rg (reciprocal space) rg_reciprocal11.18 Å
I(0) (reciprocal space) i0_reciprocal376300000.0000
Solution quality estimate total_estimate0.7041
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary14.3 Å
Skewness Skewness skewness0.362
Kurtosis Kurtosis kurtosis0.223
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha115300.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.395; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.963; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd6cpka_
Class classb — All beta proteins
Fold Fold foldb.34 — SH3-like barrel
Superfamily Superfamily superfamilyb.34.2 — SH3-domain
Family Family familyb.34.2.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id6cpkA00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily40 — SH3 Domains
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8. Citations (1)

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9. Files and Curves (10)