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5ixf

Solution structure of the STAM2 SH3 with AMSH derived peptide complex

Method: SOLUTION NMR Dmax: 43.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Signal transducing adapter molecule 2

Homo sapiens

UniProt O75886

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 162–265 Fragment：SH3 domain, residues 196-263 STAM-binding protein × 1 （C9JK83） SOLUTION NMR NMR measurement conditions：pH 6.8；293 K；Ionic strength (raw mmCIF value) 20；Pressure 1 NMR sample composition：250 uM [U-13C; U-15N] UIM-SH3, 250 uM SBM motif of AMSH, 20 mM sodium phosphate, 0.02 % sodium azide, 90% H2O/10% D2O | 90% H2O/10% 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 5IXF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1X2Q Solution structure of the SH3 domain of the Signal transducing adaptor molecule 2 Deposited 2005-04-26 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 195–269（75 aa） Fragment：SH3 domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition 1.00mM SH3 domain U-15N,13C; 20mM d-tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O | 90% H2O/10% D2O
Resolution not provided
1X5B The solution structure of the VHS domain of human Signal transducing adaptor molecule 2 Deposited 2005-05-15 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–150（150 aa） Fragment：VHS domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition 1.5mM VHS domain U-15N,13C; 20mM d-Tris HCl; 100mM NaCl; 5mM d-DTT; 0.02% NaN3; 10% D2O | 90% H2O/10% D2O
Resolution not provided
2L0T Solution structure of the complex of ubiquitin and the VHS domain of Stam2 Deposited 2010-07-15 Different construct Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–150（150 aa） Fragment：VHS Domain (UNP residues 1-150)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；288 K；Ionic strength (raw mmCIF value) 20；Pressure ambient
NMR sample composition 250 uM [U-99% 15N] Ubiquitin protein, 250 uM [U-99% 15N] VHS domain of Stam2, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
5CRV Crystal structure of the Bro domain of HD-PTP in a complex with the core region of STAM2 Deposited 2015-07-23 Different construct 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 350–370（21 aa） Fragment：UNP residues 350-370
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1 M Bis-Tris, 30%(w/v) polyethylene glycol 3350, 4%(v/v) acetonitrile
Resolution 2.00 Å R-free 0.241
5CRV Crystal structure of the Bro domain of HD-PTP in a complex with the core region of STAM2 Deposited 2015-07-23 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 350–370（21 aa） Fragment：UNP residues 350-370
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1 M Bis-Tris, 30%(w/v) polyethylene glycol 3350, 4%(v/v) acetonitrile
Resolution 2.00 Å R-free 0.241

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name STAM2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 6–109； UniProt 162–265

STAM-binding protein

OrganismNot specified

UniProt C9JK83

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 228–241 Fragment：SBM motif, UNP residues 228-241 Signal transducing adapter molecule 2 × 1 （O75886） SOLUTION NMR NMR measurement conditions：pH 6.8；293 K；Ionic strength (raw mmCIF value) 20；Pressure 1 NMR sample composition：250 uM [U-13C; U-15N] UIM-SH3, 250 uM SBM motif of AMSH, 20 mM sodium phosphate, 0.02 % sodium azide, 90% H2O/10% D2O | 90% H2O/10% 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.

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

View Construct and Data Evidence
UniProt name C9JK83_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–14； UniProt 228–241

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 5ixf

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5ixf
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5ixf
Deposition date deposition_date2016-03-23
Structure title titleSolution structure of the STAM2 SH3 with AMSH derived peptide complex
Keywords keywordsSTAM2, SH3, endosome, traffic, AMSH, Signaling protein; SIGNALING PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier13.49 Å
Radius of gyration Rg (electron density) rg_electron13.25 Å
Forward intensity I(0) i0121793000.00
Molecular weight molecular_weight92734.0 kDa
Excluded volume excluded_volume116320 ų
Envelope volume envelope_volume20752 ų
Hydration-shell volume shell_volume12232 ų
Envelope diameter envelope_diameter48.8 Å
Shell Rg shell_rg20.31 Å
Envelope Rg envelope_rg15.34 Å
Shape Rg shape_rg13.19 Å
Total Rg total_rg13.71 Å
Total atoms total_atoms13050
Residues n_residues820
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 dmax43.5 Å
Rg (real space) rg_real13.48 Å
Rg uncertainty (real space) rg_real_error0.31 Å
I(0) (real space) i0_real1.2180e+08
I(0) uncertainty (real space) i0_real_error1.2930e+06
Rg (reciprocal space) rg_reciprocal13.48 Å
I(0) (reciprocal space) i0_reciprocal121800000.0000
Solution quality estimate total_estimate0.8102
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary16.5 Å
Skewness Skewness skewness0.297
Kurtosis Kurtosis kurtosis-0.307
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha137200.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.845; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id5ixfA00
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)