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9ezn

Canonical class 1 structure of the human cortactin SH3 domain in complex with WIP-derived peptide

Method: SOLUTION NMR Dmax: 37.5 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

cDNA FLJ34459 fis, clone HLUNG2002916, highly similar to SRC SUBSTRATE CORTACTIN

Homo sapiens

UniProt B3KRK4

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 178–234 Not recorded WAS/WASL-interacting protein family member 1 × 1 （O43516） SOLUTION NMR NMR measurement conditions：pH 6.6；298 K；Ionic strength (raw mmCIF value) 0.055；Pressure 1 NMR sample composition：0.7 mM Human WIP (165-183), 20 mM potassium phosphate, 20 mM sodium chloride, 0.02 % sodium azide, 93% H2O/7% D2O | 93% H2O/7% D2O NMR sample composition：0.7 mM Human WIP (165-183), 20 mM potassium phosphate, 20 mM sodium chloride, 0.02 % sodium azide, 100% D2O | 100% D2O NMR sample composition：1.1 mM Human WIP (165-183), 0.22 mM [U-99% 15N; U-80% 2H] Human cortactin SH3 domain (494-550), 20 mM potassium phosphate, 20 mM sodium chloride, 1 mM dithiothreitol, 0.02 % sodium azide, 93% H2O/7% D2O | 93% H2O/7% D2O NMR sample composition：1.1 mM Human WIP (165-183), 0.22 mM [U-99% 15N; U-80% 2H] Human cortactin SH3 domain (494-550), 20 mM potassium phosphate, 20 mM sodium chloride, 1 mM dithiothreitol, 0.02 % sodium azide, 100% D2O | 100% D2O NMR sample composition：1.1 mM Human WIP (165-183), 0.22 mM [U-99% 13C; U-99% 15N] Human cortactin SH3 domain (494-550), 20 mM potassium phosphate, 20 mM sodium chloride, 1 mM dithiothreitol, 0.02 % sodium azide, 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 9EZN Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9EZO Canonical class 2 structure of the human cortactin SH3 domain in complex with WIP-derived peptide Deposited 2024-04-13 Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 178–234（57 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.6；298 K；Ionic strength (raw mmCIF value) 0.055；Pressure 1
NMR sample composition 0.7 mM Human WIP (165-183), 20 mM potassium phosphate, 20 mM sodium chloride, 0.02 % sodium azide, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 0.7 mM Human WIP (165-183), 20 mM potassium phosphate, 20 mM sodium chloride, 0.02 % sodium azide, 100% D2O | 100% D2O
NMR sample composition 0.22 mM [U-99% 15N; U-80% 2H] Human cortactin SH3 domain (494-550), 1.1 mM Human WIP (165-183), 20 mM potassium phosphate, 20 mM sodium chloride, 0.02 % sodium azide, 1 mM dithiothreitol, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 0.22 mM [U-99% 15N; U-80% 2H] Human cortactin SH3 domain (494-550), 1.1 mM Human WIP (165-183), 20 mM potassium phosphate, 20 mM sodium chloride, 0.02 % sodium azide, 1 mM dithiothreitol, 100% D2O | 100% D2O
NMR sample composition 0.22 mM [U-99% 13C; U-99% 15N] Human cortactin SH3 domain (494-550), 1.1 mM Human WIP (165-183), 20 mM potassium phosphate, 20 mM sodium chloride, 0.02 % sodium azide, 1 mM dithiothreitol, 100% D2O | 100% D2O
Resolution not provided
9EZP Non-canonical structure of the human cortactin SH3 domain in complex with WIP-derived peptide Deposited 2024-04-13 Parsed fields agree Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 178–234（57 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.6；298 K；Ionic strength (raw mmCIF value) 0.055；Pressure 1
NMR sample composition 0.7 mM Human WIP (165-183), 20 mM potassium phosphate, 20 mM sodium chloride, 0.02 % sodium azide, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 0.7 mM Human WIP (165-183), 20 mM potassium phosphate, 20 mM sodium chloride, 0.02 % sodium azide, 100% D2O | 100% D2O
NMR sample composition 1.1 mM Human WIP (165-183), 0.22 mM [U-99% 15N; U-80% 2H] Human cortactin SH3 domain (494-550), 20 mM potassium phosphate, 20 mM sodium chloride, 1 mM dithiothreitol, 0.02 % sodium azide, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 1.1 mM Human WIP (165-183), 0.22 mM [U-99% 15N; U-80% 2H] Human cortactin SH3 domain (494-550), 20 mM potassium phosphate, 20 mM sodium chloride, 1 mM dithiothreitol, 0.02 % sodium azide, 100% D2O | 100% D2O
NMR sample composition 1.1 mM Human WIP (165-183), 0.22 mM [U-99% 13C; U-99% 15N] Human cortactin SH3 domain (494-550), 20 mM potassium phosphate, 20 mM sodium chloride, 1 mM dithiothreitol, 0.02 % sodium azide, 100% D2O | 100% D2O
Resolution not provided

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

View Construct and Data Evidence
UniProt name B3KRK4_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–57； UniProt 178–234

WAS/WASL-interacting protein family member 1

OrganismNot specified

UniProt O43516

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 165–183 Not recorded cDNA FLJ34459 fis, clone HLUNG2002916, highly similar to SRC SUBSTRATE CORTACTIN × 1 （B3KRK4） SOLUTION NMR NMR measurement conditions：pH 6.6；298 K；Ionic strength (raw mmCIF value) 0.055；Pressure 1 NMR sample composition：0.7 mM Human WIP (165-183), 20 mM potassium phosphate, 20 mM sodium chloride, 0.02 % sodium azide, 93% H2O/7% D2O | 93% H2O/7% D2O NMR sample composition：0.7 mM Human WIP (165-183), 20 mM potassium phosphate, 20 mM sodium chloride, 0.02 % sodium azide, 100% D2O | 100% D2O NMR sample composition：1.1 mM Human WIP (165-183), 0.22 mM [U-99% 15N; U-80% 2H] Human cortactin SH3 domain (494-550), 20 mM potassium phosphate, 20 mM sodium chloride, 1 mM dithiothreitol, 0.02 % sodium azide, 93% H2O/7% D2O | 93% H2O/7% D2O NMR sample composition：1.1 mM Human WIP (165-183), 0.22 mM [U-99% 15N; U-80% 2H] Human cortactin SH3 domain (494-550), 20 mM potassium phosphate, 20 mM sodium chloride, 1 mM dithiothreitol, 0.02 % sodium azide, 100% D2O | 100% D2O NMR sample composition：1.1 mM Human WIP (165-183), 0.22 mM [U-99% 13C; U-99% 15N] Human cortactin SH3 domain (494-550), 20 mM potassium phosphate, 20 mM sodium chloride, 1 mM dithiothreitol, 0.02 % sodium azide, 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 9EZN Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1MKE Structure of the N-WASP EVH1 Domain-WIP complex Deposited 2002-08-29 Different construct Different oligomeric state Different experimental conditions Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 461–485（25 aa） Fragment：WIP peptide and N-WASP EVH1 domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 20 mM NaCl；Pressure ambient
NMR sample composition U-15N protein 20 mM PO4 buffer 1 mM dithiothreitol | 90% H2O/10% D2O
NMR sample composition U-13C/15N protein 20 mM PO4 buffer 1 mM dithiothreitol | 90% H2O/10% D2O
Resolution not provided
2A41 Ternary complex of the WH2 Domain of WIP with Actin-DNAse I Deposited 2005-06-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 29–60（32 aa） Fragment：first WH2 domain
Not recorded CA CALCIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 FMT FORMIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；sodium formate, PEG3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.219
2IFS Structure of the N-WASP EVH1 domain in complex with an extended WIP peptide Deposited 2006-09-21 Different construct Different oligomeric state Different experimental conditions Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 451–485（35 aa） Fragment：WIP peptide (residues 451-485) and N-WASP EVH1 domain (Residues 26-147)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 0.044 mM；Pressure 1
NMR sample composition 1.0 mM U-15N/13C protein, 20 mM sodium phosphate, 1 mM Dithiothreitol, 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
9EZO Canonical class 2 structure of the human cortactin SH3 domain in complex with WIP-derived peptide Deposited 2024-04-13 Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 165–183（19 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.6；298 K；Ionic strength (raw mmCIF value) 0.055；Pressure 1
NMR sample composition 0.7 mM Human WIP (165-183), 20 mM potassium phosphate, 20 mM sodium chloride, 0.02 % sodium azide, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 0.7 mM Human WIP (165-183), 20 mM potassium phosphate, 20 mM sodium chloride, 0.02 % sodium azide, 100% D2O | 100% D2O
NMR sample composition 0.22 mM [U-99% 15N; U-80% 2H] Human cortactin SH3 domain (494-550), 1.1 mM Human WIP (165-183), 20 mM potassium phosphate, 20 mM sodium chloride, 0.02 % sodium azide, 1 mM dithiothreitol, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 0.22 mM [U-99% 15N; U-80% 2H] Human cortactin SH3 domain (494-550), 1.1 mM Human WIP (165-183), 20 mM potassium phosphate, 20 mM sodium chloride, 0.02 % sodium azide, 1 mM dithiothreitol, 100% D2O | 100% D2O
NMR sample composition 0.22 mM [U-99% 13C; U-99% 15N] Human cortactin SH3 domain (494-550), 1.1 mM Human WIP (165-183), 20 mM potassium phosphate, 20 mM sodium chloride, 0.02 % sodium azide, 1 mM dithiothreitol, 100% D2O | 100% D2O
Resolution not provided
9EZP Non-canonical structure of the human cortactin SH3 domain in complex with WIP-derived peptide Deposited 2024-04-13 Parsed fields agree Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 165–183（19 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.6；298 K；Ionic strength (raw mmCIF value) 0.055；Pressure 1
NMR sample composition 0.7 mM Human WIP (165-183), 20 mM potassium phosphate, 20 mM sodium chloride, 0.02 % sodium azide, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 0.7 mM Human WIP (165-183), 20 mM potassium phosphate, 20 mM sodium chloride, 0.02 % sodium azide, 100% D2O | 100% D2O
NMR sample composition 1.1 mM Human WIP (165-183), 0.22 mM [U-99% 15N; U-80% 2H] Human cortactin SH3 domain (494-550), 20 mM potassium phosphate, 20 mM sodium chloride, 1 mM dithiothreitol, 0.02 % sodium azide, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 1.1 mM Human WIP (165-183), 0.22 mM [U-99% 15N; U-80% 2H] Human cortactin SH3 domain (494-550), 20 mM potassium phosphate, 20 mM sodium chloride, 1 mM dithiothreitol, 0.02 % sodium azide, 100% D2O | 100% D2O
NMR sample composition 1.1 mM Human WIP (165-183), 0.22 mM [U-99% 13C; U-99% 15N] Human cortactin SH3 domain (494-550), 20 mM potassium phosphate, 20 mM sodium chloride, 1 mM dithiothreitol, 0.02 % sodium azide, 100% D2O | 100% D2O
Resolution not provided

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

View Construct and Data Evidence
UniProt name WIPF1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–19； UniProt 165–183

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 9ezn

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9ezn
Deposition date deposition_date2024-04-13
Structure title titleCanonical class 1 structure of the human cortactin SH3 domain in complex with WIP-derived peptide
Keywords keywordsSH3 domain, cortactin, WASp-interacting protein (WIP), cytoskeletal regulation, cortactin-WIP complex, 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_guinier13.53 Å
Radius of gyration Rg (electron density) rg_electron13.31 Å
Forward intensity I(0) i0444767000.00
Molecular weight molecular_weight172010.0 kDa
Excluded volume excluded_volume212400 ų
Envelope volume envelope_volume27375 ų
Hydration-shell volume shell_volume13831 ų
Envelope diameter envelope_diameter58.9 Å
Shell Rg shell_rg23.09 Å
Envelope Rg envelope_rg18.96 Å
Shape Rg shape_rg13.23 Å
Total Rg total_rg13.82 Å
Total atoms total_atoms23620
Residues n_residues1520
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 dmax37.5 Å
Rg (real space) rg_real12.95 Å
Rg uncertainty (real space) rg_real_error0.06 Å
I(0) (real space) i0_real4.2600e+08
I(0) uncertainty (real space) i0_real_error3.2690e+06
Rg (reciprocal space) rg_reciprocal13.62 Å
I(0) (reciprocal space) i0_reciprocal444800000.0000
Solution quality estimate total_estimate0.6680
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary15.2 Å
Skewness Skewness skewness0.403
Kurtosis Kurtosis kurtosis-0.140
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha5.5100
Highest regularization parameter α highest_alpha236000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.925; Stabil: 0.970; Sysdev: 0.000; Positv: 1.000; Valcen: 0.998; 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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8. Citations (1)

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9. Files and Curves (10)