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7pll

Structure of the murine cortactin C-SH3 domain in complex with a Pyk2 proline-rich ligand

Method: SOLUTION NMR Dmax: 31.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Src substrate cortactin

Mus musculus

UniProt Q60598

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 490–546 Fragment：SH3 domain, UNP Residues 490-546 Pyk2-PRR2 peptide × 1 SOLUTION NMR NMR measurement conditions：pH 6.5；296 K；Ionic strength (raw mmCIF value) 123；Pressure 1 NMR sample composition：0.8 mM cortactin C-terminal SH3 domain, 0.8 mM Pyk2-PRR2 peptide, 30 mM sodium phosphate, 0.01 % w/v sodium azide, 93% H2O/7% D2O | 93% H2O/7% D2O NMR sample composition：0.5 mM Pyk2-PRR2 peptide, 30 mM sodium phosphate, 0.01 % w/v sodium azide, 93% H2O/7% D2O | 93% H2O/7% D2O NMR sample composition：0.8 mM 2H,13C,15N cortactin C-terminal SH3 domain, 0.8 mM Pyk2-PRR2 peptide, 30 mM sodium phosphate, 0.01 % w/v sodium azide, 100% D2O | 100% D2O NMR sample composition：0.8 mM cortactin C-terminal SH3 domain, 0.8 mM Pyk2-PRR2 peptide, 30 mM sodium phosphate, 0.01 % w/v 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 7PLL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3ULR Lysozyme contamination facilitates crystallization of a hetero-trimericCortactin:Arg:Lysozyme complex Deposited 2011-11-11 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 487–546（60 aa） Fragment：SH3 domain (UNP residues 487-546)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；297 K；1.0M Na Citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Resolution 1.65 Å R-free 0.225
5NV1 SH3 domain from Mouse cortactin (C 2 2 21 crystal form) Deposited 2017-05-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 490–546（57 aa）
Not recorded MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 GOL GLYCEROL × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；1.6 M Mg-sulfate, 0.1 M MES pH 6.5
Resolution 1.51 Å
5NVJ SH3 domain from Mouse cortactin (C 1 2 1 crystal form) Deposited 2017-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 490–546（57 aa）
Not recorded BEN BENZAMIDINE × 1 GOL GLYCEROL × 1 CIT CITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；289 K；1.2 M (NH4)2SO4, 0.1 M sodium citrate pH 5, 1% benzamidine hydrochloride.
Resolution 1.18 Å R-free 0.201
5NVJ SH3 domain from Mouse cortactin (C 1 2 1 crystal form) Deposited 2017-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 490–546（57 aa）
Not recorded BEN BENZAMIDINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；289 K；1.2 M (NH4)2SO4, 0.1 M sodium citrate pH 5, 1% benzamidine hydrochloride.
Resolution 1.18 Å R-free 0.201
5NXJ SH3 domain from Mouse cortactin (P 1 21 1 crystal form) Deposited 2017-05-10 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 490–546（57 aa） Fragment：SH3 domain, UNP Residues 490-546
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；289 K；1.2 M (NH4)2SO4, 0.1 M sodium citrate pH 5, 3% 2_propanol
Resolution 2.28 Å R-free 0.248
5NXJ SH3 domain from Mouse cortactin (P 1 21 1 crystal form) Deposited 2017-05-10 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 490–546（57 aa） Fragment：SH3 domain, UNP Residues 490-546
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；289 K；1.2 M (NH4)2SO4, 0.1 M sodium citrate pH 5, 3% 2_propanol
Resolution 2.28 Å R-free 0.248
5NXJ SH3 domain from Mouse cortactin (P 1 21 1 crystal form) Deposited 2017-05-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 490–546（57 aa） Fragment：SH3 domain, UNP Residues 490-546
Not recorded IPA ISOPROPYL ALCOHOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；289 K；1.2 M (NH4)2SO4, 0.1 M sodium citrate pH 5, 3% 2_propanol
Resolution 2.28 Å R-free 0.248
5NXJ SH3 domain from Mouse cortactin (P 1 21 1 crystal form) Deposited 2017-05-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 490–546（57 aa） Fragment：SH3 domain, UNP Residues 490-546
Not recorded IPA ISOPROPYL ALCOHOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；289 K；1.2 M (NH4)2SO4, 0.1 M sodium citrate pH 5, 3% 2_propanol
Resolution 2.28 Å R-free 0.248
5NXJ SH3 domain from Mouse cortactin (P 1 21 1 crystal form) Deposited 2017-05-10 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 490–546（57 aa） Fragment：SH3 domain, UNP Residues 490-546
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；289 K；1.2 M (NH4)2SO4, 0.1 M sodium citrate pH 5, 3% 2_propanol
Resolution 2.28 Å R-free 0.248
5NXJ SH3 domain from Mouse cortactin (P 1 21 1 crystal form) Deposited 2017-05-10 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 490–546（57 aa） Fragment：SH3 domain, UNP Residues 490-546
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；289 K；1.2 M (NH4)2SO4, 0.1 M sodium citrate pH 5, 3% 2_propanol
Resolution 2.28 Å R-free 0.248
8P94 Cryo-EM structure of cortactin stabilized Arp2/3-complex nucleated actin branches Deposited 2023-06-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain I 1–546（546 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 12 MG MAGNESIUM ION × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 50mM KCl, 1mM EGTA, 1mM MgCl2, 0.2 mM ATP and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE；Back blotting
Resolution 3.30 Å
8TAH Cryo-EM structure of Cortactin-bound to Arp2/3 complex Deposited 2023-06-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain H 1–76（76 aa）
Not recorded MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；10 mM imidazole pH 7.0, 50 mM KCl, 2 mM MgCl2, 1 mM EGTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.89 Å

6 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SRC8_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–60； UniProt 490–546

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 7pll

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7pll
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7pll
Deposition date deposition_date2021-08-31
Structure title titleStructure of the murine cortactin C-SH3 domain in complex with a Pyk2 proline-rich ligand
Keywords keywordsSH3 domain, cortactin, Pyk2, signaling, cancer, CELL INVASION; CELL INVASION
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier12.60 Å
Radius of gyration Rg (electron density) rg_electron12.59 Å
Forward intensity I(0) i0412636000.00
Molecular weight molecular_weight173170.0 kDa
Excluded volume excluded_volume216560 ų
Envelope volume envelope_volume20058 ų
Hydration-shell volume shell_volume11844 ų
Envelope diameter envelope_diameter59.0 Å
Shell Rg shell_rg20.16 Å
Envelope Rg envelope_rg15.78 Å
Shape Rg shape_rg12.55 Å
Total Rg total_rg12.87 Å
Total atoms total_atoms23880
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 dmax31.8 Å
Rg (real space) rg_real11.89 Å
Rg uncertainty (real space) rg_real_error0.03 Å
I(0) (real space) i0_real3.9410e+08
I(0) uncertainty (real space) i0_real_error2.6160e+06
Rg (reciprocal space) rg_reciprocal12.64 Å
I(0) (reciprocal space) i0_reciprocal412600000.0000
Solution quality estimate total_estimate0.6842
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary15.7 Å
Skewness Skewness skewness0.137
Kurtosis Kurtosis kurtosis-0.382
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha2.5100
Highest regularization parameter α highest_alpha166400.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.004; Oscil: 0.984; Stabil: 0.983; Sysdev: 0.000; Positv: 1.000; Valcen: 0.992; 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_id7pllA01
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily40 — SH3 Domains
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8. Citations (2)

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9. Files and Curves (10)