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5xq1

Structural basis of kindlin-mediated integrin recognition and activation

Method: X-RAY DIFFRACTION Dmax: 136.2 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Fermitin family homolog 2,Integrin beta-3

Mus musculus

UniProt O54890

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 773–787 Chain B； UniProt 773–787 Fragment：UNP residues 773-787 Mutation：168-217 deletion, 337-512 deletion No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；0.2 M potassium chloride, 0.05 M HEPES pH 7.5, 35% v/v pentaerythritol propoxylate Resolution 2.95 Å R-free 0.260

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 5XQ1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6VGU Crystal structure of FERM-folded talin head domain bound to the NPLY motif of beta3-integrin Deposited 2020-01-09 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 745–775（31 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.2 M sodium chloride 0.1 M MES pH6.5 10 % w/v PEG 4000
Resolution 2.78 Å R-free 0.263

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ITB3_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 471–485； UniProt 773–787 Author chain B； PDBConstruct 471–485； UniProt 773–787

Fermitin family homolog 2,Integrin beta-3

Mus musculus

UniProt Q8CIB5

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–680 Chain B； UniProt 1–680 Fragment：UNP residues 773-787 Mutation：168-217 deletion, 337-512 deletion No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；0.2 M potassium chloride, 0.05 M HEPES pH 7.5, 35% v/v pentaerythritol propoxylate Resolution 2.95 Å R-free 0.260

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 5XQ1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5XPY Structural basis of kindlin-mediated integrin recognition and activation Deposited 2017-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 15–680（666 aa） Fragment：UNP residues 15-680
Mutation：168-217 deletion, 367-512 deletion ACT ACETATE ION × 5 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；289 K；0.1 M Tris pH 8.5, 4.0 M Ammonium acetate
Resolution 2.10 Å R-free 0.196
5XPZ Structural basis of kindlin-mediated integrin recognition and activation Deposited 2017-06-05 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–680（680 aa）
Chain B 1–680（680 aa）
Mutation：168-217 deletion, 337-512 deletion Mutation：168-217 deletion, 337-512 deletion GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；0.2 M potassium chloride, 0.05 M HEPES pH 7.5, 35% v/v pentaerythritol propoxylate
Resolution 2.60 Å R-free 0.283
5XQ0 Structural basis of kindlin-mediated integrin recognition and activation Deposited 2017-06-05 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–680（680 aa） Fragment：UNP residues 784-798
Chain B 1–680（680 aa） Fragment：UNP residues 784-798
Mutation：168-217 deletion, 337-512 deletion Mutation：168-217 deletion, 337-512 deletion GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；0.2 M potassium chloride, 0.05 M HEPES pH 7.5, 35% v/v pentaerythritol propoxylate
Resolution 2.75 Å R-free 0.284
8TEC Crystal structure of Kindlin2 in complex with acylated beta1 integrin peptide Deposited 2023-07-06 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–336（336 aa） Fragment：UNP residues 1-336,513-680
Chain A 513–680（168 aa） Fragment：UNP residues 1-336,513-680
Chain B 1–336（336 aa） Fragment：UNP residues 1-336,513-680
Chain B 513–680（168 aa） Fragment：UNP residues 1-336,513-680
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；0.1 M Tris, pH 8.5, 10% isopropanal
Resolution 2.04 Å R-free 0.230
8TEE Crystal structure of Kindlin2 in complex with K794Q mutated beta1 integrin Deposited 2023-07-06 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–336（336 aa） Fragment：UNP residues 1-336,513-680
Chain A 513–680（168 aa） Fragment：UNP residues 1-336,513-680
Chain B 1–336（336 aa） Fragment：UNP residues 1-336,513-680
Chain B 513–680（168 aa） Fragment：UNP residues 1-336,513-680
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M Tris, pH 8.5, 10% isopropanal
Resolution 2.49 Å R-free 0.275

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

View Construct and Data Evidence
UniProt name FERM2_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 5–458； UniProt 1–680 Author chain B； PDBConstruct 5–458； UniProt 1–680

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 5xq1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5xq1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5xq1
Deposition date deposition_date2017-06-05
Structure title titleStructural basis of kindlin-mediated integrin recognition and activation
Keywords keywordsIntegrin Binding, Multi-domain containing protein, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier37.41 Å
Radius of gyration Rg (electron density) rg_electron37.38 Å
Forward intensity I(0) i0131367000.00
Molecular weight molecular_weight95210.0 kDa
Excluded volume excluded_volume120350 ų
Envelope volume envelope_volume163260 ų
Hydration-shell volume shell_volume37696 ų
Envelope diameter envelope_diameter141.2 Å
Shell Rg shell_rg41.61 Å
Envelope Rg envelope_rg37.52 Å
Shape Rg shape_rg37.38 Å
Total Rg total_rg37.67 Å
Total atoms total_atoms6707
Residues n_residues840
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 dmax136.2 Å
Rg (real space) rg_real39.79 Å
Rg uncertainty (real space) rg_real_error0.69 Å
I(0) (real space) i0_real1.3250e+08
I(0) uncertainty (real space) i0_real_error2.1760e+06
Rg (reciprocal space) rg_reciprocal37.53 Å
I(0) (reciprocal space) i0_reciprocal131300000.0000
Solution quality estimate total_estimate0.6198
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary35.7 Å
Skewness Skewness skewness0.583
Kurtosis Kurtosis kurtosis-0.117
Angular range angular_range— – 0.2100 Å−1
Current regularization parameter α current_alpha2.0480
Highest regularization parameter α highest_alpha18090000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.780; Stabil: 0.843; Sysdev: 0.000; Positv: 1.000; Valcen: 0.776; Smooth: 0.469
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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)