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8tec

Crystal structure of Kindlin2 in complex with acylated beta1 integrin peptide

Method: X-RAY DIFFRACTION Dmax: 110.2 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Fermitin family homolog 2

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 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 1–336 Chain A； UniProt 513–680 Chain B； UniProt 1–336 Chain B； UniProt 513–680 Fragment：UNP residues 1-336,513-680 Integrin beta-1 × 1 （P09055） 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

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 8TEC 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions 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
5XQ1 Structural basis of kindlin-mediated integrin recognition and activation Deposited 2017-06-05 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–680（680 aa） Fragment：UNP residues 773-787
Chain B 1–680（680 aa） Fragment：UNP residues 773-787
Mutation：168-217 deletion, 337-512 deletion Mutation：168-217 deletion, 337-512 deletion No recorded non-water small molecule 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
8TEE Crystal structure of Kindlin2 in complex with K794Q mutated beta1 integrin Deposited 2023-07-06 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 30–365； UniProt 1–336 Author chain A； PDBConstruct 366–533； UniProt 513–680 Author chain B； PDBConstruct 30–365； UniProt 1–336 Author chain B； PDBConstruct 366–533； UniProt 513–680

Integrin beta-1

OrganismNot specified

UniProt P09055

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain C； UniProt 784–798 Non-standard monomer：Yes (specific site not provided by mmCIF) Fermitin family homolog 2 × 2 （Q8CIB5） 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

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 8TEC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5XQ0 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 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 784–798（15 aa） Fragment：UNP residues 784-798
Chain B 784–798（15 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
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 C 784–798（15 aa）
Chain D 784–798（15 aa）
Mutation：K794Q Mutation：K794Q 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

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

View Construct and Data Evidence
UniProt name ITB1_MOUSE
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–15； UniProt 784–798

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 8tec

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8tec
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8tec
Deposition date deposition_date2023-07-06
Structure title titleCrystal structure of Kindlin2 in complex with acylated beta1 integrin peptide
Keywords keywordskindlin, integrin, acylation, CELL ADHESION; CELL ADHESION
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_guinier34.66 Å
Radius of gyration Rg (electron density) rg_electron33.83 Å
Forward intensity I(0) i0138652000.00
Molecular weight molecular_weight96412.0 kDa
Excluded volume excluded_volume121480 ų
Envelope volume envelope_volume167180 ų
Hydration-shell volume shell_volume41013 ų
Envelope diameter envelope_diameter112.9 Å
Shell Rg shell_rg40.75 Å
Envelope Rg envelope_rg33.40 Å
Shape Rg shape_rg33.78 Å
Total Rg total_rg34.55 Å
Total atoms total_atoms6797
Residues n_residues878
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 dmax110.2 Å
Rg (real space) rg_real34.55 Å
Rg uncertainty (real space) rg_real_error0.83 Å
I(0) (real space) i0_real1.3870e+08
I(0) uncertainty (real space) i0_real_error2.1670e+06
Rg (reciprocal space) rg_reciprocal34.62 Å
I(0) (reciprocal space) i0_reciprocal138700000.0000
Solution quality estimate total_estimate0.9066
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary40.7 Å
Skewness Skewness skewness0.146
Kurtosis Kurtosis kurtosis-0.641
Angular range angular_range— – 0.2300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha19050000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.948; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.937
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)