4cak

Three-dimensional reconstruction of intact human integrin alphaIIbbeta3 in a phospholipid bilayer nanodisc

Method: ELECTRON MICROSCOPY Dmax: 114.8 Å Quality: REASONABLE

1. Protein Identity and Related Structures Protein Identity & Related Structures

Integrin alpha-IIb

OrganismNot specified

UniProt P08514

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 2 其他Polymer 5 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 32–990 Fragment:ECTODOMAIN, UNP RESIDUES 32-990 Integrin beta-3 × 1 (P05106) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ELECTRON MICROSCOPY cryo-EM buffer:150 MM NACL, 10 MM HEPES, PH 7.4, 1 MM CACL2 AND 1 MM MGCL2;pH 7.4;150 MM NACL, 10 MM HEPES, PH 7.4, 1 MM CACL2 AND 1 MM MGCL2 cryo-EM vitrification conditions:VITRIFICATION 1 -- CRYOGEN- NONE, INSTRUMENT- NONE, Resolution 20.50 Å

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.

76 other PDB entries and 116 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ITA2B_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–959; UniProt 32–990

Integrin beta-3

OrganismNot specified

UniProt P05106

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 2 其他Polymer 5 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 27–716 Fragment:RESIDUES 27-716 Integrin alpha-IIb × 1 (P08514) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ELECTRON MICROSCOPY cryo-EM buffer:150 MM NACL, 10 MM HEPES, PH 7.4, 1 MM CACL2 AND 1 MM MGCL2;pH 7.4;150 MM NACL, 10 MM HEPES, PH 7.4, 1 MM CACL2 AND 1 MM MGCL2 cryo-EM vitrification conditions:VITRIFICATION 1 -- CRYOGEN- NONE, INSTRUMENT- NONE, Resolution 20.50 Å

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.

124 other PDB entries and 176 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ITB3_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–690; UniProt 27–716

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 4cak

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4cak
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4cak
Deposition date deposition_date2013-10-08
Structure title titleThree-dimensional reconstruction of intact human integrin alphaIIbbeta3 in a phospholipid bilayer nanodisc
Keywords keywordsCELL ADHESION, INTEGRIN, SINGLE PARTICLE RECONSTRUCTION; CELL ADHESION
Experimental Method methodELECTRON MICROSCOPY

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier35.60
Radius of gyration Rg (electron density) rg_electron34.96
Forward intensity I(0) i0506834000.00
Molecular weight molecular_weight177250.0 kDa
Excluded volume excluded_volume219140 ų
Envelope volume envelope_volume256830 ų
Hydration-shell volume shell_volume58595 ų
Envelope diameter envelope_diameter125.6
Shell Rg shell_rg43.16
Envelope Rg envelope_rg35.51
Shape Rg shape_rg34.95
Total Rg total_rg35.47
Total atoms total_atoms15673
Residues n_residues1593
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax114.8
Rg (real space) rg_real35.45
Rg uncertainty (real space) rg_real_error0.86
I(0) (real space) i0_real5.0680e+08
I(0) uncertainty (real space) i0_real_error8.9360e+06
Rg (reciprocal space) rg_reciprocal35.54
I(0) (reciprocal space) i0_reciprocal506900000.0000
Solution quality estimate total_estimate0.6735
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary47.0
Skewness Skewness skewness0.170
Kurtosis Kurtosis kurtosis-0.458
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha31990000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.901; Stabil: 1.000; Sysdev: 0.028; Positv: 1.000; Valcen: 0.997; Smooth: 0.967

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

8. Citations (1)

9. Files and Curves (10)