3h6a

Structure of the Calx-beta domain of integrin beta4 crystallized in the presence of calcium

Method: X-RAY DIFFRACTION Dmax: 79.0 Å Quality: GOOD

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

Integrin beta-4

Homo sapiens

UniProt P16144

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 989–1107 Fragment:CALX-BETA DOMAIN, RESIDUES 989-1107 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.9;298 K;50MM TRIS-HCL, 2MM CACL2, 26% PEG 1500, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.61 Å R-free 0.212
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 989–1107 Fragment:CALX-BETA DOMAIN, RESIDUES 989-1107 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.9;298 K;50MM TRIS-HCL, 2MM CACL2, 26% PEG 1500, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.61 Å R-free 0.212

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.

12 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ITB4_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 5–123; UniProt 989–1107 Author chain B; PDBConstruct 5–123; UniProt 989–1107

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 3h6a

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3h6a
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3h6a
Deposition date deposition_date2009-04-23
Structure title titleStructure of the Calx-beta domain of integrin beta4 crystallized in the presence of calcium
Keywords keywords;IMMUNOGLOBULIN FOLD, INTEGRIN, CELL ADHESION, EPIDERMOLYSIS BULLOSA, GLYCOPROTEIN, MEMBRANE, RECEPTOR, TRANSMEMBRANE, Alternative splicing, Disease mutation, Disulfide bond, Phosphoprotein, Polymorphism ;; CELL ADHESION
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier21.66
Radius of gyration Rg (electron density) rg_electron20.67
Forward intensity I(0) i012065500.00
Molecular weight molecular_weight25499.0 kDa
Excluded volume excluded_volume31818 ų
Envelope volume envelope_volume38669 ų
Hydration-shell volume shell_volume16824 ų
Envelope diameter envelope_diameter84.8
Shell Rg shell_rg25.73
Envelope Rg envelope_rg21.14
Shape Rg shape_rg20.62
Total Rg total_rg21.57
Total atoms total_atoms3598
Residues n_residues224
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 dmax79.0
Rg (real space) rg_real21.81
Rg uncertainty (real space) rg_real_error0.69
I(0) (real space) i0_real1.2070e+07
I(0) uncertainty (real space) i0_real_error1.8110e+05
Rg (reciprocal space) rg_reciprocal21.78
I(0) (reciprocal space) i0_reciprocal12070000.0000
Solution quality estimate total_estimate0.8218
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.2
Skewness Skewness skewness0.506
Kurtosis Kurtosis kurtosis-0.140
Angular range angular_range— – 0.3650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3651000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.692; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.640; Smooth: 0.963

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3h6aa1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.27 — CalX-like
Family Family familyb.1.27.0 — automated matches
Domain ID domain_idd3h6aa2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3h6ab1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.27 — CalX-like
Family Family familyb.1.27.0 — automated matches
Domain ID domain_idd3h6ab2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id3h6aA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily2030 — CalX-beta domain
Domain ID domain_id3h6aB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily2030 — CalX-beta domain

8. Citations (1)

9. Files and Curves (10)