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9p96

CryoEM structure of the apo integrin alpha4beta7

Method: ELECTRON MICROSCOPY Dmax: 109.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Integrin alpha-4

Homo sapiens

UniProt P13612

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 1–970 Not recorded Integrin beta-7 × 1 （P26010） CA CALCIUM ION × 6 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.10 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.

Other PDB Difference from Current Entry 9P96 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3V4P crystal structure of a4b7 headpiece complexed with Fab ACT-1 Deposited 2011-12-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 34–620（587 aa） Fragment：unp residues 34-620
Mutation：R558A CA CALCIUM ION × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 15P POLYETHYLENE GLYCOL (N=34) × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1 M Tris, 0.1 M NaCl, 8-10% PEG 20,000, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 8.5
Resolution 3.15 Å R-free 0.251
3V4P crystal structure of a4b7 headpiece complexed with Fab ACT-1 Deposited 2011-12-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 34–620（587 aa） Fragment：unp residues 34-620
Mutation：R558A CA CALCIUM ION × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 MG MAGNESIUM ION × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1 M Tris, 0.1 M NaCl, 8-10% PEG 20,000, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 8.5
Resolution 3.15 Å R-free 0.251
3V4V crystal structure of a4b7 headpiece complexed with Fab ACT-1 and RO0505376 Deposited 2011-12-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 34–620（587 aa） Fragment：unp residues 34-620
Mutation：R558A CA CALCIUM ION × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 MG MAGNESIUM ION × 1 0DU N-(2,6-dichlorobenzoyl)-4-[1,6-dimethyl-2-oxo-4-(trifluoromethyl)-1,2-dihydropyridin-3-yl]-L-phenylalanine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1 M Tris pH 8.5, 0.1 M NaCl, 8-10% PEG 20,000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.10 Å R-free 0.231
3V4V crystal structure of a4b7 headpiece complexed with Fab ACT-1 and RO0505376 Deposited 2011-12-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 34–620（587 aa） Fragment：unp residues 34-620
Mutation：R558A CA CALCIUM ION × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 MG MAGNESIUM ION × 1 0DU N-(2,6-dichlorobenzoyl)-4-[1,6-dimethyl-2-oxo-4-(trifluoromethyl)-1,2-dihydropyridin-3-yl]-L-phenylalanine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1 M Tris pH 8.5, 0.1 M NaCl, 8-10% PEG 20,000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.10 Å R-free 0.231
4HKC 14-3-3-zeta in complex with S1011 phosphorylated integrin alpha-4 peptide Deposited 2012-10-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1003–1032（30 aa） Fragment：UNP residues 1003-1032
Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1M Na HEPES (pH 7.5), 25% PEG 2000 MME, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.20 Å R-free 0.239
5C7Z AP2 Mu2 adaptin C-terminal domain complexed with integrin alpha-4 peptide Deposited 2015-06-25 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1008–1015（8 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；293 K；2.2M NaCl, 0.4M Na/K phosphate, 10MM DTT 0.1M MES pH 7.1, 15% glycerol, molar ratio of peptide to protein 3:1
Resolution 2.77 Å R-free 0.224
9P95 CryoEM structure of integrin alpha4beta7 bound to MAdCAM-1 Deposited 2025-06-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–970（970 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 3 MN MANGANESE (II) ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；0.05% CHAPS added immediately before vitrification
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å

5 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ITA4_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–970； UniProt 1–970

Integrin beta-7

Homo sapiens

UniProt P26010

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 B； UniProt 101–473 Not recorded Integrin alpha-4 × 1 （P13612） CA CALCIUM ION × 6 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.10 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.

Other PDB Difference from Current Entry 9P96 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2BRQ Crystal structure of the filamin A repeat 21 complexed with the integrin beta7 cytoplasmic tail peptide Deposited 2005-05-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 768–798（31 aa） Fragment：RESIDUES 768-798
Chain D 768–798（31 aa） Fragment：RESIDUES 768-798
Not recorded GSH Glutathione × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；1.26 M SODIUM CITRATE, 0.1 M CITRIC ACID PH 5.5
Resolution 2.10 Å R-free 0.243
3V4P crystal structure of a4b7 headpiece complexed with Fab ACT-1 Deposited 2011-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 20–512（493 aa） Fragment：unp residues 20-512
Not recorded CA CALCIUM ION × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 15P POLYETHYLENE GLYCOL (N=34) × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1 M Tris, 0.1 M NaCl, 8-10% PEG 20,000, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 8.5
Resolution 3.15 Å R-free 0.251
3V4P crystal structure of a4b7 headpiece complexed with Fab ACT-1 Deposited 2011-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 20–512（493 aa） Fragment：unp residues 20-512
Not recorded CA CALCIUM ION × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 MG MAGNESIUM ION × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1 M Tris, 0.1 M NaCl, 8-10% PEG 20,000, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 8.5
Resolution 3.15 Å R-free 0.251
3V4V crystal structure of a4b7 headpiece complexed with Fab ACT-1 and RO0505376 Deposited 2011-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 20–512（493 aa） Fragment：unp residues 20-512
Not recorded CA CALCIUM ION × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 MG MAGNESIUM ION × 1 0DU N-(2,6-dichlorobenzoyl)-4-[1,6-dimethyl-2-oxo-4-(trifluoromethyl)-1,2-dihydropyridin-3-yl]-L-phenylalanine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1 M Tris pH 8.5, 0.1 M NaCl, 8-10% PEG 20,000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.10 Å R-free 0.231
3V4V crystal structure of a4b7 headpiece complexed with Fab ACT-1 and RO0505376 Deposited 2011-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 20–512（493 aa） Fragment：unp residues 20-512
Not recorded CA CALCIUM ION × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 MG MAGNESIUM ION × 1 0DU N-(2,6-dichlorobenzoyl)-4-[1,6-dimethyl-2-oxo-4-(trifluoromethyl)-1,2-dihydropyridin-3-yl]-L-phenylalanine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1 M Tris pH 8.5, 0.1 M NaCl, 8-10% PEG 20,000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.10 Å R-free 0.231
8ZJF Cryo-EM structure of human integrin alpha-E beta-7 Deposited 2024-05-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–798（797 aa）
Not recorded MG MAGNESIUM ION × 1 CA CALCIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
9P95 CryoEM structure of integrin alpha4beta7 bound to MAdCAM-1 Deposited 2025-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–723（723 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 3 MN MANGANESE (II) ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；0.05% CHAPS added immediately before vitrification
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
9P97 CryoEM structure of the closed integrin alphaEbeta7 bound to fab LF61 Deposited 2025-06-24 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–723（723 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.92 Å
9P98 CryoEM structure of the open integrin alphaEbeta7 bound to fab LF61 Deposited 2025-06-24 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–723（723 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.93 Å
9P99 CryoEM structure of integrin alphaEbeta7 bound to E-cadherin Deposited 2025-06-24 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–723（723 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 3 MN MANGANESE (II) ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.37 Å

8 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ITB7_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–373； UniProt 101–473

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 9p96

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9p96
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9p96
Deposition date deposition_date2025-06-24
最后修订 last_revision2025-09-24
Structure title titleCryoEM structure of the apo integrin alpha4beta7
Keywords keywordsa4b7, gut adhesion, lymphocyte homing, membrane receptor, CELL ADHESION; CELL ADHESION
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier34.17 Å
Radius of gyration Rg (electron density) rg_electron33.54 Å
Forward intensity I(0) i0180861000.00
Molecular weight molecular_weight105890.0 kDa
Excluded volume excluded_volume131710 ų
Envelope volume envelope_volume171810 ų
Hydration-shell volume shell_volume42966 ų
Envelope diameter envelope_diameter119.9 Å
Shell Rg shell_rg39.95 Å
Envelope Rg envelope_rg33.95 Å
Shape Rg shape_rg33.52 Å
Total Rg total_rg34.08 Å
Total atoms total_atoms14703
Residues n_residues960
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 dmax109.8 Å
Rg (real space) rg_real34.19 Å
Rg uncertainty (real space) rg_real_error0.88 Å
I(0) (real space) i0_real1.8090e+08
I(0) uncertainty (real space) i0_real_error2.6640e+06
Rg (reciprocal space) rg_reciprocal34.18 Å
I(0) (reciprocal space) i0_reciprocal180900000.0000
Solution quality estimate total_estimate0.6904
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.8 Å
Skewness Skewness skewness0.317
Kurtosis Kurtosis kurtosis-0.510
Angular range angular_range— – 0.2300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha30890000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 0.122; Positv: 1.000; Valcen: 0.992; Smooth: 0.825
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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)