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9p99

CryoEM structure of integrin alphaEbeta7 bound to E-cadherin

Method: ELECTRON MICROSCOPY Dmax: 188.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Integrin alpha-E

Homo sapiens

UniProt P38570

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 × 3 其他Polymer 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 1–1123 Not recorded Integrin beta-7 × 1 （P26010） Cadherin-1 × 1 （P12830） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 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 × 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

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 9P99 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
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 A 2–1179（1178 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
9P97 CryoEM structure of the closed integrin alphaEbeta7 bound to fab LF61 Deposited 2025-06-24 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1123（1123 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 oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1123（1123 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

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ITAE_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–1123； UniProt 1–1123

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 Other combination Heteromer Protein × 3 其他Polymer 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain B； UniProt 1–723 Not recorded Integrin alpha-E × 1 （P38570） Cadherin-1 × 1 （P12830） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 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 × 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

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 9P99 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 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
9P96 CryoEM structure of the apo integrin alpha4beta7 Deposited 2025-06-24 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 101–473（373 aa）
Not recorded CA CALCIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9P97 CryoEM structure of the closed integrin alphaEbeta7 bound to fab LF61 Deposited 2025-06-24 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 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

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 1–723； UniProt 1–723

Cadherin-1

Homo sapiens

UniProt P12830

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 × 3 其他Polymer 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain C； UniProt 155–371 Not recorded Integrin alpha-E × 1 （P38570） Integrin beta-7 × 1 （P26010） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 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 × 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

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 9P99 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1O6S Internalin (Listeria monocytogenes) / E-Cadherin (human) Recognition Complex Deposited 2002-10-13 Different construct Different oligomeric state 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 156–255（100 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 156-253
Not recorded CA CALCIUM ION × 2 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；VAPOUR DIFFUSION / HANGING DROP 10 MG/ML IN 10 MM HEPES PH 7.0, 26% PEG 4000, 100 MM MES/TRIS PH 7.0, 100 MM SODIUM ACETATE, 50 MM CACL2
Resolution 1.80 Å R-free 0.221
2O72 Crystal Structure Analysis of human E-cadherin (1-213) Deposited 2006-12-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 155–367（213 aa） Fragment：N-Terminal domains 1 and 2, residues 155-317
Mutation：C9S CA CALCIUM ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；10% PEG 8000, 0.2M calcium chloride, 5% DMSO, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 4K, temperature 277K
Resolution 2.00 Å R-free 0.234
2OMT Crystal structure of InlA G194S+S/hEC1 complex Deposited 2007-01-23 Different construct Different oligomeric state 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 156–255（100 aa） Fragment：N-terminal domain of human E-cadherin
Not recorded CA CALCIUM ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 4000, CaCl2, Na-Acetate, Tris/MES, pH 6.0, vapor diffusion, hanging drop, temperature 298K
Resolution 2.00 Å R-free 0.283
2OMU Crystal structure of InlA G194S+S Y369S/hEC1 complex Deposited 2007-01-23 Different construct Different oligomeric state 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 156–255（100 aa） Fragment：N-terminal domain of human E-cadherin
Not recorded CA CALCIUM ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 4000, CaCl2, Na-Acetate, Tris/MES, pH 6.0, vapor diffusion, hanging drop, temperature 298K
Resolution 1.80 Å R-free 0.217
2OMV Crystal structure of InlA S192N Y369S/hEC1 complex Deposited 2007-01-23 Different construct Different oligomeric state 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 156–255（100 aa） Fragment：N-terminal domain of human E-cadherin
Not recorded CA CALCIUM ION × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 4000, CaCl2, Na-Acetate, Tris/MES, pH 6.0, vapor diffusion, hanging drop, temperature 298K
Resolution 1.90 Å R-free 0.219
2OMX Crystal structure of InlA S192N G194S+S/hEC1 complex Deposited 2007-01-23 Different construct Different oligomeric state 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 156–258（103 aa） Fragment：N-terminal domain of human E-cadherin
Not recorded CL CHLORIDE ION × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 4000, CaCl2, Na-Acetate, Tris/MES, pH 6.0, vapor diffusion, hanging drop, temperature 298K
Resolution 1.70 Å R-free 0.223
2OMY Crystal structure of InlA S192N/hEC1 complex Deposited 2007-01-23 Different construct Different oligomeric state 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 156–254（99 aa） Fragment：N-terminal domain of human E-cadherin
Not recorded CA CALCIUM ION × 2 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 4000, CaCl2, Na-Acetate, Tris/MES, pH 6.0, vapor diffusion, hanging drop, temperature 298K
Resolution 1.70 Å R-free 0.211
2OMZ Crystal structure of InlA Y369A/hEC1 complex Deposited 2007-01-23 Different construct Different oligomeric state 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 156–254（99 aa） Fragment：N-terminal domain of human E-cadherin
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 4000, CaCl2, Na-Acetate, Tris/MES, pH 6.0, vapor diffusion, hanging drop, temperature 298K
Resolution 1.60 Å R-free 0.186
3FF7 Structure of NK cell receptor KLRG1 bound to E-cadherin Deposited 2008-12-02 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 A 155–253（99 aa） Fragment：UNP residues 155-253, Cadherin 1 domain
Chain B 155–253（99 aa） Fragment：UNP residues 155-253, Cadherin 1 domain
Mutation：C9L Mutation：C9L ACY ACETIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.6；298 K；PEG4000, pH 4.6, vapor diffusion, temperature 298K
Resolution 1.80 Å R-free 0.246
3FF8 Structure of NK cell receptor KLRG1 bound to E-cadherin Deposited 2008-12-02 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 A 155–254（100 aa） Fragment：UNP residues 155-254, Cadherin 1 domain
Chain B 155–254（100 aa） Fragment：UNP residues 155-254, Cadherin 1 domain
Mutation：C9L Mutation：C9L CA CALCIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；PEG8000, pH 6.5, vapor diffusion, temperature 298K
Resolution 2.00 Å R-free 0.253
4ZT1 Crystal structure of human E-Cadherin (residues 3-213) in x-dimer conformation Deposited 2015-05-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 157–367（211 aa） Fragment：UNP residues 157-367
Chain B 157–367（211 aa） Fragment：UNP residues 157-367
Not recorded CA CALCIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；TRIS 0.1 M, ammonium sulfate 1.3 M, calcium chloride 50 mM
Resolution 1.92 Å R-free 0.219
4ZTE Crystal structure of human E-Cadherin (residues 3-213) in complex with a peptidomimetic inhibitor Deposited 2015-05-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 157–367（211 aa） Fragment：residues 157-367
Chain B 157–367（211 aa） Fragment：residues 157-367
Not recorded CA CALCIUM ION × 6 4RL N-{[(2S,5S)-1-benzyl-5-(2-{[(2S,3S)-1-(tert-butylamino)-3-methyl-1-oxopentan-2-yl]amino}-2-oxoethyl)-3,6-dioxopiperazin-2-yl]methyl}-L-alpha-asparagine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；TRIS 0.1 M, ammonium sulfate 1.3 M, calcium chloride 80 mM
Resolution 2.13 Å R-free 0.230
6CXY Crystal Structure of Human E-cadherin bound by mouse monoclonal antibody Fab mAb-1_19A11 Deposited 2018-04-04 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 155–371（217 aa）
Not recorded CA CALCIUM ION × 3 EDO 1,2-ETHANEDIOL × 18 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；290 K；HosaA.19747.a.KW2.PC00156 at 10.3 mg/ml in a buffer containing 50 mM Tris, pH = 8, 150 mM NaCl, and 3 mM CaCl2 was mixed 0.1 uL + 0.1 uL with Wizard 3/4 (h12): 15% (w/v) PEG-20,000, 0.1 M HEPES/ NaOH, pH = 7.0. The crystal was cryoprotected with 20% ethylene glycol. Tray: 299140h12, puck: qxp2-3
Resolution 2.20 Å R-free 0.197
6OLE Human ribosome nascent chain complex (CDH1-RNC) stalled by a drug-like molecule with AP and PE tRNAs Deposited 2019-04-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain y 693–730（38 aa）
Not recorded MG MAGNESIUM ION × 31 ZN ZINC ION × 6 MVM N-(3-chloropyridin-2-yl)-N-[(3R)-piperidin-3-yl]-4-(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl)benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6OLF Human ribosome nascent chain complex (CDH1-RNC) stalled by a drug-like molecule with AA and PE tRNAs Deposited 2019-04-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain y 693–730（38 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 31 MVM N-(3-chloropyridin-2-yl)-N-[(3R)-piperidin-3-yl]-4-(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl)benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6OLG Human ribosome nascent chain complex stalled by a drug-like small molecule (CDH1_RNC with PP tRNA) Deposited 2019-04-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain A 693–730（38 aa）
Not recorded MG MAGNESIUM ION × 326 ZN ZINC ION × 5 MVM N-(3-chloropyridin-2-yl)-N-[(3R)-piperidin-3-yl]-4-(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl)benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6VEL Crystal Structure of Human E-cadherin bound by mouse monoclonal antibody 66E8Fab Deposited 2020-01-02 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 155–371（217 aa）
Not recorded SO4 SULFATE ION × 6 CA CALCIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；A complex of HosaA.19747.a.KW2, MumuA.20194.a.LG23, and MumuA.20195.a.LH23 was crystallized at 10.4 mg/ml at 14C and mixed 1:1 with 12.5% (w/v) PEG 4000, 20% (v/v) 1,2,6-hexanetriol, 0.1M GlyGly/AMPD pH 8.5, 0.03M of each Lithium sulfate, Sodium sulfate, and Potassium sulfate. Tray 307437a10: puck ckt8-9.
Resolution 2.65 Å R-free 0.236
7STZ Crystal Structure of Human E-cadherin EC1-5 bound by mouse monoclonal antibody Fab mAb-1_19A11 Deposited 2021-11-15 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 × 6 PDB declaration: hexameric
Chain C 155–698（544 aa）
Chain D 155–698（544 aa）
Not recorded EDO 1,2-ETHANEDIOL × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PG4 TETRAETHYLENE GLYCOL × 5 MAN alpha-D-mannopyranose × 3 BMA beta-D-mannopyranose × 12 CA CALCIUM ION × 24 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；290 K；HosaA.19747.a.LS31.PC00180 at 11.5 mg/mL was mixed 2:1 (0.2 uL protein and 0.1 uL precipitant) with 0.1M sodium HEPES pH 7.0 and 15% w/v PEG4000 (ProPlex B11) and stored at 14C. The crystal was cryoprotected with 15% ethylene glycol. Tray: 321285b11, puck: ygq5-2.
Resolution 2.95 Å R-free 0.208
8H62 Crystal structure of Internalin A from Listeria monocytogenes with human E-cadherin EC12 Deposited 2022-10-14 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 × 2 PDB declaration: dimeric
Chain B 155–367（213 aa）
Mutation：C163S CA CALCIUM ION × 4 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M Ammonium acetate 45% MPD
Resolution 1.91 Å R-free 0.210

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

View Construct and Data Evidence
UniProt name CADH1_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 115–331； UniProt 155–371

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 9p99

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9p99
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9p99
Deposition date deposition_date2025-06-24
最后修订 last_revision2025-09-24
Structure title titleCryoEM structure of integrin alphaEbeta7 bound to E-cadherin
Keywords keywordsaEb7, gut adhesion, tissue residence, 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_guinier46.96 Å
Radius of gyration Rg (electron density) rg_electron47.89 Å
Forward intensity I(0) i0303613000.00
Molecular weight molecular_weight139430.0 kDa
Excluded volume excluded_volume173360 ų
Envelope volume envelope_volume253740 ų
Hydration-shell volume shell_volume50512 ų
Envelope diameter envelope_diameter199.3 Å
Shell Rg shell_rg43.48 Å
Envelope Rg envelope_rg49.45 Å
Shape Rg shape_rg47.85 Å
Total Rg total_rg47.79 Å
Total atoms total_atoms19367
Residues n_residues1250
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 dmax188.0 Å
Rg (real space) rg_real47.73 Å
Rg uncertainty (real space) rg_real_error3.02 Å
I(0) (real space) i0_real3.0360e+08
I(0) uncertainty (real space) i0_real_error6.6030e+06
Rg (reciprocal space) rg_reciprocal46.96 Å
I(0) (reciprocal space) i0_reciprocal303300000.0000
Solution quality estimate total_estimate0.7598
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary38.7 Å
Skewness Skewness skewness0.674
Kurtosis Kurtosis kurtosis0.258
Angular range angular_range— – 0.1700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha25310000.0000
Real-space data points n_real_points35
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.461; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.560; Smooth: 0.932
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

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8. Citations (1)

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9. Files and Curves (10)