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- EMDB-71403: CryoEM structure of integrin alphaEbeta7 bound to E-cadherin -

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Basic information

Entry
Database: EMDB / ID: EMD-71403
TitleCryoEM structure of integrin alphaEbeta7 bound to E-cadherin
Map dataSharpened, locally-refined map of integrin alphaEbeta7 bound to E-cadherin
Sample
  • Complex: Protein complex of integrin alphaEbeta7 bound to E-cadherin
    • Protein or peptide: Integrin alpha-E
    • Protein or peptide: Integrin beta-7
    • Protein or peptide: Cadherin-1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
  • Ligand: MANGANESE (II) ION
KeywordsaEb7 / gut adhesion / tissue residence / membrane receptor / CELL ADHESION
Function / homology
Function and homology information


immune response in gut-associated lymphoid tissue / cell-matrix adhesion involved in ameboidal cell migration / integrin alpha4-beta7 complex / response to heparin / desmosome assembly / response to Gram-positive bacterium / pituitary gland development / gamma-catenin binding / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / negative regulation of axon extension ...immune response in gut-associated lymphoid tissue / cell-matrix adhesion involved in ameboidal cell migration / integrin alpha4-beta7 complex / response to heparin / desmosome assembly / response to Gram-positive bacterium / pituitary gland development / gamma-catenin binding / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / negative regulation of axon extension / desmosome / cellular response to indole-3-methanol / calcium-dependent cell-cell adhesion / flotillin complex / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / cell-cell adhesion mediated by cadherin / adherens junction organization / Formation of definitive endoderm / catenin complex / leukocyte tethering or rolling / Apoptotic cleavage of cell adhesion proteins / cell-cell junction assembly / Adherens junctions interactions / GTPase activating protein binding / integrin complex / ankyrin binding / heterotypic cell-cell adhesion / negative regulation of cell-cell adhesion / leukocyte migration / cellular response to lithium ion / cell adhesion mediated by integrin / apical junction complex / receptor clustering / homophilic cell-cell adhesion / lateral plasma membrane / Integrin cell surface interactions / RHO GTPases activate IQGAPs / T cell migration / synapse assembly / cell adhesion molecule binding / positive regulation of protein localization / Degradation of the extracellular matrix / Transcriptional and post-translational regulation of MITF-M expression and activity / substrate adhesion-dependent cell spreading / InlA-mediated entry of Listeria monocytogenes into host cells / protein tyrosine kinase binding / negative regulation of cell migration / cell-matrix adhesion / integrin-mediated signaling pathway / protein localization to plasma membrane / adherens junction / trans-Golgi network / cell-cell adhesion / beta-catenin binding / positive regulation of protein import into nucleus / response to toxic substance / cytoplasmic side of plasma membrane / integrin binding / cell morphogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / neuron projection development / cell junction / cell migration / lamellipodium / actin cytoskeleton / virus receptor activity / regulation of gene expression / receptor complex / postsynapse / cell adhesion / endosome / cadherin binding / response to xenobiotic stimulus / external side of plasma membrane / focal adhesion / calcium ion binding / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / glutamatergic synapse / cell surface / extracellular exosome / extracellular region / metal ion binding / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Cadherin / Catenin binding domain superfamily / Integrin beta subunit, cytoplasmic domain / Cadherin conserved site / Integrin beta cytoplasmic domain ...Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Cadherin / Catenin binding domain superfamily / Integrin beta subunit, cytoplasmic domain / Cadherin conserved site / Integrin beta cytoplasmic domain / Cadherin domain signature. / Integrin_b_cyt / Cadherin repeats. / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / EGF-like domain, extracellular / EGF-like domain / Integrin alpha cytoplasmic region / Integrins beta chain EGF (I-EGF) domain profile. / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor / : / Integrin alpha Ig-like domain 2 / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin alpha, N-terminal / Integrin domain superfamily / von Willebrand factor type A domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2.
Similarity search - Domain/homology
Cadherin-1 / Integrin beta-7 / Integrin alpha-E
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsHollis JA / Campbell MG
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM147414 United States
National Science Foundation (NSF, United States) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008268 United States
CitationJournal: Sci Adv / Year: 2025
Title: Molecular exaptation by the integrin αI domain.
Authors: Jeremy A Hollis / Matthew C Chan / Harmit S Malik / Melody G Campbell /
Abstract: Integrins bind ligands between their alpha (α) and beta (β) subunits and transmit signals through conformational changes. Early in chordate evolution, some α subunits acquired an "inserted" (I) ...Integrins bind ligands between their alpha (α) and beta (β) subunits and transmit signals through conformational changes. Early in chordate evolution, some α subunits acquired an "inserted" (I) domain that expanded integrin's ligand-binding repertoire but obstructed the ancestral ligand pocket, seemingly blocking conventional integrin activation. Here, we compare cryo-electron microscopy structures of apo and ligand-bound states of the I domain-containing αEβ integrin and the I domain-lacking αβ integrin to illuminate how the I domain intrinsically mimics an extrinsic ligand to preserve integrin function. We trace the I domain's evolutionary origin to an ancestral collagen-collagen interaction domain, identifying an ancient molecular exaptation that facilitated integrin activation immediately upon I domain insertion. Our analyses reveal the evolutionary and biochemical basis of expanded cellular communication in vertebrates.
History
DepositionJun 24, 2025-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71403.png

Downloads & links

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Map

FileDownload / File: emd_71403.map.gz / Format: CCP4 / Size: 184 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened, locally-refined map of integrin alphaEbeta7 bound to E-cadherin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 364 pix.
= 408.408 Å		1.12 Å/pix.
x 364 pix.
= 408.408 Å		1.12 Å/pix.
x 364 pix.
= 408.408 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.122 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.019389587 - 1.7211169
Average (Standard dev.)0.00031074876 (±0.009919908)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions364364364
Spacing364364364
CellA=B=C: 408.408 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Non-uniform refined half map B of integrin alphaEbeta7...

Fileemd_71403_additional_1.map
AnnotationNon-uniform refined half map B of integrin alphaEbeta7 bound to E-cadherin
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Non-uniform refined half map A of integrin alphaEbeta7...

Fileemd_71403_additional_2.map
AnnotationNon-uniform refined half map A of integrin alphaEbeta7 bound to E-cadherin
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened, locally-refined map of integrin alphaEbeta7 bound to...

Fileemd_71403_additional_3.map
AnnotationUnsharpened, locally-refined map of integrin alphaEbeta7 bound to E-cadherin
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened, non-uniform refined map of integrin alphaEbeta7 bound...

Fileemd_71403_additional_4.map
AnnotationUnsharpened, non-uniform refined map of integrin alphaEbeta7 bound to E-cadherin
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Locally-refined half map B of integrin alphaEbeta7 bound...

Fileemd_71403_half_map_1.map
AnnotationLocally-refined half map B of integrin alphaEbeta7 bound to E-cadherin
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Locally-refined half map A of integrin alphaEbeta7 bound...

Fileemd_71403_half_map_2.map
AnnotationLocally-refined half map A of integrin alphaEbeta7 bound to E-cadherin
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Protein complex of integrin alphaEbeta7 bound to E-cadherin

EntireName: Protein complex of integrin alphaEbeta7 bound to E-cadherin
Components
  • Complex: Protein complex of integrin alphaEbeta7 bound to E-cadherin
    • Protein or peptide: Integrin alpha-E
    • Protein or peptide: Integrin beta-7
    • Protein or peptide: Cadherin-1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
  • Ligand: MANGANESE (II) ION

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Supramolecule #1: Protein complex of integrin alphaEbeta7 bound to E-cadherin

SupramoleculeName: Protein complex of integrin alphaEbeta7 bound to E-cadherin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Integrin alpha-E

MacromoleculeName: Integrin alpha-E / type: protein_or_peptide / ID: 1 / Details: Ectodomain / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 129.950203 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MWLFHTLLCI ASLALLAAFN VDVARPWLTP KGGAPFVLSS LLHQDPSTNQ TWLLVTSPRT KRTPGPLHRC SLVQDEILCH PVEHVPIPK GRHRGVTVVR SHHGVLICIQ VLVRRPHSLS SELTGTCSLL GPDLRPQAQA NFFDLENLLD PDARVDTGDC Y SNKEGGGE ...String:
MWLFHTLLCI ASLALLAAFN VDVARPWLTP KGGAPFVLSS LLHQDPSTNQ TWLLVTSPRT KRTPGPLHRC SLVQDEILCH PVEHVPIPK GRHRGVTVVR SHHGVLICIQ VLVRRPHSLS SELTGTCSLL GPDLRPQAQA NFFDLENLLD PDARVDTGDC Y SNKEGGGE DDVNTARQRR ALEKEEEEDK EEEEDEEEEE AGTEIAIILD GSGSIDPPDF QRAKDFISNM MRNFYEKCFE CN FALVQYG GVIQTEFDLR DSQDVMASLA RVQNITQVGS VTKTASAMQH VLDSIFTSSH GSRRKASKVM VVLTDGGIFE DPL NLTTVI NSPKMQGVER FAIGVGEEFK SARTARELNL IASDPDETHA FKVTNYMALD GLLSKLRYNI ISMEGTVGDA LHYQ LAQIG FSAQILDERQ VLLGAVGAFD WSGGALLYDT RSRRGRFLNQ TAAAAADAEA AQYSYLGYAV AVLHKTCSLS YIAGA PRYK HHGAVFELQK EGREASFLPV LEGEQMGSYF GSELCPVDID MDGSTDFLLV AAPFYHVHGE EGRVYVYRLS EQDGSF SLA RILSGHPGFT NARFGFAMAA MGDLSQDKLT DVAIGAPLEG FGADDGASFG SVYIYNGHWD GLSASPSQRI RASTVAP GL QYFGMSMAGG FDISGDGLAD ITVGTLGQAV VFRSRPVVRL KVSMAFTPSA LPIGFNGVVN VRLCFEISSV TTASESGL R EALLNFTLDV DVGKQRRRLQ CSDVRSCLGC LREWSSGSQL CEDLLLMPTE GELCEEDCFS NASVKVSYQL QTPEGQTDH PQPILDRYTE PFAIFQLPYE KACKNKLFCV AELQLATTVS QQELVVGLTK ELTLNINLTN SGEDSYMTSM ALNYPRNLQL KRMQKPPSP NIQCDDPQPV ASVLIMNCRI GHPVLKRSSA HVSVVWQLEE NAFPNRTADI TVTVTNSNER RSLANETHTL Q FRHGFVAV LSKPSIMYVN TGQGLSHHKE FLFHVHGENL FGAEYQLQIC VPTKLRGLQV VAVKKLTRTQ ASTVCTWSQE RA CAYSSVQ HVEEWHSVSC VIASDKENVT VAAEISWDHS EELLKDVTEL QILGEISFNK SLYEGLNAEN HRTKITVVFL KDE KYHGTG GLEVLFQGPG ENAQCEKELQ ALEKENAQLE WELQALEKEL AQWSHPQFEK

UniProtKB: Integrin alpha-E

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Macromolecule #2: Integrin beta-7

MacromoleculeName: Integrin beta-7 / type: protein_or_peptide / ID: 2 / Details: Ectodomain / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 84.538789 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MVALPMVLVL LLVLSRGESE LDAKIPSTGD ATEWRNPHLS MLGSCQPAPS CQKCILSHPS CAWCKQLNFT ASGEAEARRC ARREELLAR GCPLEELEEP RGQQEVLQDQ PLSQGARGEG ATQLAPQRVR VTLRPGEPQQ LQVRFLRAEG YPVDLYYLMD L SYSMKDDL ...String:
MVALPMVLVL LLVLSRGESE LDAKIPSTGD ATEWRNPHLS MLGSCQPAPS CQKCILSHPS CAWCKQLNFT ASGEAEARRC ARREELLAR GCPLEELEEP RGQQEVLQDQ PLSQGARGEG ATQLAPQRVR VTLRPGEPQQ LQVRFLRAEG YPVDLYYLMD L SYSMKDDL ERVRQLGHAL LVRLQEVTHS VRIGFGSFVD KTVLPFVSTV PSKLRHPCPT RLERCQSPFS FHHVLSLTGD AQ AFEREVG RQSVSGNLDS PEGGFDAILQ AALCQEQIGW RNVSRLLVFT SDDTFHTAGD GKLGGIFMPS DGHCHLDSNG LYS RSTEFD YPSVGQVAQA LSAANIQPIF AVTSAALPVY QELSKLIPKS AVGELSEDSS NVVQLIMDAY NSLSSTVTLE HSSL PPGVH ISYESQCEGP EKREGKAEDR GQCNHVRINQ TVTFWVSLQA THCLPEPHLL RLRALGFSEE LIVELHTLCD CNCSD TQPQ APHCSDGQGH LQCGVCSCAP GRLGRLCECS VAELSSPDLE SGCRAPNGTG PLCSGKGHCQ CGRCSCSGQS SGHLCE CDD ASCERHEGIL CGGFGRCQCG VCHCHANRTG RACECSGDMD SCISPEGGLC SGHGRCKCNR CQCLDGYYGA LCDQCPG CK TPCERHRDCA ECGAFRTGPL ATNCSTACAH TNVTLALAPI LDDGWCKERT LDNQLFFFLV EDDARGTVVL RVRPQEKG A DHDTSGLEVL FQGPGKNAQC KKKLQALKKK NAQLKWKLQA LKKKLAQGGH HHHHH

UniProtKB: Integrin beta-7

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Macromolecule #3: Cadherin-1

MacromoleculeName: Cadherin-1 / type: protein_or_peptide / ID: 3 / Details: First two domains of mature molecule / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.625715 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MASMHHHHHH GSSMASMSDS EVNQEAKPEV KPEVKPETHI NLKVSDGSSE IFFKIKKTTP LRRLMEAFAK RQGKEMDSLR FLYDGIRIQ ADQTPEDLDM EDNDIIEAHR EQIGGDWVIP PISCPENEKG PFPKNLVQIK SNKDKEGKVF YSITGQGADT P PVGVFIIE ...String:
MASMHHHHHH GSSMASMSDS EVNQEAKPEV KPEVKPETHI NLKVSDGSSE IFFKIKKTTP LRRLMEAFAK RQGKEMDSLR FLYDGIRIQ ADQTPEDLDM EDNDIIEAHR EQIGGDWVIP PISCPENEKG PFPKNLVQIK SNKDKEGKVF YSITGQGADT P PVGVFIIE RETGWLKVTE PLDRERIATY TLFSHAVSSN GNAVEDPMEI LITVTDQNDN KPEFTQEVFK GSVMEGALPG TS VMEVTAT DADDDVNTYN AAIAYTILSQ DPELPDKNMF TINRNTGVIS VVTTGLDRES FPTYTLVVQA ADLQGEGLST TAT AVITVT DTNDN

UniProtKB: Cadherin-1

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #7: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 7 / Number of copies: 3 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #8: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 8 / Number of copies: 4 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.15 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 487193
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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