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- EMDB-71399: CryoEM structure of integrin alpha4beta7 bound to MAdCAM-1 -

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Basic information

Entry
Database: EMDB / ID: EMD-71399
TitleCryoEM structure of integrin alpha4beta7 bound to MAdCAM-1
Map dataSharpened, locally-refined map of integrin alpha4beta7 bound to MAdCAM-1
Sample
  • Complex: Protein complex of integrin alpha4beta7 bound to MAdCAM-1
    • Protein or peptide: Integrin alpha-4
    • Protein or peptide: Integrin beta-7
    • Protein or peptide: Mucosal addressin cell adhesion molecule 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
  • Ligand: MANGANESE (II) ION
Keywordsa4b7 / gut adhesion / lymphocyte homing / membrane receptor / CELL ADHESION
Function / homology
Function and homology information


positive regulation of lymphocyte migration / clathrin-dependent extracellular exosome endocytosis / : / diapedesis / immune response in gut-associated lymphoid tissue / cell-matrix adhesion involved in ameboidal cell migration / integrin alpha4-beta7 complex / integrin binding involved in cell-matrix adhesion / integrin alpha4-beta1 complex / cell-cell adhesion mediated by integrin ...positive regulation of lymphocyte migration / clathrin-dependent extracellular exosome endocytosis / : / diapedesis / immune response in gut-associated lymphoid tissue / cell-matrix adhesion involved in ameboidal cell migration / integrin alpha4-beta7 complex / integrin binding involved in cell-matrix adhesion / integrin alpha4-beta1 complex / cell-cell adhesion mediated by integrin / positive regulation of leukocyte tethering or rolling / axonogenesis involved in innervation / leukocyte tethering or rolling / RUNX3 Regulates Immune Response and Cell Migration / protein antigen binding / positive regulation of leukocyte migration / integrin complex / positive regulation of vascular endothelial cell proliferation / neuron projection extension / heterotypic cell-cell adhesion / leukocyte migration / negative regulation of vasoconstriction / leukocyte cell-cell adhesion / cell adhesion mediated by integrin / receptor clustering / cellular response to cytokine stimulus / endodermal cell differentiation / fibronectin binding / positive regulation of endothelial cell apoptotic process / Integrin cell surface interactions / positive regulation of T cell migration / coreceptor activity / T cell migration / cell adhesion molecule binding / substrate adhesion-dependent cell spreading / B cell differentiation / cell-matrix adhesion / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / cell-cell adhesion / integrin binding / cellular response to amyloid-beta / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / growth cone / virus receptor activity / Potential therapeutics for SARS / receptor complex / cell adhesion / immune response / external side of plasma membrane / focal adhesion / neuronal cell body / cell surface / signal transduction / extracellular exosome / metal ion binding / membrane / plasma membrane
Similarity search - Function
Adhesion molecule, immunoglobulin-like / Mucosal addressin cell adhesion molecule 1 / Adhesion molecule, immunoglobulin-like / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin alpha Ig-like domain 3 / Integrin beta subunit, tail / Integrin beta tail domain superfamily ...Adhesion molecule, immunoglobulin-like / Mucosal addressin cell adhesion molecule 1 / Adhesion molecule, immunoglobulin-like / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin alpha Ig-like domain 3 / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / EGF-like domain, extracellular / EGF-like domain / 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) / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / 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 / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Integrin alpha-4 / Integrin beta-7 / Mucosal addressin cell adhesion molecule 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.05 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_71399.png

Downloads & links

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Map

FileDownload / File: emd_71399.map.gz / Format: CCP4 / Size: 184 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened, locally-refined map of integrin alpha4beta7 bound to MAdCAM-1
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: 0.045
Minimum - Maximum-0.024773287 - 1.9567537
Average (Standard dev.)0.00030398453 (±0.010157577)
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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Mask #1

Fileemd_71399_msk_1.map
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 alpha4beta7...

Fileemd_71399_additional_1.map
AnnotationNon-uniform refined half map A of integrin alpha4beta7 bound to MAdCAM-1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Non-uniform refined half map B of integrin alpha4beta7...

Fileemd_71399_additional_2.map
AnnotationNon-uniform refined half map B of integrin alpha4beta7 bound to MAdCAM-1
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 alpha4beta7 bound...

Fileemd_71399_additional_3.map
AnnotationUnsharpened, non-uniform refined map of integrin alpha4beta7 bound to MAdCAM-1
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 alpha4beta7 bound to...

Fileemd_71399_additional_4.map
AnnotationUnsharpened, locally-refined map of integrin alpha4beta7 bound to MAdCAM-1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened, non-uniform refined map of integrin alpha4beta7 bound...

Fileemd_71399_additional_5.map
AnnotationSharpened, non-uniform refined map of integrin alpha4beta7 bound to MAdCAM-1
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 alpha4beta7 bound to MAdCAM-1

Fileemd_71399_half_map_1.map
AnnotationLocally-refined half map A of integrin alpha4beta7 bound to MAdCAM-1
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 alpha4beta7 bound to MAdCAM-1

Fileemd_71399_half_map_2.map
AnnotationLocally-refined half map B of integrin alpha4beta7 bound to MAdCAM-1
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 alpha4beta7 bound to MAdCAM-1

EntireName: Protein complex of integrin alpha4beta7 bound to MAdCAM-1
Components
  • Complex: Protein complex of integrin alpha4beta7 bound to MAdCAM-1
    • Protein or peptide: Integrin alpha-4
    • Protein or peptide: Integrin beta-7
    • Protein or peptide: Mucosal addressin cell adhesion molecule 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 alpha4beta7 bound to MAdCAM-1

SupramoleculeName: Protein complex of integrin alpha4beta7 bound to MAdCAM-1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Integrin alpha-4

MacromoleculeName: Integrin alpha-4 / type: protein_or_peptide / ID: 1 / Details: Ectodomain / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 113.632453 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MAWEARREPG PRRAAVRETV MLLLCLGVPT GRPYNVDTES ALLYQGPHNT LFGYSVVLHS HGANRWLLVG APTANWLANA SVINPGAIY RCRIGKNPGQ TCEQLQLGSP NGEPCGKTCL EERDNQWLGV TLSRQPGENG SIVTCGHRWK NIFYIKNENK L PTGGCYGV ...String:
MAWEARREPG PRRAAVRETV MLLLCLGVPT GRPYNVDTES ALLYQGPHNT LFGYSVVLHS HGANRWLLVG APTANWLANA SVINPGAIY RCRIGKNPGQ TCEQLQLGSP NGEPCGKTCL EERDNQWLGV TLSRQPGENG SIVTCGHRWK NIFYIKNENK L PTGGCYGV PPDLRTELSK RIAPCYQDYV KKFGENFASC QAGISSFYTK DLIVMGAPGS SYWTGSLFVY NITTNKYKAF LD KQNQVKF GSYLGYSVGA GHFRSQHTTE VVGGAPQHEQ IGKAYIFSID EKELNILHEM KGKKLGSYFG ASVCAVDLNA DGF SDLLVG APMQSTIREE GRVFVYINSG SGAVMNAMET NLVGSDKYAA RFGESIVNLG DIDNDGFEDV AIGAPQEDDL QGAI YIYNG RADGISSTFS QRIEGLQISK SLSMFGQSIS GQIDADNNGY VDVAVGAFRS DSAVLLRTRP VVIVDASLSH PESVN RTKF DCVENGWPSV CIDLTLCFSY KGKEVPGYIV LFYNMSLDVN RKAESPPRFY FSSNGTSDVI TGSIQVSSRE ANCRTH QAF MRKDVRDILT PIQIEAAYHL GPHVISKRST EEFPPLQPIL QQKKEKDIMK KTINFARFCA HENCSADLQV SAKIGFL KP HENKTYLAVG SMKTLMLNVS LFNAGDDAYE TTLHVKLPVG LYFIKILELE EKQINCEVTD NSGVVQLDCS IGYIYVDH L SRIDISFLLD VSSLSRAEED LSITVHATCE NEEEMDNLKH SRVTVAIPLK YEVKLTVHGF VNPTSFVYGS NDENEPETC MVEKMNLTFH VINTGNSMAP NVSVEIMVPN SFSPQTDKLF NILDVQTTTG ECHFENYQRV CALEQQKSAM QTLKGIVRFL SKTDKRLLY CIKADPHCLN FLCNFGKMES GKEASVHIQL EGRPSILEMD ETSALKFEIR ATGFPEPNPR VIELNKDENV A HVLLEGLH HQGTGGLEVL FQGPGENAQC EKELQALEKE NAQLEWELQA LEKELAQWSH PQFEK

UniProtKB: Integrin alpha-4

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Macromolecule #2: Integrin beta-7

MacromoleculeName: Integrin beta-7 / type: protein_or_peptide / ID: 2 / 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: Mucosal addressin cell adhesion molecule 1

MacromoleculeName: Mucosal addressin cell adhesion molecule 1 / type: protein_or_peptide / ID: 3 / Details: Ectodomain without mucin domain / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.205062 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MDFGLALLLA GLLGLLLGQS LQVKPLQVEP PEPVVAVALG ASRQLTCRLA CADRGASVQW RGLDTSLGAV QSDTGRSVLT VRNASLSAA GTRVCVGSCG GRTFQHTVQL LVYAFPDQLT VSPAALVPGD PEVACTAHKV TPVDPNALSF SLLVGGQELE G AQALGPEV ...String:
MDFGLALLLA GLLGLLLGQS LQVKPLQVEP PEPVVAVALG ASRQLTCRLA CADRGASVQW RGLDTSLGAV QSDTGRSVLT VRNASLSAA GTRVCVGSCG GRTFQHTVQL LVYAFPDQLT VSPAALVPGD PEVACTAHKV TPVDPNALSF SLLVGGQELE G AQALGPEV QEEEEEPQGD EDVLFRVTER WRLPPLGTPV PPALYCQATM RLPGLELSHR QAIPVLHSPT SPEPPDTTSP ES PDTTSPE SPDTTSQEPP DTTSPEPPDK TSPEPAPQQG STHTPRSPGS TRTRRPEISQ AGPTQGEVIP TGSSKPAGDQ DTS GLEVLF QGPGKNAQCK KKLQALKKKN AQLKWKLQAL KKKLAQGGHH HHHH

UniProtKB: Mucosal addressin cell adhesion molecule 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: 3 / 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

Concentration1.0 mg/mL
BufferpH: 7.4 / Details: 0.05% CHAPS added immediately before vitrification
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: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 188443
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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