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- EMDB-71400: CryoEM structure of the apo integrin alpha4beta7 -

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Basic information

Entry
Database: EMDB / ID: EMD-71400
TitleCryoEM structure of the apo integrin alpha4beta7
Map dataSharpened, locally-refined map of apo integrin alpha4beta7
Sample
  • Complex: Heterodimer of integrin alpha4beta7
    • Protein or peptide: Integrin alpha-4
    • Protein or peptide: Integrin beta-7
  • Ligand: CALCIUM ION
Keywordsa4b7 / gut adhesion / lymphocyte homing / membrane receptor / CELL ADHESION
Function / homology
Function and homology information


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 alpha4-beta1 complex / cell-cell adhesion mediated by integrin / positive regulation of leukocyte tethering or rolling / axonogenesis involved in innervation ...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 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 vascular endothelial cell proliferation / neuron projection extension / integrin complex / heterotypic cell-cell adhesion / negative regulation of vasoconstriction / leukocyte migration / 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 / external side of plasma membrane / focal adhesion / neuronal cell body / cell surface / extracellular exosome / metal ion binding / membrane / plasma membrane
Similarity search - Function
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 ...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.
Similarity search - Domain/homology
Integrin alpha-4 / Integrin beta-7
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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_71400.png

Downloads & links

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Map

FileDownload / File: emd_71400.map.gz / Format: CCP4 / Size: 134.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened, locally-refined map of apo integrin alpha4beta7
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 328 pix.
= 368.016 Å		1.12 Å/pix.
x 328 pix.
= 368.016 Å		1.12 Å/pix.
x 328 pix.
= 368.016 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: 0.07
Minimum - Maximum-0.04757852 - 1.8796173
Average (Standard dev.)0.0003101277 (±0.012770528)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions328328328
Spacing328328328
CellA=B=C: 368.016 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71400_msk_1.map
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 apo integrin alpha4beta7

Fileemd_71400_additional_1.map
AnnotationUnsharpened, non-uniform refined map of apo integrin alpha4beta7
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Non-uniform refined half map A of apo integrin alpha4beta7

Fileemd_71400_additional_2.map
AnnotationNon-uniform refined half map A of apo integrin alpha4beta7
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 apo integrin alpha4beta7

Fileemd_71400_additional_3.map
AnnotationNon-uniform refined half map B of apo integrin alpha4beta7
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened, non-uniform refined half map B of apo integrin alpha4beta7

Fileemd_71400_additional_4.map
AnnotationSharpened, non-uniform refined half map B of apo integrin alpha4beta7
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened, locally-refined map of apo integrin alpha4beta7

Fileemd_71400_additional_5.map
AnnotationUnsharpened, locally-refined map of apo integrin alpha4beta7
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 apo integrin alpha4beta7

Fileemd_71400_half_map_1.map
AnnotationLocally refined half map A of apo integrin alpha4beta7
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 apo integrin alpha4beta7

Fileemd_71400_half_map_2.map
AnnotationLocally refined half map B of apo integrin alpha4beta7
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Heterodimer of integrin alpha4beta7

EntireName: Heterodimer of integrin alpha4beta7
Components
  • Complex: Heterodimer of integrin alpha4beta7
    • Protein or peptide: Integrin alpha-4
    • Protein or peptide: Integrin beta-7
  • Ligand: CALCIUM ION

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Supramolecule #1: Heterodimer of integrin alpha4beta7

SupramoleculeName: Heterodimer of integrin alpha4beta7 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
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 / Details: ectodomain / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.204266 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: GQQEVLQDQP LSQGARGEGA TQLAPQRVRV TLRPGEPQQL QVRFLRAEGY PVDLYYLMDL SYSMKDDLER VRQLGHALLV RLQEVTHSV RIGFGSFVDK TVLPFVSTVP SKLRHPCPTR LERCQSPFSF HHVLSLTGDA QAFEREVGRQ SVSGNLDSPE G GFDAILQA ...String:
GQQEVLQDQP LSQGARGEGA TQLAPQRVRV TLRPGEPQQL QVRFLRAEGY PVDLYYLMDL SYSMKDDLER VRQLGHALLV RLQEVTHSV RIGFGSFVDK TVLPFVSTVP SKLRHPCPTR LERCQSPFSF HHVLSLTGDA QAFEREVGRQ SVSGNLDSPE G GFDAILQA ALCQEQIGWR NVSRLLVFTS DDTFHTAGDG KLGGIFMPSD GHCHLDSNGL YSRSTEFDYP SVGQVAQALS AA NIQPIFA VTSAALPVYQ ELSKLIPKSA VGELSEDSSN VVQLIMDAYN SLSSTVTLEH SSLPPGVHIS YESQCEGPEK REG KAEDRG QCNHVRINQT VTFWVSLQAT HCLPEPHLLR LRALGFSEEL IVELHTL

UniProtKB: Integrin beta-7

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 6 / Formula: CA
Molecular weightTheoretical: 40.078 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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 202130
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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