[English] 日本語
Yorodumi
- EMDB-71402: CryoEM structure of the open integrin alphaEbeta7 bound to fab LF61 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-71402
TitleCryoEM structure of the open integrin alphaEbeta7 bound to fab LF61
Map dataSharpened, locally refined map of the open integrin alphaEbeta7 bound to fab LF61
Sample
  • Complex: Protein complex of open integrin alphaEbeta7 with fab LF61
    • Protein or peptide: Integrin alpha-E
    • Protein or peptide: Integrin beta-7
    • Protein or peptide: Fab LF61 Heavy Chain
    • Protein or peptide: Fab LF61 Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM 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 / leukocyte tethering or rolling / integrin complex / heterotypic cell-cell adhesion / leukocyte migration / cell adhesion mediated by integrin / receptor clustering / Integrin cell surface interactions ...immune response in gut-associated lymphoid tissue / cell-matrix adhesion involved in ameboidal cell migration / integrin alpha4-beta7 complex / leukocyte tethering or rolling / integrin complex / heterotypic cell-cell adhesion / leukocyte migration / cell adhesion mediated by integrin / receptor clustering / Integrin cell surface interactions / T cell migration / cell adhesion molecule binding / substrate adhesion-dependent cell spreading / cell-matrix adhesion / integrin-mediated signaling pathway / cell-cell adhesion / integrin binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / virus receptor activity / receptor complex / cell adhesion / external side of plasma membrane / focal adhesion / 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 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, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / 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) / 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
Integrin beta-7 / Integrin alpha-E
Similarity search - Component
Biological speciesMus musculus (house mouse) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 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

-
Structure visualization

Supplemental images

emd_71402.png

Downloads & links

-
Map

FileDownload / File: emd_71402.map.gz / Format: CCP4 / Size: 134.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened, locally refined map of the open integrin alphaEbeta7 bound to fab LF61
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: 0.04
Minimum - Maximum-0.04479464 - 1.7332332
Average (Standard dev.)0.00025709975 (±0.012933662)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_71402_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Non-uniform refined half map A of the open...

Fileemd_71402_additional_1.map
AnnotationNon-uniform refined half map A of the open integrin alphaEbeta7 bound to fab LF61
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Non-uniform refined half map B of the open...

Fileemd_71402_additional_2.map
AnnotationNon-uniform refined half map B of the open integrin alphaEbeta7 bound to fab LF61
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Unsharpened, locally refined map of the open integrin...

Fileemd_71402_additional_3.map
AnnotationUnsharpened, locally refined map of the open integrin alphaEbeta7 bound to fab LF61
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Unsharpened, non-uniform refined map of the open integrin...

Fileemd_71402_additional_4.map
AnnotationUnsharpened, non-uniform refined map of the open integrin alphaEbeta7 bound to fab LF61
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Locally refined half map A of the open...

Fileemd_71402_half_map_1.map
AnnotationLocally refined half map A of the open integrin alphaEbeta7 bound to fab LF61
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Locally refined half map B of the open...

Fileemd_71402_half_map_2.map
AnnotationLocally refined half map B of the open integrin alphaEbeta7 bound to fab LF61
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Protein complex of open integrin alphaEbeta7 with fab LF61

EntireName: Protein complex of open integrin alphaEbeta7 with fab LF61
Components
  • Complex: Protein complex of open integrin alphaEbeta7 with fab LF61
    • Protein or peptide: Integrin alpha-E
    • Protein or peptide: Integrin beta-7
    • Protein or peptide: Fab LF61 Heavy Chain
    • Protein or peptide: Fab LF61 Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION

-
Supramolecule #1: Protein complex of open integrin alphaEbeta7 with fab LF61

SupramoleculeName: Protein complex of open integrin alphaEbeta7 with fab LF61
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Mus musculus (house mouse)

-
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

-
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

-
Macromolecule #3: Fab LF61 Heavy Chain

MacromoleculeName: Fab LF61 Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.634564 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: MVQLQRAGPT IVKPGSAVKL SCKATGFAYE DYYIFWVRQR EGGNGQKWIG RIHPGSGETK YNDKFKGKAT LTADTEASSA YMRLTSLTS EDTAVWYCGW ERSVGRATFA YWGQGTSVTV SSAKTTPPSV YPLAPGSAAQ TNSMVTLGCL VKGYFPEPVT V TWNSGSLS ...String:
MVQLQRAGPT IVKPGSAVKL SCKATGFAYE DYYIFWVRQR EGGNGQKWIG RIHPGSGETK YNDKFKGKAT LTADTEASSA YMRLTSLTS EDTAVWYCGW ERSVGRATFA YWGQGTSVTV SSAKTTPPSV YPLAPGSAAQ TNSMVTLGCL VKGYFPEPVT V TWNSGSLS SGVHTFPAVL QSDLYTLSSS VTVPSSTWPS ETVTCNVAHP ASSTKVDKKI VP

-
Macromolecule #4: Fab LF61 Light Chain

MacromoleculeName: Fab LF61 Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.439385 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: AAITFNLAPE SLVVTAGSKV TFSCKASQDF LNSATKRNYL TWYQQRDGKP PKLLIYWASA RLSGVPARFT GSGGGGTEFT LTISSVKAA DIGTYYCRQL RSRPLTFGGG TKLTVKQPKS SPSVTLFPPS SEELETNKAT LVCTITDFYP GVVTVDWKVD G TPVTQGME ...String:
AAITFNLAPE SLVVTAGSKV TFSCKASQDF LNSATKRNYL TWYQQRDGKP PKLLIYWASA RLSGVPARFT GSGGGGTEFT LTISSVKAA DIGTYYCRQL RSRPLTFGGG TKLTVKQPKS SPSVTLFPPS SEELETNKAT LVCTITDFYP GVVTVDWKVD G TPVTQGME TTQPSKQSNN KYMASSYLTL TARAWERHSS YSCQVTHEGH TVEKSLS

-
Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Macromolecule #8: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 8 / Number of copies: 6 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

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

-
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

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 379901
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more