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- EMDB-79038: CryoEM structure of integrin aEb7 bound to Bly7 fab -

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Basic information

Entry
Database: EMDB / ID: EMD-79038
TitleCryoEM structure of integrin aEb7 bound to Bly7 fab
Map dataNon-uniform refinement final map
Sample
  • Complex: Protein complex of open integrin alphaEbeta7 with fab Bly7
    • Protein or peptide: Integrin alpha-E
    • Protein or peptide: Integrin beta-7
    • Protein or peptide: Fab Bly7 Heavy Chain
    • Protein or peptide: Fab Bly7 Light Chain
KeywordsaEb7 / gut adhesion / tissue residence / membrane receptor / CELL ADHESION
Biological speciesMus musculus (house mouse) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 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: To Be Published
Title: Molecular exaptation by the integrin alpha I domain
Authors: Hollis JA / Campbell MG
History
DepositionSep 10, 2026-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_79038.png

Downloads & links

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Map

FileDownload / File: emd_79038.map.gz / Format: CCP4 / Size: 134.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNon-uniform refinement final map
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: 0.12
Minimum - Maximum-0.4870575 - 1.5200828
Average (Standard dev.)-0.00055815035 (±0.02971142)
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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Additional map: Sharpened non-uniform refinement map

Fileemd_79038_additional_1.map
AnnotationSharpened non-uniform refinement map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Non-uniform refinement half map A

Fileemd_79038_half_map_1.map
AnnotationNon-uniform refinement half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Non-uniform refinement half map A

Fileemd_79038_half_map_2.map
AnnotationNon-uniform refinement half map A
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 open integrin alphaEbeta7 with fab Bly7

EntireName: Protein complex of open integrin alphaEbeta7 with fab Bly7
Components
  • Complex: Protein complex of open integrin alphaEbeta7 with fab Bly7
    • Protein or peptide: Integrin alpha-E
    • Protein or peptide: Integrin beta-7
    • Protein or peptide: Fab Bly7 Heavy Chain
    • Protein or peptide: Fab Bly7 Light Chain

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Supramolecule #1: Protein complex of open integrin alphaEbeta7 with fab Bly7

SupramoleculeName: Protein complex of open integrin alphaEbeta7 with fab Bly7
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Integrin alpha-E

MacromoleculeName: Integrin alpha-E / type: protein_or_peptide / ID: 1 / 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

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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

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Macromolecule #3: Fab Bly7 Heavy Chain

MacromoleculeName: Fab Bly7 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: IQLVQSGPEL KKPGETVKIS CKASGYTFTN YGMNWVKQAP GKGLKWMGWI NTYTGSPTYA EEFKGRFAFS LETSASTAYL QINNLKNEDT ATYFCARSFT TTACGAQDYW GQGTTVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS WNSGALTSGV ...String:
IQLVQSGPEL KKPGETVKIS CKASGYTFTN YGMNWVKQAP GKGLKWMGWI NTYTGSPTYA EEFKGRFAFS LETSASTAYL QINNLKNEDT ATYFCARSFT TTACGAQDYW GQGTTVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKKVEP

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Macromolecule #4: Fab Bly7 Light Chain

MacromoleculeName: Fab Bly7 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: DIQMTQSPSS LSASLGDTIT ITCHASQNIE TWLNWFQQKP GSIPKLLIYK ASRLFEGVPS RFSGSGSGTG FTLTISSLQP EDIATYYCQQ GNSFPLVFGG GTKLEIKRAD AAPTVSIFPP SSEQLTSGGA SVVCFLNNFY PKDINVKWKI DGSERQNGVL NSWTDQDSKD ...String:
DIQMTQSPSS LSASLGDTIT ITCHASQNIE TWLNWFQQKP GSIPKLLIYK ASRLFEGVPS RFSGSGSGTG FTLTISSLQP EDIATYYCQQ GNSFPLVFGG GTKLEIKRAD AAPTVSIFPP SSEQLTSGGA SVVCFLNNFY PKDINVKWKI DGSERQNGVL NSWTDQDSKD STYSMSSTLT LTKDEYERHN SYTCEATHKT STSPIVKSFN RNE

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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: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 950417
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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