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- EMDB-79037: CryoEM structure of integrin a4b7 bound to act1 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-79037
TitleCryoEM structure of integrin a4b7 bound to act1 Fab
Map dataNon-uniform refinement final map
Sample
  • Complex: Protein complex of integrin alpha4beta7 bound to act1 fab
    • Protein or peptide: Integrin alpha-4
    • Protein or peptide: Integrin beta-7
    • Protein or peptide: Act1 heavy chain
    • Protein or peptide: Act1 light chain
Keywordsa4b7 / gut adhesion / lymphocyte homing / membrane receptor / CELL ADHESION
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 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: Structure of integrin a4b7 bound to act1 fab
Authors: Campbell MG / Hollis JA
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_79037.png

Downloads & links

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Map

FileDownload / File: emd_79037.map.gz / Format: CCP4 / Size: 290.8 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 424 pix.
= 475.728 Å		1.12 Å/pix.
x 424 pix.
= 475.728 Å		1.12 Å/pix.
x 424 pix.
= 475.728 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: 0.225
Minimum - Maximum-0.5835246 - 1.9519267
Average (Standard dev.)-0.0005339354 (±0.027600288)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions424424424
Spacing424424424
CellA=B=C: 475.728 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened non-uniform refinement map

Fileemd_79037_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_79037_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 B

Fileemd_79037_half_map_2.map
AnnotationNon-uniform refinement half map B
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 act1 fab

EntireName: Protein complex of integrin alpha4beta7 bound to act1 fab
Components
  • Complex: Protein complex of integrin alpha4beta7 bound to act1 fab
    • Protein or peptide: Integrin alpha-4
    • Protein or peptide: Integrin beta-7
    • Protein or peptide: Act1 heavy chain
    • Protein or peptide: Act1 light chain

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Supramolecule #1: Protein complex of integrin alpha4beta7 bound to act1 fab

SupramoleculeName: Protein complex of integrin alpha4beta7 bound to act1 fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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

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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 #9: Act1 heavy chain

MacromoleculeName: Act1 heavy chain / type: protein_or_peptide / ID: 9 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQQPGAE LVKPGTSVKL SCKGYGYTFT SYWMHWVKQR PGQGLEWIGE IDPSESNTNY NQKFKGKATL TVDISSSTAY MQLSSLTSED SAVYYCARGG YDGWDYAIDY WGQGTSVTVS SAKTTPPSVY PLAPGSAAQT NSMVTLGCLV KGYFPEPVTV TWNSGSLSSG ...String:
QVQLQQPGAE LVKPGTSVKL SCKGYGYTFT SYWMHWVKQR PGQGLEWIGE IDPSESNTNY NQKFKGKATL TVDISSSTAY MQLSSLTSED SAVYYCARGG YDGWDYAIDY WGQGTSVTVS SAKTTPPSVY PLAPGSAAQT NSMVTLGCLV KGYFPEPVTV TWNSGSLSSG VHTFPAVLES DLYTLSSSVT VPSSPRPSET VTCNVAHPAS STKVDKKIV

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Macromolecule #10: Act1 light chain

MacromoleculeName: Act1 light chain / type: protein_or_peptide / ID: 10 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DVVVTQTPLS LPVSFGDQVS ISCRSSQSLA KSYGNTYLSW YLHKPGQSPQ LLIYGISNRF SGVPDRFSGS GSGTDFTLKI STIKPEDLGM YYCLQGTHQP YTFGGGTKLE IKRADAAPTV SIFPPSSEQL TSGGASVVCF LNNFYPKDIN VKWNIDGSER QNGVLNSWTD ...String:
DVVVTQTPLS LPVSFGDQVS ISCRSSQSLA KSYGNTYLSW YLHKPGQSPQ LLIYGISNRF SGVPDRFSGS GSGTDFTLKI STIKPEDLGM YYCLQGTHQP YTFGGGTKLE IKRADAAPTV SIFPPSSEQL TSGGASVVCF LNNFYPKDIN VKWNIDGSER QNGVLNSWTD QDSKDSTYSM SSTLTLTKDE YERHNSYTCE ATHKTSTSPI VKSFNRN

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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: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 241041
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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