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- EMDB-42607: Apo integrin a4b7 in the compact state -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-42607
TitleApo integrin a4b7 in the compact state
Map data
Sample
  • Complex: Apo integrin a4b7 in the compact conformation
    • Protein or peptide: Integrin Alpha-4
    • Protein or peptide: Integrin Beta-7
KeywordsT cell residence / Adhesion / Signaling / Cell-cell interaction / IMMUNE SYSTEM
Function / homology
Function and homology information


clathrin-dependent extracellular exosome endocytosis / negative regulation of protein homodimerization activity / immune response in gut-associated lymphoid tissue / cell-matrix adhesion involved in ameboidal cell migration / integrin alpha4-beta7 complex / diapedesis / 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 / negative regulation of protein homodimerization activity / immune response in gut-associated lymphoid tissue / cell-matrix adhesion involved in ameboidal cell migration / integrin alpha4-beta7 complex / diapedesis / integrin alpha4-beta1 complex / cell-cell adhesion mediated by integrin / positive regulation of leukocyte tethering or rolling / axonogenesis involved in innervation / protein antigen binding / leukocyte tethering or rolling / RUNX3 Regulates Immune Response and Cell Migration / integrin complex / positive regulation of vascular endothelial cell proliferation / heterotypic cell-cell adhesion / neuron projection extension / 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 / T cell migration / coreceptor activity / 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 / cellular response to amyloid-beta / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / virus receptor activity / growth cone / 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 / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / 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: 3.2 Å
AuthorsHollis JA / Campbell MG / Malik HS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM147414 United States
CitationJournal: To Be Published
Title: Evolutionary origin and structural ligand mimicry mediated by the inserted domain of alpha-integrin proteins
Authors: Hollis JA / Campbell MG / Malik HS / Chan MC
History
DepositionNov 2, 2023-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42607.png

Downloads & links

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Map

FileDownload / File: emd_42607.map.gz / Format: CCP4 / Size: 134.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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: 0.13
Minimum - Maximum-0.60652447 - 1.5983708
Average (Standard dev.)-0.0007788928 (±0.029223297)
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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Half map: #1

Fileemd_42607_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_42607_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Apo integrin a4b7 in the compact conformation

EntireName: Apo integrin a4b7 in the compact conformation
Components
  • Complex: Apo integrin a4b7 in the compact conformation
    • Protein or peptide: Integrin Alpha-4
    • Protein or peptide: Integrin Beta-7

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Supramolecule #1: Apo integrin a4b7 in the compact conformation

SupramoleculeName: Apo integrin a4b7 in the compact conformation / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 270 KDa

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Macromolecule #1: Integrin Alpha-4

MacromoleculeName: Integrin Alpha-4 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: YNVDTESALL YQGPHNTLFG YSVVLHSHGA NRWLLVGAPT ANWLANASVI NPGAIYRCRI GKNPGQTCEQ LQLGSPNGEP CGKTCLEERD NQWLGVTLSR QPGENGSIVT CGHRWKNIFY IKNENKLPTG GCYGVPPDLR TELSKRIAPC YQDYVKKFGE NFASCQAGIS ...String:
YNVDTESALL YQGPHNTLFG YSVVLHSHGA NRWLLVGAPT ANWLANASVI NPGAIYRCRI GKNPGQTCEQ LQLGSPNGEP CGKTCLEERD NQWLGVTLSR QPGENGSIVT CGHRWKNIFY IKNENKLPTG GCYGVPPDLR TELSKRIAPC YQDYVKKFGE NFASCQAGIS SFYTKDLIVM GAPGSSYWTG SLFVYNITTN KYKAFLDKQN QVKFGSYLGY SVGAGHFRSQ HTTEVVGGAP QHEQIGKAYI FSIDEKELNI LHEMKGKKLG SYFGASVCAV DLNADGFSDL LVGAPMQSTI REEGRVFVYI NSGSGAVMNA METNLVGSDK YAARFGESIV NLGDIDNDGF EDVAIGAPQE DDLQGAIYIY NGRADGISST FSQRIEGLQI SKSLSMFGQS ISGQIDADNN GYVDVAVGAF RSDSAVLLRT RPVVIVDASL SHPESVNRTK FDCVENGWPS VCIDLTLCFS YKGKEVPGYI VLFYNMSLDV NRKAESPPRF YFSSNGTSDV ITGSIQVSSR EANCRTHQAF MRKDVRDILT PIQIEAAYHL GPHVISKRST EEFPPLQPIL QQKKEKDIMK KTINFARFCA HENCSADLQV SAKIGFLKPH ENKTYLAVGS MKTLMLNVSL FNAGDDAYET TLHVKLPVGL YFIKILELEE KQINCEVTDN SGVVQLDCSI GYIYVDHLSR IDISFLLDVS SLSRAEEDLS ITVHATCENE EEMDNLKHSR VTVAIPLKYE VKLTVHGFVN PTSFVYGSND ENEPETCMVE KMNLTFHVIN TGNSMAPNVS VEIMVPNSFS PQTDKLFNIL DVQTTTGECH FENYQRVCAL EQQKSAMQTL KGIVRFLSKT DKRLLYCIKA DPHCLNFLCN FGKMESGKEA SVHIQLEGRP SILEMDETSA LKFEIRATGF PEPNPRVIEL NKDENVAHVL LEGLHHQGTG GLEVLFQGPG ENAQCEKELQ ALEKENAQLE WELQALEKEL AQWSHPQFEK

UniProtKB: Integrin alpha-4

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Macromolecule #2: Integrin Beta-7

MacromoleculeName: Integrin Beta-7 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
SequenceString: ELDAKIPSTG DATEWRNPHL SMLGSCQPAP SCQKCILSHP SCAWCKQLNF TASGEAEARR CARREELLAR GCPLEELEEP RGQQEVLQDQ PLSQGARGEG ATQLAPQRVR VTLRPGEPQQ LQVRFLRAEG YPVDLYYLMD LSYSMKDDLE RVRQLGHALL VRLQEVTHSV ...String:
ELDAKIPSTG DATEWRNPHL SMLGSCQPAP SCQKCILSHP SCAWCKQLNF TASGEAEARR CARREELLAR GCPLEELEEP RGQQEVLQDQ PLSQGARGEG ATQLAPQRVR VTLRPGEPQQ LQVRFLRAEG YPVDLYYLMD LSYSMKDDLE RVRQLGHALL VRLQEVTHSV RIGFGSFVDK TVLPFVSTVP SKLRHPCPTR LERCQSPFSF HHVLSLTGDA QAFEREVGRQ SVSGNLDSPE GGFDAILQAA LCQEQIGWRN VSRLLVFTSD DTFHTAGDGK LGGIFMPSDG HCHLDSNGLY SRSTEFDYPS VGQVAQALSA ANIQPIFAVT SAALPVYQEL SKLIPKSAVG ELSEDSSNVV QLIMDAYNSL SSTVTLEHSS LPPGVHISYE SQCEGPEKRE GKAEDRGQCN HVRINQTVTF WVSLQATHCL PEPHLLRLRA LGFSEELIVE LHTLCDCNCS DTQPQAPHCS DGQGHLQCGV CSCAPGRLGR LCECSVAELS SPDLESGCRA PNGTGPLCSG KGHCQCGRCS CSGQSSGHLC ECDDASCERH EGILCGGFGR CQCGVCHCHA NRTGRACECS GDMDSCISPE GGLCSGHGRC KCNRCQCLDG YYGALCDQCP GCKTPCERHR DCAECGAFRT GPLATNCSTA CAHTNVTLAL APILDDGWCK ERTLDNQLFF FLVEDDARGT VVLRVRPQEK GADHDTSGLE VLFQGPGKNA QCKKKLQALK KKNAQLKWKL QALKKKLAQG GHHHHHH

UniProtKB: Integrin beta-7

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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

Concentration.2 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 239117
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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