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- EMDB-60143: Cryo-EM structure of human integrin alpha-E beta-7 -

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Basic information

Entry
Database: EMDB / ID: EMD-60143
TitleCryo-EM structure of human integrin alpha-E beta-7
Map data
Sample
  • Complex: Integrin alpha-E beta-7
    • Protein or peptide: Integrin beta-7
    • Protein or peptide: Integrin alpha-E
  • Ligand: MAGNESIUM ION
  • Ligand: CALCIUM ION
KeywordsComplex / Cryo-EM / 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 / T cell migration / leukocyte tethering or rolling / heterotypic cell-cell adhesion / integrin complex / cell adhesion mediated by integrin / leukocyte migration / receptor clustering ...immune response in gut-associated lymphoid tissue / cell-matrix adhesion involved in ameboidal cell migration / integrin alpha4-beta7 complex / T cell migration / leukocyte tethering or rolling / heterotypic cell-cell adhesion / integrin complex / cell adhesion mediated by integrin / leukocyte migration / receptor clustering / Integrin cell surface interactions / cell adhesion molecule binding / substrate adhesion-dependent cell spreading / cell-matrix adhesion / integrin-mediated signaling pathway / cell-cell adhesion / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / virus receptor activity / receptor complex / cell adhesion / external side of plasma membrane / focal adhesion / cell surface / extracellular exosome / membrane / metal ion binding / 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 / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain ...Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain cysteine-rich domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin alpha cytoplasmic region / EGF-like domain, extracellular / EGF-like domain / : / Integrin alpha Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / 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 / von Willebrand factor type A domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1.
Similarity search - Domain/homology
Integrin beta-7 / Integrin alpha-E
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsAkasaka H / Nureki O / Kise Y
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22H02555 Japan
CitationJournal: Biochem Biophys Res Commun / Year: 2024
Title: Cryo-EM structure of I domain-containing integrin αEβ7.
Authors: Hiroaki Akasaka / Dan Sato / Wataru Shihoya / Osamu Nureki / Yoshiaki Kise /
Abstract: The integrin family is a transmembrane receptor that plays critical roles in the cell-cell and cell-extracellular matrix adhesion, signal transduction such as cell cycle regulation, organization of ...The integrin family is a transmembrane receptor that plays critical roles in the cell-cell and cell-extracellular matrix adhesion, signal transduction such as cell cycle regulation, organization of the intracellular cytoskeleton, and immune responses. Consequently, dysfunction of integrins is associated with a wide range of human diseases, including cancer and immune diseases, which makes integrins therapeutic targets for drug discovery. Here we report the cryo-EM structure of the human α-I domain-containing full-length integrin αEβ7, which is expressed in the leukocytes of the immune system and a drug target for inflammatory bowel disease (IBD). The structure reveals the half-bent conformation, an intermediate between the close and the open conformation, while the α-I domain responsible for the ligand binding covers the headpiece domain by a unique spatial arrangement. Our results provide the structural information for the drug design targeting IBD.
History
DepositionMay 14, 2024-
Header (metadata) releaseJun 5, 2024-
Map releaseJun 5, 2024-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60143.png

Downloads & links

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Map

FileDownload / File: emd_60143.map.gz / Format: CCP4 / Size: 35.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 210 pix.
= 233.1 Å		1.11 Å/pix.
x 210 pix.
= 233.1 Å		1.11 Å/pix.
x 210 pix.
= 233.1 Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.95777845 - 1.4249634
Average (Standard dev.)0.00062077906 (±0.027468132)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions210210210
Spacing210210210
CellA=B=C: 233.1 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_60143_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_60143_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_60143_half_map_2.map
Projections & Slices
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Sample components

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Entire : Integrin alpha-E beta-7

EntireName: Integrin alpha-E beta-7
Components
  • Complex: Integrin alpha-E beta-7
    • Protein or peptide: Integrin beta-7
    • Protein or peptide: Integrin alpha-E
  • Ligand: MAGNESIUM ION
  • Ligand: CALCIUM ION

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Supramolecule #1: Integrin alpha-E beta-7

SupramoleculeName: Integrin alpha-E beta-7 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Integrin beta-7

MacromoleculeName: Integrin beta-7 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 90.055438 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VALPMVLVLL LVLSRGESEL DAKIPSTGDA TEWRNPHLSM LGSCQPAPSC QKCILSHPSC AWCKQLNFTA SGEAEARRCA RREELLARG CPLEELEEPR GQQEVLQDQP LSQGARGEGA TQLAPQRVRV TLRPGEPQQL QVRFLRAEGY PVDLYYLMDL S YSMKDDLE ...String:
VALPMVLVLL LVLSRGESEL DAKIPSTGDA TEWRNPHLSM LGSCQPAPSC QKCILSHPSC AWCKQLNFTA SGEAEARRCA RREELLARG CPLEELEEPR GQQEVLQDQP LSQGARGEGA TQLAPQRVRV TLRPGEPQQL QVRFLRAEGY PVDLYYLMDL S YSMKDDLE RVRQLGHALL VRLQEVTHSV RIGFGSFVDK TVLPFVSTVP SKLRHPCPTR LERCQSPFSF HHVLSLTGDA QA FEREVGR QSVSGNLDSP EGGFDAILQA ALCQEQIGWR NVSRLLVFTS DDTFHTAGDG KLGGIFMPSD GHCHLDSNGL YSR STEFDY PSVGQVAQAL SAANIQPIFA VTSAALPVYQ ELSKLIPKSA VGELSEDSSN VVQLIMDAYN SLSSTVTLEH SSLP PGVHI SYESQCEGPE KREGKAEDRG QCNHVRINQT VTFWVSLQAT HCLPEPHLLR LRALGFSEEL IVELHTLCDC NCSDT QPQA PHCSDGQGHL QCGVCSCAPG RLGRLCECSV AELSSPDLES GCRAPNGTGP LCSGKGHCQC GRCSCSGQSS GHLCEC DDA SCERHEGILC GGFGRCQCGV CHCHANRTGR ACECSGDMDS CISPEGGLCS GHGRCKCNRC QCLDGYYGAL CDQCPGC KT PCERHRDCAE CGAFRTGPLA TNCSTACAHT NVTLALAPIL DDGWCKERTL DNQLFFFLVE DDARGTVVLR VRPQEKGA D HTQAIVLGCV GGIVAVGLGL VLAYRLSVEI YDRREYSRFE KEQQQLNWKQ DSNPLYKSAI TTTINPRFQE ADSPTLGSG SGLNDIFEAQ KIEWHEGSGS ENLYFQ

UniProtKB: Integrin beta-7

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Macromolecule #2: Integrin alpha-E

MacromoleculeName: Integrin alpha-E / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 132.436453 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: WLFHTLLCIA SLALLAAFNV DVARPWLTPK GGAPFVLSSL LHQDPSTNQT WLLVTSPRTK RTPGPLHRCS LVQDEILCHP VEHVPIPKG RHRGVTVVRS HHGVLICIQV LVRRPHSLSS ELTGTCSLLG PDLRPQAQAN FFDLENLLDP DARVDTGDCY S NKEGGGED ...String:
WLFHTLLCIA SLALLAAFNV DVARPWLTPK GGAPFVLSSL LHQDPSTNQT WLLVTSPRTK RTPGPLHRCS LVQDEILCHP VEHVPIPKG RHRGVTVVRS HHGVLICIQV LVRRPHSLSS ELTGTCSLLG PDLRPQAQAN FFDLENLLDP DARVDTGDCY S NKEGGGED DVNTARQRRA LEKEEEEDKE EEEDEEEEEA GTEIAIILDG SGSIDPPDFQ RAKDFISNMM RNFYEKCFEC NF ALVQYGG VIQTEFDLRD SQDVMASLAR VQNITQVGSV TKTASAMQHV LDSIFTSSHG SRRKASKVMV VLTDGGIFED PLN LTTVIN SPKMQGVERF AIGVGEEFKS ARTARELNLI ASDPDETHAF KVTNYMALDG LLSKLRYNII SMEGTVGDAL HYQL AQIGF SAQILDERQV LLGAVGAFDW SGGALLYDTR SRRGRFLNQT AAAAADAEAA QYSYLGYAVA VLHKTCSLSY IAGAP RYKH HGAVFELQKE GREASFLPVL EGEQMGSYFG SELCPVDIDM DGSTDFLLVA APFYHVHGEE GRVYVYRLSE QDGSFS LAR ILSGHPGFTN ARFGFAMAAM GDLSQDKLTD VAIGAPLEGF GADDGASFGS VYIYNGHWDG LSASPSQRIR ASTVAPG LQ YFGMSMAGGF DISGDGLADI TVGTLGQAVV FRSRPVVRLK VSMAFTPSAL PIGFNGVVNV RLCFEISSVT TASESGLR E ALLNFTLDVD VGKQRRRLQC SDVRSCLGCL REWSSGSQLC EDLLLMPTEG ELCEEDCFSN ASVKVSYQLQ TPEGQTDHP QPILDRYTEP FAIFQLPYEK ACKNKLFCVA ELQLATTVSQ QELVVGLTKE LTLNINLTNS GEDSYMTSMA LNYPRNLQLK RMQKPPSPN IQCDDPQPVA SVLIMNCRIG HPVLKRSSAH VSVVWQLEEN AFPNRTADIT VTVTNSNERR SLANETHTLQ F RHGFVAVL SKPSIMYVNT GQGLSHHKEF LFHVHGENLF GAEYQLQICV PTKLRGLQVV AVKKLTRTQA STVCTWSQER AC AYSSVQH VEEWHSVSCV IASDKENVTV AAEISWDHSE ELLKDVTELQ ILGEISFNKS LYEGLNAENH RTKITVVFLK DEK YHSLPI IIKGSVGGLL VLIVILVILF KCGFFKRKYQ QLNLESIRKA QLKSENLLEE ENLELEVLFQ GPGSDYKDDD DK

UniProtKB: Integrin alpha-E

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 2 / 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 statecell

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.855 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 300397
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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