+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-60143 | |||||||||
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Title | Cryo-EM structure of human integrin alpha-E beta-7 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Complex / 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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Akasaka H / Nureki O / Kise Y | |||||||||
Funding support | Japan, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_60143.map.gz | 2.7 MB | EMDB map data format | |
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Header (meta data) | emd-60143-v30.xml emd-60143.xml | 16.5 KB 16.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_60143_fsc.xml | 6.9 KB | Display | FSC data file |
Images | emd_60143.png | 79.1 KB | ||
Masks | emd_60143_msk_1.map | 35.3 MB | Mask map | |
Filedesc metadata | emd-60143.cif.gz | 6.7 KB | ||
Others | emd_60143_half_map_1.map.gz emd_60143_half_map_2.map.gz | 32.8 MB 32.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-60143 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-60143 | HTTPS FTP |
-Validation report
Summary document | emd_60143_validation.pdf.gz | 663.5 KB | Display | EMDB validaton report |
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Full document | emd_60143_full_validation.pdf.gz | 663.1 KB | Display | |
Data in XML | emd_60143_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | emd_60143_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-60143 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-60143 | HTTPS FTP |
-Related structure data
Related structure data | 8zjfMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_60143.map.gz / Format: CCP4 / Size: 35.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.11 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_60143_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_60143_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_60143_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Integrin alpha-E beta-7
Entire | Name: Integrin alpha-E beta-7 |
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Components |
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-Supramolecule #1: Integrin alpha-E beta-7
Supramolecule | Name: Integrin alpha-E beta-7 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Integrin beta-7
Macromolecule | Name: Integrin beta-7 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 90.055438 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #2: Integrin alpha-E
Macromolecule | Name: Integrin alpha-E / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 132.436453 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.855 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |