[English] 日本語
Yorodumi
- EMDB-42608: Integrin aEb7 bound to fab LF61 with an open I domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-42608
TitleIntegrin aEb7 bound to fab LF61 with an open I domain
Map data
Sample
  • Complex: Trimeric complex of heterodimeric aEb7 bound to fab LF61
    • Protein or peptide: Integrin Beta-7
    • Protein or peptide: Integrin Alpha-E
KeywordsT cell residence / Adhesion / Signaling / Cell-cell interaction / IMMUNE SYSTEM
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 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

-
Structure visualization

Supplemental images

emd_42608.png

Downloads & links

-
Map

FileDownload / File: emd_42608.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: 0.1
Minimum - Maximum-0.4999415 - 1.687668
Average (Standard dev.)-0.0010638887 (±0.030699413)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions328328328
Spacing328328328
CellA=B=C: 368.016 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_42608_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_42608_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Trimeric complex of heterodimeric aEb7 bound to fab LF61

EntireName: Trimeric complex of heterodimeric aEb7 bound to fab LF61
Components
  • Complex: Trimeric complex of heterodimeric aEb7 bound to fab LF61
    • Protein or peptide: Integrin Beta-7
    • Protein or peptide: Integrin Alpha-E

-
Supramolecule #1: Trimeric complex of heterodimeric aEb7 bound to fab LF61

SupramoleculeName: Trimeric complex of heterodimeric aEb7 bound to fab LF61
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Integrin Beta-7

MacromoleculeName: Integrin Beta-7 / type: protein_or_peptide / ID: 1 / 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

-
Macromolecule #2: Integrin Alpha-E

MacromoleculeName: Integrin Alpha-E / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
SequenceString: FNVDVARPWL TPKGGAPFVL SSLLHQDPST NQTWLLVTSP RTKRTPGPLH RCSLVQDEIL CHPVEHVPIP KGRHRGVTVV RSHHGVLICI QVLVRRPHSL SSELTGTCSL LGPDLRPQAQ ANFFDLENLL DPDARVDTGD CYSNKEGGGE DDVNTARQGG ALEKEEEEDK ...String:
FNVDVARPWL TPKGGAPFVL SSLLHQDPST NQTWLLVTSP RTKRTPGPLH RCSLVQDEIL CHPVEHVPIP KGRHRGVTVV RSHHGVLICI QVLVRRPHSL SSELTGTCSL LGPDLRPQAQ ANFFDLENLL DPDARVDTGD CYSNKEGGGE DDVNTARQGG ALEKEEEEDK EEEEDEEEEE AGTEIAIILD GSGSIDPPDF QRAKDFISNM MRNFYEKCFE CNFALVQYGG VIQTEFDLRD SQDVMASLAR VQNITQVGSV TKTASAMQHV LDSIFTSSHG SRRKASKVMV VLTDGGIFED PLNLTTVINS PKMQGVERFA IGVGEEFKSA RTARELNLIA SDPDETHAFK VTNYMALDGL LSKLRYNIIS MEGTVGDALH YQLAQIGFSA QILDERQVLL GAVGAFDWSG GALLYDTRSR RGRFLNQTAA AAADAEAAQY SYLGYAVAVL HKTCSLSYIA GAPRYKHHGA VFELQKEGRE ASFLPVLEGE QMGSYFGSEL CPVDIDMDGS TDFLLVAAPF YHVHGEEGRV YVYRLSEQDG SFSLARILSG HPGFTNARFG FAMAAMGDLS QDKLTDVAIG APLEGFGADD GASFGSVYIY NGHWDGLSAS PSQRIRASTV APGLQYFGMS MAGGFDISGD GLADITVGTL GQAVVFRSRP VVRLKVSMAF TPSALPIGFN GVVNVRLCFE ISSVTTASES GLREALLNFT LDVDVGKQRR RLQCSDVRSC LGCLREWSSG SQLCEDLLLM PTEGELCEED CFSNASVKVS YQLQTPEGQT DHPQPILDRY TEPFAIFQLP YEKACKNKLF CVAELQLATT VSQQELVVGL TKELTLNINL TNSGEDSYMT SMALNYPRNL QLKRMQKPPS PNIQCDDPQP VASVLIMNCR IGHPVLKRSS AHVSVVWQLE ENAFPNRTAD ITVTVTNSNE RRSLANETHT LQFRHGFVAV LSKPSIMYVN TGQGLSHHKE FLFHVHGENL FGAEYQLQIC VPTKLRGLQV VAVKKLTRTQ ASTVCTWSQE RACAYSSVQH VEEWHSVSCV IASDKENVTV AAEISWDHSE ELLKDVTELQ ILGEISFNKS LYEGLNAENH RTKITVVFLK DEKYHGTGGL EVLFQGPGEN AQCEKELQAL EKENAQLEWE LQALEKELAQ WSHPQFEK

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

-
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

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 379901
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more