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- EMDB-3635: Localised Reconstruction of Integrin alpha v beta 6 bound to Foot... -

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Entry
Database: EMDB / ID: EMD-3635
TitleLocalised Reconstruction of Integrin alpha v beta 6 bound to Foot and Mouth Disease Virus O1 Manisa - Pose B
Map dataLocalised Reconstruction of Integrin alpha v beta 6 bound to Foot and Mouth Disease Virus O1 Manisa - Pose B
Sample
  • Complex: Foot-and-mouth disease virus
    • Complex: Integrin
      • Protein or peptide: Integrin alpha-V
      • Protein or peptide: Integrin beta-6
    • Virus: Foot-and-mouth disease virus
      • Protein or peptide: O1 Manisa VP1
      • Protein or peptide: O1 Manisa VP2
      • Protein or peptide: Capsid protein
      • Protein or peptide: O1 Manisa VP4
  • Ligand: MAGNESIUM ION
  • Ligand: CALCIUM ION
KeywordsFoot and Mouth Disease Virus / FMDV / virus / OpanAsia / virus-receptor / complex
Function / homology
Function and homology information


hard palate development / Langerhans cell differentiation / integrin alphav-beta8 complex / integrin alphav-beta6 complex / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / extracellular matrix protein binding / opsonin binding / enamel mineralization ...hard palate development / Langerhans cell differentiation / integrin alphav-beta8 complex / integrin alphav-beta6 complex / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / extracellular matrix protein binding / opsonin binding / enamel mineralization / symbiont-mediated perturbation of host chromatin organization / integrin alphav-beta1 complex / bronchiole development / Cross-presentation of particulate exogenous antigens (phagosomes) / Laminin interactions / negative regulation of lipoprotein metabolic process / integrin alphav-beta3 complex / entry into host cell by a symbiont-containing vacuole / alphav-beta3 integrin-PKCalpha complex / phospholipid homeostasis / alphav-beta3 integrin-HMGB1 complex / negative regulation of lipid transport / regulation of phagocytosis / : / Elastic fibre formation / alphav-beta3 integrin-IGF-1-IGF1R complex / surfactant homeostasis / transforming growth factor beta binding / positive regulation of small GTPase mediated signal transduction / filopodium membrane / extracellular matrix binding / apolipoprotein A-I-mediated signaling pathway / apoptotic cell clearance / wound healing, spreading of epidermal cells / integrin complex / heterotypic cell-cell adhesion / Molecules associated with elastic fibres / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / negative chemotaxis / cell adhesion mediated by integrin / Syndecan interactions / microvillus membrane / skin development / lung alveolus development / cell-substrate adhesion / positive regulation of osteoblast proliferation / endodermal cell differentiation / PECAM1 interactions / TGF-beta receptor signaling activates SMADs / positive regulation of intracellular signal transduction / lamellipodium membrane / fibronectin binding / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / ECM proteoglycans / Integrin cell surface interactions / voltage-gated calcium channel activity / vasculogenesis / specific granule membrane / coreceptor activity / extrinsic apoptotic signaling pathway in absence of ligand / phagocytic vesicle / ERK1 and ERK2 cascade / positive regulation of cell adhesion / transforming growth factor beta receptor signaling pathway / substrate adhesion-dependent cell spreading / ribonucleoside triphosphate phosphatase activity / molecular function activator activity / protein kinase C binding / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cell-matrix adhesion / Signal transduction by L1 / integrin-mediated signaling pathway / cellular response to ionizing radiation / negative regulation of extrinsic apoptotic signaling pathway / wound healing / T=pseudo3 icosahedral viral capsid / cell morphogenesis / bone development / calcium ion transmembrane transport / cell-cell adhesion / response to virus / host cell cytoplasmic vesicle membrane / VEGFA-VEGFR2 Pathway / ruffle membrane / integrin binding / cell migration / regulation of translation / virus receptor activity / channel activity / positive regulation of cytosolic calcium ion concentration / protease binding / monoatomic ion transmembrane transport / angiogenesis / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / receptor complex / RNA helicase activity / cell adhesion / viral protein processing
Similarity search - Function
Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Helicase/polymerase/peptidase polyprotein, Calicivirus-type ...Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / : / Integrin alpha Ig-like domain 3 / Integrin EGF domain / 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 alpha cytoplasmic region / 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 / Picornavirus coat protein / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / Papain-like cysteine peptidase superfamily / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Genome polyprotein / Integrin alpha-V / Integrin beta-6 / Genome polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human) / Foot-and-mouth disease virus
Methodsingle particle reconstruction / cryo EM / Resolution: 12.3 Å
AuthorsKotecha A / Stuart D
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G1000099 United Kingdom
Medical Research Council (United Kingdom)G1100525/1 United Kingdom
Wellcome Trust090532/Z/09/Z United Kingdom
CitationJournal: Nat Commun / Year: 2017
Title: Rules of engagement between αvβ6 integrin and foot-and-mouth disease virus.
Authors: Abhay Kotecha / Quan Wang / Xianchi Dong / Serban L Ilca / Marina Ondiviela / Rao Zihe / Julian Seago / Bryan Charleston / Elizabeth E Fry / Nicola G A Abrescia / Timothy A Springer / Juha T ...Authors: Abhay Kotecha / Quan Wang / Xianchi Dong / Serban L Ilca / Marina Ondiviela / Rao Zihe / Julian Seago / Bryan Charleston / Elizabeth E Fry / Nicola G A Abrescia / Timothy A Springer / Juha T Huiskonen / David I Stuart /
Abstract: Foot-and-mouth disease virus (FMDV) mediates cell entry by attachment to an integrin receptor, generally αvβ6, via a conserved arginine-glycine-aspartic acid (RGD) motif in the exposed, antigenic, ...Foot-and-mouth disease virus (FMDV) mediates cell entry by attachment to an integrin receptor, generally αvβ6, via a conserved arginine-glycine-aspartic acid (RGD) motif in the exposed, antigenic, GH loop of capsid protein VP1. Infection can also occur in tissue culture adapted virus in the absence of integrin via acquired basic mutations interacting with heparin sulphate (HS); this virus is attenuated in natural infections. HS interaction has been visualized at a conserved site in two serotypes suggesting a propensity for sulfated-sugar binding. Here we determined the interaction between αvβ6 and two tissue culture adapted FMDV strains by cryo-electron microscopy. In the preferred mode of engagement, the fully open form of the integrin, hitherto unseen at high resolution, attaches to an extended GH loop via interactions with the RGD motif plus downstream hydrophobic residues. In addition, an N-linked sugar of the integrin attaches to the previously identified HS binding site, suggesting a functional role.
History
DepositionMar 11, 2017-
Header (metadata) releaseApr 5, 2017-
Map releaseJun 21, 2017-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0138
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0138
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5neu
  • Surface level: 0.0138
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3635.png

Downloads & links

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Map

FileDownload / File: emd_3635.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocalised Reconstruction of Integrin alpha v beta 6 bound to Foot and Mouth Disease Virus O1 Manisa - Pose B
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 128 pix.
= 172.8 Å		1.35 Å/pix.
x 128 pix.
= 172.8 Å		1.35 Å/pix.
x 128 pix.
= 172.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0138 / Movie #1: 0.0138
Minimum - Maximum-0.010910902 - 0.04730446
Average (Standard dev.)0.0065334295 (±0.0066531715)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin163-273277
Dimensions128128128
Spacing128128128
CellA=B=C: 172.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z172.800172.800172.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-273163277
NC/NR/NS128128128
D min/max/mean-0.0110.0470.007

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Supplemental data

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Sample components

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Entire : Foot-and-mouth disease virus

EntireName: Foot-and-mouth disease virus
Components
  • Complex: Foot-and-mouth disease virus
    • Complex: Integrin
      • Protein or peptide: Integrin alpha-V
      • Protein or peptide: Integrin beta-6
    • Virus: Foot-and-mouth disease virus
      • Protein or peptide: O1 Manisa VP1
      • Protein or peptide: O1 Manisa VP2
      • Protein or peptide: Capsid protein
      • Protein or peptide: O1 Manisa VP4
  • Ligand: MAGNESIUM ION
  • Ligand: CALCIUM ION

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Supramolecule #1: Foot-and-mouth disease virus

SupramoleculeName: Foot-and-mouth disease virus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Molecular weightTheoretical: 9 MDa

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Supramolecule #3: Integrin

SupramoleculeName: Integrin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Foot-and-mouth disease virus

SupramoleculeName: Foot-and-mouth disease virus / type: virus / ID: 2 / Parent: 1 / Macromolecule list: #1-#4 / NCBI-ID: 12110 / Sci species name: Foot-and-mouth disease virus / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Bos taurus (domestic cattle)
Virus shellShell ID: 1 / Name: Foot and Mouth Disease virus / Diameter: 300.0 Å / T number (triangulation number): 3

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Macromolecule #1: O1 Manisa VP1

MacromoleculeName: O1 Manisa VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus
Molecular weightTheoretical: 22.850895 KDa
Recombinant expressionOrganism: Cricetinae gen. sp. (mammal)
SequenceString: TTSAGESADP VTATVENYGG ETQVQRRQHT DVSFILDRFV KVTPKDQINV LDLMQTPAHT LVGALLRTAT YYFADLEVAV KHEGNLTWV PNGAPEAALD NTTNPTAYHK APLTRLALPY TAPHRVLATV YNGNSKYGDG TVANVRGDLQ VLAQKAARAL P TSFNYGAI ...String:
TTSAGESADP VTATVENYGG ETQVQRRQHT DVSFILDRFV KVTPKDQINV LDLMQTPAHT LVGALLRTAT YYFADLEVAV KHEGNLTWV PNGAPEAALD NTTNPTAYHK APLTRLALPY TAPHRVLATV YNGNSKYGDG TVANVRGDLQ VLAQKAARAL P TSFNYGAI KATRVTELLY RMKRAETYCP RPLLAIHPDQ ARHKQKIVAP

UniProtKB: Genome polyprotein

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Macromolecule #2: O1 Manisa VP2

MacromoleculeName: O1 Manisa VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus
Molecular weightTheoretical: 24.41751 KDa
Recombinant expressionOrganism: Cricetinae gen. sp. (mammal)
SequenceString: DKKTEETTLL EDRILTTRNG HTTSTTQSSV GVTYGYATAE DFVSGPNTSG LETRVAQAER FFKTHLFDWV TSDPFGRCHL LELPTDHKG VYGYLTDSYA YMRNGWDVEV TAVGNQFNGG CLLVAMVPEL CSIQKRELYQ LTLFPHQFIN PRTNMTAHIT V PFVGVNRY ...String:
DKKTEETTLL EDRILTTRNG HTTSTTQSSV GVTYGYATAE DFVSGPNTSG LETRVAQAER FFKTHLFDWV TSDPFGRCHL LELPTDHKG VYGYLTDSYA YMRNGWDVEV TAVGNQFNGG CLLVAMVPEL CSIQKRELYQ LTLFPHQFIN PRTNMTAHIT V PFVGVNRY DQYKVHKPWT LVVMVVAPLT VNSEGAPQIK VYANIAPTNV HVAGEFPSKE

UniProtKB: Genome polyprotein

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Macromolecule #3: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus
Molecular weightTheoretical: 23.933879 KDa
Recombinant expressionOrganism: Cricetinae gen. sp. (mammal)
SequenceString: GIFPVACSDG YGGLVTTDPK TADPAYGKVF NPPRNMLPGR FTNFLDVAEA CPTFLHFEGD VPYVTTKTDS DRVLAQFDLS LAAKHMSNT FLAGLAQYYT QYSGTINLHF MFTGPTDAKA RYMIAYAPPG MEPPKTPEAA AHCIHAEWDT GLNSKFTFSI P YLSAADYT ...String:
GIFPVACSDG YGGLVTTDPK TADPAYGKVF NPPRNMLPGR FTNFLDVAEA CPTFLHFEGD VPYVTTKTDS DRVLAQFDLS LAAKHMSNT FLAGLAQYYT QYSGTINLHF MFTGPTDAKA RYMIAYAPPG MEPPKTPEAA AHCIHAEWDT GLNSKFTFSI P YLSAADYT YTASDVAETT NVQGWVCLFQ ITHGKADGDA LVVLASAGKD FELRLPVDAR TQ

UniProtKB: Genome polyprotein

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Macromolecule #4: O1 Manisa VP4

MacromoleculeName: O1 Manisa VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus
Molecular weightTheoretical: 8.766075 KDa
Recombinant expressionOrganism: Cricetinae gen. sp. (mammal)
SequenceString:
GAGQSSPATG SQNQSGNTGS IINNYYMQQY QNSMDTQLGD NATSGGSNEG STDTTSTHTT NTQNNDWFSK LASSAFSGLF GALLA

UniProtKB: Genome polyprotein

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Macromolecule #5: Integrin alpha-V

MacromoleculeName: Integrin alpha-V / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 64.937828 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: FNLDVDSPAE YSGPEGSYFG FAVDFFVPSS RMFLLVGAPK ANTTQPGIVE GGQVLKCDWS STRRCQPIEF DATGNRDYAK DDPLEFKSH QWFGASVRSK QDKILACAPL YHWRTEMKQE REPVGTCFLQ DGTKTVEYAP CRSQDIDADG QGFCQGGFSI D FTKADRVL ...String:
FNLDVDSPAE YSGPEGSYFG FAVDFFVPSS RMFLLVGAPK ANTTQPGIVE GGQVLKCDWS STRRCQPIEF DATGNRDYAK DDPLEFKSH QWFGASVRSK QDKILACAPL YHWRTEMKQE REPVGTCFLQ DGTKTVEYAP CRSQDIDADG QGFCQGGFSI D FTKADRVL LGGPGSFYWQ GQLISDQVAE IVSKYDPNVY SIKYNNQLAT RTAQAIFDDS YLGYSVAVGD FNGDGIDDFV SG VPRAART LGMVYIYDGK NMSSLYNFTG EQMAAYFGFS VAATDINGDD YADVFIGAPL FMDRGSDGKL QEVGQVSVSL QRA SGDFQT TKLNGFEVFA RFGSAIAPLG DLDQDGFNDI AIAAPYGGED KKGIVYIFNG RSTGLNAVPS QILEGQWAAR SCPP SFGYS MKGATDIDKN GYPDLIVGAF GVDRAILYRA RPVITVNAGL EVYPSILNQD NKTCSLPGTA LKVSCFNVRF CLKAD GKGV LPRKLNFQVE LLLDKLKGAI RRALFLYSRS PSHSKNMTIS RGGLMQCEEL IAYLRDESEF RDKLTPITIF MEYRLD YRT AADTTGLQPI LNQFTPANIS RQAHILL

UniProtKB: Integrin alpha-V

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Macromolecule #6: Integrin beta-6

MacromoleculeName: Integrin beta-6 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.53457 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GCALGGAETC EDCLLIGPQC AWCAQENFTH PSGVGERCDT PANLLAKGCQ LNFIENPVSQ VEILKNKPLS VGRQKNSSDI VQIAPQSLI LKLRPGGAQT LQVHVRQTED YPVDLYYLMD LSASMDDDLN TIKELGSRLS KEMSKLTSNF RLGFGSFVEK P VSPFVKTT ...String:
GCALGGAETC EDCLLIGPQC AWCAQENFTH PSGVGERCDT PANLLAKGCQ LNFIENPVSQ VEILKNKPLS VGRQKNSSDI VQIAPQSLI LKLRPGGAQT LQVHVRQTED YPVDLYYLMD LSASMDDDLN TIKELGSRLS KEMSKLTSNF RLGFGSFVEK P VSPFVKTT PEEIANPCSS IPYFCLPTFG FKHILPLTND AERFNEIVKN QKISANIDTP EGGFDAIMQA AVCKEKIGWR ND SLHLLVF VSDADSHFGM DSKLAGIVCP NDGLCHLDSK NEYSMSTVLE YPTIGQLIDK LVQNNVLLIF AVTQEQVHLY ENY AKLIPG ATVGLLQKDS GNILQLIISA YEELRSEVEL EVLGDTEGLN LSFTAICNNG TLFQHQKKCS HMKVGDTASF SVTV NIPHC ERRSRHIIIK PVGLGDALEL LVSPECNCDC QKEVEVNSSK CHNGNGSFQC GVCACHPGHM GPRCE

UniProtKB: Integrin beta-6

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #8: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 8 / 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 stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 8 / Component - Concentration: 50.0 mM / Component - Name: HEPES
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 5 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 294 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI POLARA 300
TemperatureMin: 70.0 K / Max: 70.0 K
Specialist opticsEnergy filter - Name: GIF / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 2-20 / Number grids imaged: 1 / Number real images: 360 / Average exposure time: 5.0 sec. / Average electron dose: 18.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 37037 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 160000
Sample stageSpecimen holder model: GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1bbt

Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 12.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 13483
Initial angle assignmentType: COMMON LINE / Software - Name: RELION (ver. 1.3)
Final angle assignmentType: COMMON LINE / Software - Name: RELION (ver. 1.3)
Final 3D classificationSoftware - Name: RELION (ver. 1.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 120 / Target criteria: Cross-correlation coefficient
Output model

PDB-5neu:
Localised Reconstruction of Integrin alpha V beta 6 bound to Foot and Mouth Disease Virus O1 Manisa - Pose B.

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