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- EMDB-3634: Localised Reconstruction of Integrin alpha V beta 6 bound to Foot... -

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Basic information

Entry
Database: EMDB / ID: EMD-3634
TitleLocalised Reconstruction of Integrin alpha V beta 6 bound to Foot and Mouth Disease Virus O1 Manisa - Pose A.
Map dataLocalised Reconstruction of Integrin alpha v beta 6 bound to Foot and Mouth Disease Virus O1 Manisa - Pose A
Sample
  • Complex: Foot and mouth virus and Integrin
    • Complex: Integrin
      • Protein or peptide: Integrin alpha-VIntegrin 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: O1 Manisa VP3
      • Protein or peptide: O1 Manisa VP4
  • Ligand: alpha-D-mannopyranose
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM IONCalcium
Function / homology
Function and homology information


Langerhans cell differentiation / icosahedral viral capsid / integrin alphav-beta6 complex / integrin alphav-beta8 complex / hard palate development / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / : / opsonin binding ...Langerhans cell differentiation / icosahedral viral capsid / integrin alphav-beta6 complex / integrin alphav-beta8 complex / hard palate development / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / : / opsonin binding / integrin alphav-beta1 complex / Cross-presentation of particulate exogenous antigens (phagosomes) / bronchiole development / enamel mineralization / extracellular matrix protein binding / modulation by virus of host chromatin organization / Laminin interactions / RNA-protein covalent cross-linking / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / phospholipid homeostasis / entry into host cell by a symbiont-containing vacuole / alphav-beta3 integrin-PKCalpha complex / alphav-beta3 integrin-HMGB1 complex / negative regulation of lipid transport / negative regulation of low-density lipoprotein receptor activity / regulation of phagocytosis / Elastic fibre formation / alphav-beta3 integrin-IGF-1-IGF1R complex / transforming growth factor beta binding / surfactant homeostasis / filopodium membrane / positive regulation of small GTPase mediated signal transduction / extracellular matrix binding / apolipoprotein A-I-mediated signaling pathway / wound healing, spreading of epidermal cells / apoptotic cell clearance / heterotypic cell-cell adhesion / integrin complex / positive regulation of intracellular signal transduction / Molecules associated with elastic fibres / cell adhesion mediated by integrin / skin development / microvillus membrane / Syndecan interactions / negative chemotaxis / lung alveolus development / endodermal cell differentiation / cell-substrate adhesion / positive regulation of osteoblast proliferation / TGF-beta receptor signaling activates SMADs / PECAM1 interactions / lamellipodium membrane / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / fibronectin binding / positive regulation of cell adhesion / ECM proteoglycans / voltage-gated calcium channel activity / vasculogenesis / Integrin cell surface interactions / specific granule membrane / coreceptor activity / phagocytic vesicle / extrinsic apoptotic signaling pathway in absence of ligand / ERK1 and ERK2 cascade / ribonucleoside triphosphate phosphatase activity / cell-matrix adhesion / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / protein kinase C binding / T=pseudo3 icosahedral viral capsid / Signal transduction by L1 / host cell cytoplasmic vesicle membrane / molecular function activator activity / integrin-mediated signaling pathway / cellular response to ionizing radiation / negative regulation of extrinsic apoptotic signaling pathway / calcium ion transmembrane transport / response to virus / wound healing / bone development / cell morphogenesis / cytoplasmic vesicle membrane / cell-cell adhesion / ruffle membrane / VEGFA-VEGFR2 Pathway / : / cell migration / integrin binding / protein complex oligomerization / regulation of translation / virus receptor activity / monoatomic ion channel activity / cell junction / positive regulation of cytosolic calcium ion concentration / clathrin-dependent endocytosis of virus by host cell / angiogenesis / protease binding / host cell cytoplasm
Similarity search - Function
Aphthovirus leader protease (L(pro)) domain profile. / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / 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 / Integrin beta subunit, cytoplasmic domain ...Aphthovirus leader protease (L(pro)) domain profile. / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / 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 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin alpha Ig-like domain 3 / Integrin beta tail domain / 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) / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Integrin alpha cytoplasmic region / EGF-like domain, extracellular / EGF-like domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / : / 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 / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor A-like domain superfamily / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / EGF-like domain signature 2. / EGF-like domain signature 1. / 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 / Papain-like cysteine peptidase superfamily / 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 / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Integrin alpha-V / Integrin beta-6 / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human) / Foot-and-mouth disease virus
Methodsingle particle reconstruction / cryo EM / Resolution: 8.6 Å
AuthorsKotecha A / Stuart D
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G1000099 United Kingdom
Wellcome Trust090532/Z/09/Z United Kingdom
Medical Research Council (United Kingdom)G1100525/1 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 19, 2017-
Map releaseJun 21, 2017-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
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  • Atomic models: PDB-5net
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3634.png

Downloads & links

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Map

FileDownload / File: emd_3634.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 A
Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.013298614 - 0.048147164
Average (Standard dev.)0.005484182 (±0.0067152213)
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-0.0130.0480.005

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Supplemental data

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Sample components

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Entire : Foot and mouth virus and Integrin

EntireName: Foot and mouth virus and Integrin
Components
  • Complex: Foot and mouth virus and Integrin
    • Complex: Integrin
      • Protein or peptide: Integrin alpha-VIntegrin 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: O1 Manisa VP3
      • Protein or peptide: O1 Manisa VP4
  • Ligand: alpha-D-mannopyranose
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM IONCalcium

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Supramolecule #1: Foot and mouth virus and Integrin

SupramoleculeName: Foot and mouth virus and Integrin / 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)
Recombinant expressionOrganism: 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 (cattle)
Host systemOrganism: Cricetinae gen. sp. (mammal)
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

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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

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Macromolecule #3: O1 Manisa VP3

MacromoleculeName: O1 Manisa VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus
Molecular weightTheoretical: 23.952924 KDa
Recombinant expressionOrganism: Cricetinae gen. sp. (mammal)
SequenceString: GIFPVACSDG YGGLVTTDPK TADPAYGKVF NPPRNMLPGR FTNFLDVAEA CPTFLRFEGD VPYVTTKTDS DRVLAQFDLS LAAKHMSNT FLAGLAQYYT QYSGTINLHF MFTGPTDAKA RYMIAYAPPG MEPPKTPEAA AHCIHAEWDT GLNSKFTFSI P YLSAADYT ...String:
GIFPVACSDG YGGLVTTDPK TADPAYGKVF NPPRNMLPGR FTNFLDVAEA CPTFLRFEGD VPYVTTKTDS DRVLAQFDLS LAAKHMSNT FLAGLAQYYT QYSGTINLHF MFTGPTDAKA RYMIAYAPPG MEPPKTPEAA AHCIHAEWDT GLNSKFTFSI P YLSAADYT YTASDVAETT NVQGWVCLFQ ITHGKADGDA LVVLASAGKD FELRLPVDAR TQ

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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

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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: 65.353293 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: FNLDVDSPAE YSGPEGSYFG FAVDFFVPSA SSRMFLLVGA PKANTTQPGI VEGGQVLKCD WSSTRRCQPI EFDATGNRDY AKDDPLEFK SHQWFGASVR SKQDKILACA PLYHWRTEMK QEREPVGTCF LQDGTKTVEY APCRSQDIDA DGQGFCQGGF S IDFTKADR ...String:
FNLDVDSPAE YSGPEGSYFG FAVDFFVPSA SSRMFLLVGA PKANTTQPGI VEGGQVLKCD WSSTRRCQPI EFDATGNRDY AKDDPLEFK SHQWFGASVR SKQDKILACA PLYHWRTEMK QEREPVGTCF LQDGTKTVEY APCRSQDIDA DGQGFCQGGF S IDFTKADR VLLGGPGSFY WQGQLISDQV AEIVSKYDPN VYSIKYNNQL ATRTAQAIFD DSYLGYSVAV GDFNGDGIDD FV SGVPRAA RTLGMVYIYD GKNMSSLYNF TGEQMAAYFG FSVAATDING DDYADVFIGA PLFMDRGSDG KLQEVGQVSV SLQ RASGDF QTTKLNGFEV FARFGSAIAP LGDLDQDGFN DIAIAAPYGG EDKKGIVYIF NGRSTGLNAV PSQILEGQWA ARSC PPSFG YSMKGATDID KNGYPDLIVG AFGVDRAILY RARPVITVNA GLEVYPSILN QDNKTCSLPG TALKVSCFNV RFCLK ADGK GVLPRKLNFQ VELLLDKLKQ KGAIRRALFL YSRSPSHSKN MTISRGGLMQ CEELIAYLRD ESEFRDKLTP ITIFME YRL DYRTAADTTG LQPILNQFTP ANISRQAHIL L

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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

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Macromolecule #11: alpha-D-mannopyranose

MacromoleculeName: alpha-D-mannopyranose / type: ligand / ID: 11 / Number of copies: 3 / Formula: MAN
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-MAN:
alpha-D-mannopyranose / Mannose

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Macromolecule #12: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 12 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Macromolecule #13: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 13 / Number of copies: 4 / 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: 5.0 nm / Pretreatment - Type: GLOW DISCHARGE / 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
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 FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 160000
Specialist opticsEnergy filter - Name: GIF / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV
Sample stageSpecimen holder model: GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
TemperatureMin: 70.0 K / Max: 70.0 K
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
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.0.17)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1bbt

Initial angle assignmentType: COMMON LINE / Software - Name: RELION (ver. 1.3)
Final 3D classificationSoftware - Name: RELION (ver. 1.3)
Final angle assignmentType: COMMON LINE / Software - Name: RELION (ver. 1.3)
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 8.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 13483
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-5net:
Localised Reconstruction of Integrin alpha V beta 6 bound to Foot and Mouth Disease Virus O1 Manisa - Pose A.

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