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- PDB-5neu: Localised Reconstruction of Integrin alpha V beta 6 bound to Foot... -

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Entry
Database: PDB / ID: 5neu
TitleLocalised Reconstruction of Integrin alpha V beta 6 bound to Foot and Mouth Disease Virus O1 Manisa - Pose B.
Components
  • Capsid proteinCapsid
  • Integrin alpha-VIntegrin alpha V
  • Integrin beta-6
  • O1 Manisa VP1
  • O1 Manisa VP2
  • O1 Manisa VP4
KeywordsVIRUS / Foot and Mouth Disease Virus / FMDV / OpanAsia / virus-receptor / complex
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 / 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 / Elastic fibre formation / regulation of phagocytosis / 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 / Molecules associated with elastic fibres / positive regulation of intracellular signal transduction / cell adhesion mediated by integrin / skin development / microvillus membrane / Syndecan interactions / negative chemotaxis / lung alveolus development / cell-substrate adhesion / endodermal cell differentiation / 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 / substrate adhesion-dependent cell spreading / cell-matrix adhesion / transforming growth factor beta receptor signaling pathway / protein kinase C binding / Signal transduction by L1 / T=pseudo3 icosahedral viral capsid / molecular function activator activity / integrin-mediated signaling pathway / cellular response to ionizing radiation / host cell cytoplasmic vesicle membrane / negative regulation of extrinsic apoptotic signaling pathway / calcium ion transmembrane transport / response to virus / wound healing / bone development / cytoplasmic vesicle membrane / cell morphogenesis / cell-cell adhesion / ruffle membrane / VEGFA-VEGFR2 Pathway / : / cell migration / integrin binding / regulation of translation / virus receptor activity / protein complex oligomerization / cell junction / monoatomic ion channel activity / positive regulation of cytosolic calcium ion concentration / clathrin-dependent endocytosis of virus by host cell / angiogenesis / protease binding / host cell cytoplasm / RNA helicase activity
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 / EGF-like domain signature 2. / EGF-like domain signature 1. / 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 / 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 / Papain-like cysteine peptidase superfamily / 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 speciesFoot-and-mouth disease virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12.3 Å
AuthorsKotecha, A. / Stuart, D.
Funding support United Kingdom, 3items
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, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Experimental preparation / Refinement description
Category: em_3d_fitting / em_sample_support ...em_3d_fitting / em_sample_support / em_software / pdbx_audit_support
Item: _em_3d_fitting.target_criteria / _em_sample_support.grid_type ..._em_3d_fitting.target_criteria / _em_sample_support.grid_type / _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2017Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Mar 28, 2018Group: Structure summary / Category: struct / Item: _struct.title

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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Structure viewerMolecule:
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Assembly

Deposited unit
1: O1 Manisa VP1
2: O1 Manisa VP2
3: Capsid protein
4: O1 Manisa VP4
A: Integrin alpha-V
B: Integrin beta-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,5459
Polymers196,4416
Non-polymers1043
Water0
1
1: O1 Manisa VP1
2: O1 Manisa VP2
3: Capsid protein
4: O1 Manisa VP4
A: Integrin alpha-V
B: Integrin beta-6
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)11,792,713540
Polymers11,786,445360
Non-polymers6,268180
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
1: O1 Manisa VP1
2: O1 Manisa VP2
3: Capsid protein
4: O1 Manisa VP4
A: Integrin alpha-V
B: Integrin beta-6
hetero molecules
x 5


  • icosahedral pentamer
  • 983 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)982,72645
Polymers982,20430
Non-polymers52215
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
1: O1 Manisa VP1
2: O1 Manisa VP2
3: Capsid protein
4: O1 Manisa VP4
A: Integrin alpha-V
B: Integrin beta-6
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 1.18 MDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)1,179,27154
Polymers1,178,64536
Non-polymers62718
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

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Protein , 6 types, 6 molecules 1234AB

#1: Protein O1 Manisa VP1


Mass: 22850.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus / Production host: Cricetinae gen. sp. (mammal) / References: UniProt: Q6PMW3
#2: Protein O1 Manisa VP2


Mass: 24417.510 Da / Num. of mol.: 1 / Mutation: S93Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus / Production host: Cricetinae gen. sp. (mammal) / References: UniProt: Q6PMW3
#3: Protein Capsid protein / Capsid


Mass: 23933.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus / Production host: Cricetinae gen. sp. (mammal) / References: UniProt: A0A1C6ZW60, UniProt: Q6PMW3*PLUS
#4: Protein O1 Manisa VP4


Mass: 8766.075 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus / Production host: Cricetinae gen. sp. (mammal) / References: UniProt: E1ACS1, UniProt: D1H101*PLUS
#5: Protein Integrin alpha-V / Integrin alpha V / Vitronectin receptor subunit alpha


Mass: 64937.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAV, MSK8, VNRA / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P06756
#6: Protein Integrin beta-6


Mass: 51534.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB6 / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P18564

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Non-polymers , 2 types, 3 molecules

#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Foot-and-mouth disease virusCOMPLEX#1-#60MULTIPLE SOURCES
2Foot-and-mouth disease virusVIRUS#1-#41RECOMBINANT
3IntegrinCOMPLEX#5-#61RECOMBINANT
Molecular weightValue: 9 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Foot-and-mouth disease virus12110
23Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Cricetinae gen. sp. (mammal)36483
23Homo sapiens (human)9606
Details of virusEmpty: NO / Enveloped: NO / Isolate: SEROTYPE / Type: VIRION
Natural hostOrganism: Bos taurus
Virus shellName: Foot and Mouth Disease virusFoot-and-mouth disease virus
Diameter: 300 nm / Triangulation number (T number): 3
Buffer solutionpH: 8
Buffer componentConc.: 50 mM / Name: HEPES
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 294 K

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 160000 X / Calibrated magnification: 37037 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Cs: 2 mm / C2 aperture diameter: 50 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER
Temperature (max): 70 K / Temperature (min): 70 K
Image recordingAverage exposure time: 5 sec. / Electron dose: 18 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 360
EM imaging opticsEnergyfilter name: GIF / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 25 / Used frames/image: 2-20

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Processing

EM software
IDNameVersionCategory
2SerialEM6image acquisition
4CTFFIND4.0.17CTF correction
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
10RELION1.3initial Euler assignment
11RELION1.3final Euler assignment
12RELION1.3classification
13RELION1.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 12.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13483 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingB value: 120 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient

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