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- PDB-3epf: CryoEM structure of poliovirus receptor bound to poliovirus type 2 -

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Basic information

Entry
Database: PDB / ID: 3epf
TitleCryoEM structure of poliovirus receptor bound to poliovirus type 2
DescriptorPoliovirus receptor
Protein VP1
Protein VP2
Protein VP4
Protein VP3
KeywordsVIRAL PROTEIN / CD155 structure Immunoglobulin Superfamily / poliovirus capsid jelly role / Cell adhesion / Cell membrane / Glycoprotein / Host-virus interaction / Immunoglobulin domain / Membrane / Receptor / Secreted / Transmembrane
Specimen sourceHomo sapiens / human
Poliovirus type 2 / virus
MethodElectron microscopy (9 Å resolution / Particle / Single particle)
AuthorsZhang, P. / Mueller, S. / Morais, M.C. / Bator, C.M. / Bowman, V.D. / Hafenstein, S. / Wimmer, E. / Rossmann, M.G.
CitationProc. Natl. Acad. Sci. U.S.A., 2008, 105, 18284-18289

Proc. Natl. Acad. Sci. U.S.A., 2008, 105, 18284-18289 StrPapers
Crystal structure of CD155 and electron microscopic studies of its complexes with polioviruses.
Ping Zhang / Steffen Mueller / Marc C Morais / Carol M Bator / Valorie D Bowman / Susan Hafenstein / Eckard Wimmer / Michael G Rossmann

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 29, 2008 / Release: Nov 11, 2008
RevisionDateData content typeGroupProviderType
1.0Nov 11, 2008Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance
1.2May 11, 2016Structure modelDerived calculations

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Assembly

Deposited unit
R: Poliovirus receptor
1: Protein VP1
2: Protein VP2
4: Protein VP4
3: Protein VP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,2267
Polyers116,5745
Non-polymers6522
Water4,882271
#1
R: Poliovirus receptor
1: Protein VP1
2: Protein VP2
4: Protein VP4
3: Protein VP3
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)7,033,546420
Polyers6,994,420300
Non-polymers39,125120
Water4,324240
TypeNameSymmetry operationNumber
point symmetry operation60
#2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
#3
R: Poliovirus receptor
1: Protein VP1
2: Protein VP2
4: Protein VP4
3: Protein VP3
hetero molecules
x 5


  • icosahedral pentamer
  • 586 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)586,12935
Polyers582,86825
Non-polymers3,26010
Water36020
TypeNameSymmetry operationNumber
point symmetry operation5
#4
R: Poliovirus receptor
1: Protein VP1
2: Protein VP2
4: Protein VP4
3: Protein VP3
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 703 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)703,35542
Polyers699,44230
Non-polymers3,91312
Water43224
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

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Components

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Polypeptide(L) , 5 types, 5 molecules R1243

#1: Polypeptide(L)Poliovirus receptor / Nectin-like protein 5 / Necl-5


Mass: 23330.514 Da / Num. of mol.: 1 / Fragment: Poliovirus receptor CD155 D1D2 / Mutation: N105D, N120S, N188Q, N218Q, N237S / Source: (gene. exp.) Homo sapiens / References: UniProt: P15151

Cellular component

Molecular function

Biological process

  • adherens junction organization (GO: 0034332)
  • cell recognition (GO: 0008037)
  • heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules (GO: 0007157)
  • homophilic cell adhesion via plasma membrane adhesion molecules (GO: 0007156)
  • positive regulation of natural killer cell mediated cytotoxicity (GO: 0045954)
  • positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO: 0002860)
  • regulation of immune response (GO: 0050776)
  • susceptibility to natural killer cell mediated cytotoxicity (GO: 0042271)
  • susceptibility to T cell mediated cytotoxicity (GO: 0060370)
#2: Polypeptide(L)Protein VP1


Mass: 30734.535 Da / Num. of mol.: 1 / Source: (gene. exp.) Poliovirus type 2 / References: UniProt: P06210

Cellular component

Molecular function

Biological process

  • DNA replication (GO: 0006260)
  • induction by virus of host autophagy (GO: 0039520)
  • pore formation by virus in membrane of host cell (GO: 0039707)
  • pore-mediated entry of viral genome into host cell (GO: 0044694)
  • positive stranded viral RNA replication (GO: 0039690)
  • protein oligomerization (GO: 0051259)
  • receptor-mediated endocytosis of virus by host cell (GO: 0019065)
  • RNA-protein covalent cross-linking (GO: 0018144)
  • suppression by virus of host gene expression (GO: 0039657)
  • suppression by virus of host mRNA export from nucleus (GO: 0039522)
  • obsolete suppression by virus of host RIG-I activity by RIG-I proteolysis (GO: 0039544)
  • suppression by virus of host translation initiation factor activity (GO: 0039611)
  • transcription, DNA-templated (GO: 0006351)
  • viral RNA genome replication (GO: 0039694)
  • virion attachment to host cell (GO: 0019062)
#3: Polypeptide(L)Protein VP2


Mass: 29045.814 Da / Num. of mol.: 1 / Source: (gene. exp.) Poliovirus type 2 / References: UniProt: P06210

Cellular component

Molecular function

Biological process

  • DNA replication (GO: 0006260)
  • induction by virus of host autophagy (GO: 0039520)
  • pore formation by virus in membrane of host cell (GO: 0039707)
  • pore-mediated entry of viral genome into host cell (GO: 0044694)
  • positive stranded viral RNA replication (GO: 0039690)
  • protein oligomerization (GO: 0051259)
  • receptor-mediated endocytosis of virus by host cell (GO: 0019065)
  • RNA-protein covalent cross-linking (GO: 0018144)
  • suppression by virus of host gene expression (GO: 0039657)
  • suppression by virus of host mRNA export from nucleus (GO: 0039522)
  • obsolete suppression by virus of host RIG-I activity by RIG-I proteolysis (GO: 0039544)
  • suppression by virus of host translation initiation factor activity (GO: 0039611)
  • transcription, DNA-templated (GO: 0006351)
  • viral RNA genome replication (GO: 0039694)
  • virion attachment to host cell (GO: 0019062)
#4: Polypeptide(L)Protein VP4


Mass: 7346.957 Da / Num. of mol.: 1 / Source: (gene. exp.) Poliovirus type 2 / References: UniProt: P06210

Cellular component

Molecular function

Biological process

  • DNA replication (GO: 0006260)
  • induction by virus of host autophagy (GO: 0039520)
  • pore formation by virus in membrane of host cell (GO: 0039707)
  • pore-mediated entry of viral genome into host cell (GO: 0044694)
  • positive stranded viral RNA replication (GO: 0039690)
  • protein oligomerization (GO: 0051259)
  • receptor-mediated endocytosis of virus by host cell (GO: 0019065)
  • RNA-protein covalent cross-linking (GO: 0018144)
  • suppression by virus of host gene expression (GO: 0039657)
  • suppression by virus of host mRNA export from nucleus (GO: 0039522)
  • obsolete suppression by virus of host RIG-I activity by RIG-I proteolysis (GO: 0039544)
  • suppression by virus of host translation initiation factor activity (GO: 0039611)
  • transcription, DNA-templated (GO: 0006351)
  • viral RNA genome replication (GO: 0039694)
  • virion attachment to host cell (GO: 0019062)
#5: Polypeptide(L)Protein VP3


Mass: 26115.852 Da / Num. of mol.: 1 / Source: (gene. exp.) Poliovirus type 2 / References: UniProt: P06210

Cellular component

Molecular function

Biological process

  • DNA replication (GO: 0006260)
  • induction by virus of host autophagy (GO: 0039520)
  • pore formation by virus in membrane of host cell (GO: 0039707)
  • pore-mediated entry of viral genome into host cell (GO: 0044694)
  • positive stranded viral RNA replication (GO: 0039690)
  • protein oligomerization (GO: 0051259)
  • receptor-mediated endocytosis of virus by host cell (GO: 0019065)
  • RNA-protein covalent cross-linking (GO: 0018144)
  • suppression by virus of host gene expression (GO: 0039657)
  • suppression by virus of host mRNA export from nucleus (GO: 0039522)
  • obsolete suppression by virus of host RIG-I activity by RIG-I proteolysis (GO: 0039544)
  • suppression by virus of host translation initiation factor activity (GO: 0039611)
  • transcription, DNA-templated (GO: 0006351)
  • viral RNA genome replication (GO: 0039694)
  • virion attachment to host cell (GO: 0019062)

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Non-polymers , 3 types, 273 molecules

#6: ChemicalChemComp-SC4 / 1[2-CHLORO-4-METHOXY-PHENYL-OXYMETHYL]-4-[2,6-DICHLORO-PHENYL-OXYMETHYL]-BENZENE


Mass: 423.717 Da / Num. of mol.: 1 / Formula: C21H17Cl3O3
#7: ChemicalChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Formula: C14H28O2
#8: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

Component
IDNameTypeParent ID
1CryoEM structure of poliovirus receptor bound to poliovirus type 2COMPLEX0
2poliovirus receptorCOMPLEX1
3poliovirus type 2VIRUS1
Buffer solutionDetails: 10mM Tris-HCl, 20mM NaCl / pH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyMicroscope model: FEI/PHILIPS CM300FEG/T
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 47000 / Nominal defocus max: 2745 nm / Nominal defocus min: 1236 nm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM softwareName: EMFit / Category: MODEL FITTING
SymmetryPoint symmetry: I
3D reconstructionResolution: 9 Å / Nominal pixel size: 2.69 / Actual pixel size: 2.66 / Symmetry type: POINT
Atomic model buildingRef space: REAL
Number of atoms included #LASTProtein: 8152 / Nucleic acid: 0 / Ligand: 38 / Solvent: 271 / Total: 8461

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