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- PDB-3epc: CryoEM structure of poliovirus receptor bound to poliovirus type 1 -

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Entry
Database: PDB / ID: 3epc
TitleCryoEM structure of poliovirus receptor bound to poliovirus type 1
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
Human poliovirus 1 Mahoney / virus
MethodElectron microscopy (8 A resolution)
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

DateDeposition: Sep 29, 2008 / Release: Nov 11, 2008 / Last modification: May 11, 2016

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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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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)118,6077
Polyers118,0795
Non-polymers5282
Water0
#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)7,116,422420
Polyers7,084,750300
Non-polymers31,672120
Water0
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
  • 593 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)593,03535
Polyers590,39625
Non-polymers2,63910
Water0
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
  • 712 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)711,64242
Polyers708,47530
Non-polymers3,16712
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
PAU


  • 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: 23330.672 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: 31455.607 Da / Num. of mol.: 1 / Source: (gene. exp.) Human poliovirus 1 Mahoney / References: UniProt: P03300

Cellular component

Molecular function

Biological process

  • endocytosis involved in viral entry into host cell (GO: 0075509)
  • 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)
  • RNA-protein covalent cross-linking (GO: 0018144)
  • suppression by virus of host mRNA export from nucleus (GO: 0039522)
  • 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: 29664.516 Da / Num. of mol.: 1 / Source: (gene. exp.) Human poliovirus 1 Mahoney / References: UniProt: P03300

Cellular component

Molecular function

Biological process

  • endocytosis involved in viral entry into host cell (GO: 0075509)
  • 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)
  • RNA-protein covalent cross-linking (GO: 0018144)
  • suppression by virus of host mRNA export from nucleus (GO: 0039522)
  • 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: 7393.119 Da / Num. of mol.: 1 / Source: (gene. exp.) Human poliovirus 1 Mahoney / References: UniProt: P03300

Cellular component

Molecular function

Biological process

  • endocytosis involved in viral entry into host cell (GO: 0075509)
  • 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)
  • RNA-protein covalent cross-linking (GO: 0018144)
  • suppression by virus of host mRNA export from nucleus (GO: 0039522)
  • 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: 26235.246 Da / Num. of mol.: 1 / Source: (gene. exp.) Human poliovirus 1 Mahoney / References: UniProt: P03300

Cellular component

Molecular function

Biological process

  • endocytosis involved in viral entry into host cell (GO: 0075509)
  • 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)
  • RNA-protein covalent cross-linking (GO: 0018144)
  • suppression by virus of host mRNA export from nucleus (GO: 0039522)
  • 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 , 2 types, 2 molecules

#6: ChemicalChemComp-MYR / MYRISTIC ACID


Mass: 228.374 Da / Num. of mol.: 1 / Formula: C14H28O2
#7: ChemicalChemComp-SPH / SPHINGOSINE


Mass: 299.496 Da / Num. of mol.: 1 / Formula: C18H37NO2

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Details

Sequence detailsTHERE IS A PHE -> SER SEQUENCE CONFLICT AT RESIDUE 464 IN UNIPROT DATABASE.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY

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Processing

Image selectionSoftware name: EMfit
3D reconstructionResolution: 8 A / Nominal pixel size: 2.69 A/pix / Actual pixel size: 2.65 A/pix
Atomic model buildingSoftware name: EMfit / Ref space: REAL
Number of atoms included #LASTProtein: 8256 / Nucleic acid: 0 / Ligand: 36 / Solvent: 0 / Total: 8292

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