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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
Components
  • Poliovirus receptor
  • Protein VP1
  • Protein VP2
  • Protein VP3
  • Protein VP4
KeywordsVIRUS / CD155 structure Immunoglobulin Superfamily / poliovirus capsid jelly role / Cell adhesion / Cell membrane / Glycoprotein / Host-virus interaction / Immunoglobulin domain / Membrane / Receptor / Secreted / Transmembrane / VIRAL PROTEIN
Function / homology
Function and homology information


susceptibility to T cell mediated cytotoxicity / susceptibility to natural killer cell mediated cytotoxicity / Nectin/Necl trans heterodimerization / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / positive regulation of natural killer cell mediated cytotoxicity / negative regulation of natural killer cell mediated cytotoxicity / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / natural killer cell mediated cytotoxicity / homophilic cell adhesion via plasma membrane adhesion molecules / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity ...susceptibility to T cell mediated cytotoxicity / susceptibility to natural killer cell mediated cytotoxicity / Nectin/Necl trans heterodimerization / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / positive regulation of natural killer cell mediated cytotoxicity / negative regulation of natural killer cell mediated cytotoxicity / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / natural killer cell mediated cytotoxicity / homophilic cell adhesion via plasma membrane adhesion molecules / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / cell adhesion molecule binding / receptor-mediated endocytosis of virus by host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / adherens junction / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / signaling receptor activity / nucleoside-triphosphate phosphatase / virus receptor activity / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / receptor ligand activity / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / focal adhesion / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / cell surface / proteolysis / extracellular space / RNA binding / zinc ion binding / ATP binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A ...: / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Immunoglobulin V-Type / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Immunoglobulin V-set domain / 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 / Immunoglobulin V-set domain / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Immunoglobulin subtype / Immunoglobulin / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Immunoglobulin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
MYRISTIC ACID / Chem-SC4 / Genome polyprotein / Poliovirus receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Poliovirus type 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9 Å
AuthorsZhang, P. / Mueller, S. / Morais, M.C. / Bator, C.M. / Bowman, V.D. / Hafenstein, S. / Wimmer, E. / Rossmann, M.G.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2008
Title: Crystal structure of CD155 and electron microscopic studies of its complexes with polioviruses.
Authors: Ping Zhang / Steffen Mueller / Marc C Morais / Carol M Bator / Valorie D Bowman / Susan Hafenstein / Eckard Wimmer / Michael G Rossmann /
Abstract: When poliovirus (PV) recognizes its receptor, CD155, the virus changes from a 160S to a 135S particle before releasing its genome into the cytoplasm. CD155 is a transmembrane protein with 3 Ig-like ...When poliovirus (PV) recognizes its receptor, CD155, the virus changes from a 160S to a 135S particle before releasing its genome into the cytoplasm. CD155 is a transmembrane protein with 3 Ig-like extracellular domains, D1-D3, where D1 is recognized by the virus. The crystal structure of D1D2 has been determined to 3.5-A resolution and fitted into approximately 8.5-A resolution cryoelectron microscopy reconstructions of the virus-receptor complexes for the 3 PV serotypes. These structures show that, compared with human rhinoviruses, the virus-receptor interactions for PVs have a greater dependence on hydrophobic interactions, as might be required for a virus that can inhabit environments of different pH. The pocket factor was shown to remain in the virus during the first recognition stage. The present structures, when combined with earlier mutational investigations, show that in the subsequent entry stage the receptor moves further into the canyon when at a physiological temperature, thereby expelling the pocket factor and separating the viral subunits to form 135S particles. These results provide a detailed analysis of how a nonenveloped virus can enter its host cell.
History
DepositionSep 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 11, 2016Group: Derived calculations
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.name
Revision 1.4Oct 31, 2018Group: Data collection / Structure summary / Category: diffrn / struct_keywords
Item: _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Apr 17, 2024Group: Data collection / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_database_status / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_sf / _pdbx_struct_oper_list.name ..._pdbx_database_status.status_code_sf / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type
Revision 1.7Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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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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
Polymers116,5745
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
Polymers6,994,420300
Non-polymers39,125120
Water4,324240
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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
Polymers582,86825
Non-polymers3,26010
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
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
Polymers699,44230
Non-polymers3,91312
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
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 , 5 types, 5 molecules R1243

#1: Protein 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 method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PVR, PVS / Production host: Escherichia coli (E. coli) / References: UniProt: P15151
#2: Protein Protein VP1


Mass: 30734.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Poliovirus type 2 / Production host: Escherichia coli (E. coli) / References: UniProt: P06210
#3: Protein Protein VP2


Mass: 29045.814 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Poliovirus type 2 / Production host: Escherichia coli (E. coli) / References: UniProt: P06210
#4: Protein Protein VP4


Mass: 7346.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Poliovirus type 2 / Production host: Escherichia coli (E. coli) / References: UniProt: P06210
#5: Protein Protein VP3


Mass: 26115.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Poliovirus type 2 / Production host: Escherichia coli (E. coli) / References: UniProt: P06210

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Non-polymers , 3 types, 273 molecules

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


Mass: 423.717 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H17Cl3O3
#7: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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

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Electron microscopy imaging

MicroscopyModel: 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 X / 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 (icosahedral)
3D reconstructionResolution: 9 Å / Nominal pixel size: 2.69 Å / Actual pixel size: 2.66 Å / Symmetry type: POINT
Atomic model buildingSpace: REAL
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms8152 0 38 271 8461

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