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- PDB-1nn8: CryoEM structure of poliovirus receptor bound to poliovirus -

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Basic information

Entry
Database: PDB / ID: 1nn8
TitleCryoEM structure of poliovirus receptor bound to poliovirus
Components
  • (coat protein ...) x 4
  • poliovirus receptorCD155
KeywordsVirus/Receptor / icosahedral virus / picornavirus / Virus-Receptor COMPLEX
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 / symbiont-mediated suppression of host translation initiation / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / positive regulation of 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 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 / symbiont-mediated suppression of host translation initiation / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / positive regulation of 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 / 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 / picornain 2A / cell adhesion molecule binding / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / adherens junction / endocytosis involved in viral entry into host cell / : / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / nucleoside-triphosphate phosphatase / virus receptor activity / signaling receptor activity / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / focal adhesion / DNA-templated transcription / host cell nucleus / structural molecule activity / virion attachment to host cell / cell surface / proteolysis / extracellular space / RNA binding / ATP binding / membrane / metal ion binding / 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 / Picornavirus coat protein VP4 ...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) / 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 / Immunoglobulin V-Type / Picornavirus/Calicivirus coat protein / Immunoglobulin V-set domain / Viral coat protein subunit / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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. / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
MYRISTIC ACID / Genome polyprotein / Poliovirus receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Human poliovirus 1 Mahoney
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 15 Å
AuthorsHe, Y. / Mueller, S. / Chipman, P.R. / Bator, C.M. / Peng, X. / Bowman, V.D. / Mukhopadhyay, S. / Wimmer, E. / Kuhn, R.J. / Rossmann, M.G.
CitationJournal: J Virol / Year: 2003
Title: Complexes of poliovirus serotypes with their common cellular receptor, CD155.
Authors: Yongning He / Steffen Mueller / Paul R Chipman / Carol M Bator / Xiaozhong Peng / Valorie D Bowman / Suchetana Mukhopadhyay / Eckard Wimmer / Richard J Kuhn / Michael G Rossmann /
Abstract: Structures of all three poliovirus (PV) serotypes (PV1, PV2, and PV3) complexed with their cellular receptor, PV receptor (PVR or CD155), were determined by cryoelectron microscopy. Both glycosylated ...Structures of all three poliovirus (PV) serotypes (PV1, PV2, and PV3) complexed with their cellular receptor, PV receptor (PVR or CD155), were determined by cryoelectron microscopy. Both glycosylated and fully deglycosylated CD155 exhibited similar binding sites and orientations in the viral canyon for all three PV serotypes, showing that all three serotypes use a common mechanism for cell entry. Difference maps between the glycosylated and deglycosylated CD155 complexes determined the sites of the carbohydrate moieties that, in turn, helped to verify the position of the receptor relative to the viral surface. The proximity of the CD155 carbohydrate site at Asn105 to the viral surface in the receptor-virus complex suggests that it might interfere with receptor docking, an observation consistent with the properties of mutant CD155. The footprints of CD155 on PV surfaces indicate that the south rim of the canyon dominates the virus-receptor interactions and may correspond to the initial CD155 binding state of the receptor-mediated viral uncoating. In contrast, the interaction of CD155 with the north rim of the canyon, especially the region immediately outside the viral hydrophobic pocket that normally binds a cellular "pocket factor," may be critical for the release of the pocket factor, decreasing the virus stability and hence initiating uncoating. The large area of the CD155 footprint on the PV surface, in comparison with other picornavirus-receptor interactions, could be a potential limitation on the viability of PV escape mutants from antibody neutralization. Many of these are likely to have lost their ability to bind CD155, resulting in there being only three PV serotypes.
History
DepositionJan 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_image_scans / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref_seq_dif.details
Remark 999Authors submitted coordinates for alpha carbons only.
Remark 99CHAINS R, S, and T REPRESENT THE DOCKING POSITIONS OF CD155 FITTED INTO PV1, PV2 and PV3 EM MAPS, ...CHAINS R, S, and T REPRESENT THE DOCKING POSITIONS OF CD155 FITTED INTO PV1, PV2 and PV3 EM MAPS, RESPECTIVELY.

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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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Assembly

Deposited unit
R: poliovirus receptor
S: poliovirus receptor
T: poliovirus receptor
1: coat protein VP1
2: coat protein VP2
3: coat protein VP3
4: coat protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,0518
Polymers195,8237
Non-polymers2281
Water0
1
R: poliovirus receptor
S: poliovirus receptor
T: poliovirus receptor
1: coat protein VP1
2: coat protein VP2
3: coat protein VP3
4: coat protein VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)11,763,066480
Polymers11,749,364420
Non-polymers13,70260
Water0
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
S: poliovirus receptor
T: poliovirus receptor
1: coat protein VP1
2: coat protein VP2
3: coat protein VP3
4: coat protein VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 980 kDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)980,25640
Polymers979,11435
Non-polymers1,1425
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
R: poliovirus receptor
S: poliovirus receptor
T: poliovirus receptor
1: coat protein VP1
2: coat protein VP2
3: coat protein VP3
4: coat protein VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 1.18 MDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)1,176,30748
Polymers1,174,93642
Non-polymers1,3706
Water0
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: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))

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Components

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Coat protein ... , 4 types, 4 molecules 1234

#2: Protein coat protein VP1 / Coordinate model: Cα atoms only


Mass: 33334.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 Mahoney / Genus: Enterovirus / Species: Poliovirus / Cellular location (production host): Hela cells / Production host: Homo sapiens (human) / References: UniProt: P03300
#3: Protein coat protein VP2 / Coordinate model: Cα atoms only


Mass: 30075.783 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 Mahoney / Genus: Enterovirus / Species: Poliovirus / Cellular location (production host): Hela cells / Production host: Homo sapiens (human) / References: UniProt: P03300
#4: Protein coat protein VP3 / Coordinate model: Cα atoms only


Mass: 26235.115 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 Mahoney / Genus: Enterovirus / Species: Poliovirus / Cellular location (production host): Hela cells / Production host: Homo sapiens (human) / References: UniProt: P03300
#5: Protein coat protein VP4 / Coordinate model: Cα atoms only


Mass: 7393.050 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 Mahoney / Genus: Enterovirus / Species: Poliovirus / Cellular location (production host): Hela cells / Production host: Homo sapiens (human) / References: UniProt: P03300

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Protein / Non-polymers , 2 types, 4 molecules RST

#1: Protein poliovirus receptor / CD155 / CD155 antigen / Coordinate model: Cα atoms only


Mass: 32928.160 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location (production host): 293 cells / Production host: Homo sapiens (human) / References: UniProt: P15151
#6: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2

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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

ComponentName: poliovirus receptor bound to poliovirus / Type: VIRUS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Crystal grow
*PLUS
Method: electron microscopy / Details: electron microscopy

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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 FIELDBright-field microscopy / Nominal defocus max: 3700 nm / Nominal defocus min: 1400 nm

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Processing

CTF correctionDetails: CTF is corrected for each image
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: polar fourier transform (PFT) / Resolution: 15 Å / Num. of particles: 2022 / Nominal pixel size: 3.11 Å / Actual pixel size: 2.91 Å / Magnification calibration: 45000
Details: 4799 particles are collected, defocus range: 1.4um-3.7um
Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms1756 0 1 0 1757

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