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- PDB-1dgi: Cryo-EM structure of human poliovirus(serotype 1)complexed with t... -

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Basic information

Entry
Database: PDB / ID: 1dgi
TitleCryo-EM structure of human poliovirus(serotype 1)complexed with three domain CD155
Components
  • POLIOVIRUS RECEPTORCD155
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVirus/Receptor / CD155 / PVR / HUMAN POLIOVIRUS / POLIOVIRUS-RECEPTOR COMPLEX / Icosahedral virus / 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 MDA-5 activity / 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 / 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 MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / cell adhesion molecule binding / ribonucleoside triphosphate phosphatase activity / 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 / protein complex oligomerization / virus receptor activity / signaling receptor activity / 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 / Picornavirus/Calicivirus coat protein / Immunoglobulin V-Type / 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
Genome polyprotein / Poliovirus receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Human poliovirus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 22 Å
AuthorsHe, Y. / Bowman, V.D. / Mueller, S. / Bator, C.M. / Bella, J. / Peng, X. / Baker, T.S. / Wimmer, E. / Kuhn, R.J. / Rossmann, M.G.
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2000
Title: Interaction of the poliovirus receptor with poliovirus.
Authors: Y He / V D Bowman / S Mueller / C M Bator / J Bella / X Peng / T S Baker / E Wimmer / R J Kuhn / M G Rossmann /
Abstract: The structure of the extracellular, three-domain poliovirus receptor (CD155) complexed with poliovirus (serotype 1) has been determined to 22-A resolution by means of cryo-electron microscopy and ...The structure of the extracellular, three-domain poliovirus receptor (CD155) complexed with poliovirus (serotype 1) has been determined to 22-A resolution by means of cryo-electron microscopy and three-dimensional image-reconstruction techniques. Density corresponding to the receptor was isolated in a difference electron density map and fitted with known structures, homologous to those of the three individual CD155 Ig-like domains. The fit was confirmed by the location of carbohydrate moieties in the CD155 glycoprotein, the conserved properties of elbow angles in the structures of cell surface molecules with Ig-like folds, and the concordance with prior results of CD155 and poliovirus mutagenesis. CD155 binds in the poliovirus "canyon" and has a footprint similar to that of the intercellular adhesion molecule-1 receptor on human rhinoviruses. However, the orientation of the long, slender CD155 molecule relative to the poliovirus surface is quite different from the orientation of intercellular adhesion molecule-1 on rhinoviruses. In addition, the residues that provide specificity of recognition differ for the two receptors. The principal feature of receptor binding common to these two picornaviruses is the site in the canyon at which binding occurs. This site may be a trigger for initiation of the subsequent uncoating step required for viral infection.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: The Structure of the Two Amino-Terminal Domain of Human Icam-1 Suggests How It Functions as a Rhinovirus Receptor and as an Lfa-1 Integrin Ligand
Authors: Bella, J. / Kolatkar, P. / Marlor, C.W. / Greve, J. / Rossmann, M.G.
#2: Journal: Science / Year: 1985
Title: Three-Dimensional Structure of Poliovirus at 2.9A Resolution
Authors: Hogle, J. / Chow, M. / Filman, D.J.
History
DepositionNov 24, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 30, 2015Group: Structure summary
Revision 1.4Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.5Dec 18, 2019Group: Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.length_a / _cell.length_b / _cell.length_c
Revision 1.6Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
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

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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
1: VP1
2: VP2
3: VP3
4: VP4


Theoretical massNumber of molelcules
Total (without water)127,6865
Polymers127,6865
Non-polymers00
Water0
1
R: POLIOVIRUS RECEPTOR
1: VP1
2: VP2
3: VP3
4: VP4
x 60


Theoretical massNumber of molelcules
Total (without water)7,661,164300
Polymers7,661,164300
Non-polymers00
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
1: VP1
2: VP2
3: VP3
4: VP4
x 5


  • icosahedral pentamer
  • 638 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)638,43025
Polymers638,43025
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
R: POLIOVIRUS RECEPTOR
1: VP1
2: VP2
3: VP3
4: VP4
x 6


  • icosahedral 23 hexamer
  • 766 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)766,11630
Polymers766,11630
Non-polymers00
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

#1: Protein POLIOVIRUS RECEPTOR / CD155 / Coordinate model: Cα atoms only


Mass: 32928.160 Da / Num. of mol.: 1 / Fragment: THREE EXTRACELLULAR DOMAINS OF CD155
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): KIDNEY CELLS / Production host: Homo sapiens (human) / References: UniProt: P15151
#2: Protein VP1 / Coordinate model: Cα atoms only


Mass: 31874.705 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Cell (production host): HELA CELLS / Production host: Homo sapiens (human) / References: UniProt: P03300
#3: Protein VP2 / Coordinate model: Cα atoms only


Mass: 29664.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Cell (production host): HELA CELLS / Production host: Homo sapiens (human) / References: UniProt: P03300
#4: 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 / Genus: Enterovirus / Species: Poliovirus / Cell (production host): HELA CELLS / Production host: Homo sapiens (human) / References: UniProt: P03300
#5: Protein VP4


Mass: 6983.754 Da / Num. of mol.: 1 / Fragment: POLIOVIRUS FRAGMENTS VP1,VP2,VP3,VP4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Cell (production host): HELA CELLS / Production host: Homo sapiens (human) / References: UniProt: P03300*PLUS

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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: human poliovirus(serotype 1)complexed with three domain CD155
Type: COMPLEX
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationDetails: POLIOVIRUS WAS INCUBATED WITH CD155-AP FOR 1 HOURS AT 4 DEGREES CELSIUS (277 KELVIN) USING A EIGHT-FOLD EXCESS OF CD155-AP FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER ...Details: POLIOVIRUS WAS INCUBATED WITH CD155-AP FOR 1 HOURS AT 4 DEGREES CELSIUS (277 KELVIN) USING A EIGHT-FOLD EXCESS OF CD155-AP FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER.
Crystal growpH: 7.5
Details: WARNING: THIS IS AN ELECTRON MICROSCOPY MODEL DEPOSITION. CRYO-EM INFORMATION HAS BEEN INCLUDED IN THE FORM OF REMARK 250 RECORDS AT THE TOP OF THE PDB COORDINATE FILE., pH 7.5, ELECTRON ...Details: WARNING: THIS IS AN ELECTRON MICROSCOPY MODEL DEPOSITION. CRYO-EM INFORMATION HAS BEEN INCLUDED IN THE FORM OF REMARK 250 RECORDS AT THE TOP OF THE PDB COORDINATE FILE., pH 7.5, ELECTRON MICROSCOPY RECONSTRUCTION
Crystal grow
*PLUS
Method: unknown / Details: electron microscopy

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM200FEG / Date: Jun 1, 1999
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 80 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 38000 X / Nominal defocus max: 2100 nm / Nominal defocus min: 1300 nm
Specimen holderTemperature: 120 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM softwareName: PURDUE PROGRAMS / Category: 3D reconstruction
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: COMMON-LINES AND POLAR-FOURIER-TRANSFORM FULLER ET AL. 1996, J.STRUC.BIOL.c 116, 48-55; BAKER AND CHENG, 1996, J.STRUC.BIOL. 116, 120-130
Resolution: 22 Å / Resolution method: OTHER / Num. of particles: 1156 / Actual pixel size: 3.68 Å
Magnification calibration: THE PIXEL SIZE OF THE CRYO-EM MAP WAS CALIBRATED AGAINST A LOW RESOLUTION DENSITY MAP CALCULATED FROM THE CRYSTAL STRUCTURE OF POLIOVIRUS. DENSITIES WERE COMPARED BY CROSS- ...Magnification calibration: THE PIXEL SIZE OF THE CRYO-EM MAP WAS CALIBRATED AGAINST A LOW RESOLUTION DENSITY MAP CALCULATED FROM THE CRYSTAL STRUCTURE OF POLIOVIRUS. DENSITIES WERE COMPARED BY CROSS- CORRELATION WITHIN A SPHERICAL SHELL OF INTERNAL RADIUS 110 ANGSTROMS AND EXTERNAL RADIUS OF 145 ANGSTROMS.
Details: THE RESOLUTION OF THE FINAL RECONSTRUCTED DENSITY WAS DETERMINED TO BE AT LEAST 22 ANGSTROMS, AS MEASURED BY RANDOMLY SPLITTING THE PARTICLES INTO TWO SETS AND COMPARING STRUCTURE FACTORS ...Details: THE RESOLUTION OF THE FINAL RECONSTRUCTED DENSITY WAS DETERMINED TO BE AT LEAST 22 ANGSTROMS, AS MEASURED BY RANDOMLY SPLITTING THE PARTICLES INTO TWO SETS AND COMPARING STRUCTURE FACTORS OBTAINED FROM SEPARATE RECONSTRUCTIONS (BAKER ET AL. 1991, BIOPHYS.J. 60, 1445-1456). THE EIGENVALUE SPECTRUM GAVE AN INDICATION OF THE RANDOMNESS OF THE DATA THAT WAS INCLUDED IN THE RECONSTRUCTION. THE COMPLETENESS OF THE DATA WAS VERIFIED IN THAT ALL EIGENVALUES EXCEEDED 1.0.
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: VISUAL AGREEMENT
Details: METHOD--MANUAL REFINEMENT PROTOCOL--MANUAL ADJUSTMENT DETAILS--THE CRYSTAL STRUCTURE OF POLIOVIRUS WAS PLACED INTO THE CALIBRATED CRYO-EM DENSITY MAP BY ALIGNING THE ICOSAHEDRAL SYMMETRY ...Details: METHOD--MANUAL REFINEMENT PROTOCOL--MANUAL ADJUSTMENT DETAILS--THE CRYSTAL STRUCTURE OF POLIOVIRUS WAS PLACED INTO THE CALIBRATED CRYO-EM DENSITY MAP BY ALIGNING THE ICOSAHEDRAL SYMMETRY AXES. APPROPRIATELY GLYCOSYLATED MODELS OF CD155 WITH VARIOUS INTERDOMAIN ANGLES WERE MANUALLY FITTED INTO THE DIFFERENCE DENSITY CALCULAT BY SUBSTRACTING POLIOVIRUS NATIVE RECONSTRUCTION FROM THE COMPLEX RECONSTRUCTION. THE COORDINATES ARE IN THE P, Q, R FRAME IN ANGSTROM UNITS AND CORRESPOND TO ICOSAHEDRAL SYMMETRY AXES. THE ORIGIN IS CHOSEN AT THE CENTER OF THE VIRUS WITH P, Q AND R ALONG MUTUALLY PERPENDICULAR TWO-FOLD AXES OF THE ICOSAHEDRON. THEY SHOULD REMAIN IN THAT FRAME FOR THE EASE OF THE USER IN CREATING THE BIOLOGICALLY SIGNIFICANT VIRAL COMPLEX PARTICLE USING THE 60 ICOSAHEDRAL SYMMETRY OPERATORS. CD155 MODEL BUILDING (D1-D2-D3)-- ATOMIC MODEL OF D1 WAS BUILT BASED ON MYELIN PROTEIN ZERO(1NEU). ATOMIC MODEL OF D2 WAS BUILT FROM A FAB FRAGMENT(1CIC).ATOMIC MODEL OF D3 WAS BUILT FROM AN INSECT IMMUNE PROTEIN(1BIH).THE ELBOW ANGLE BETWEEN D1 AND D2 WAS DETERMINED BY LEAST-SQUARE-FITTING THESE TWO DOMAINS THE CRYSTAL STRUCTURE OF CD2(1HNF).
RefinementHighest resolution: 22 Å
Refinement stepCycle: LAST / Highest resolution: 22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1155 0 0 0 1155

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