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- PDB-3uro: Poliovirus receptor CD155 D1D2 -

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Basic information

Entry
Database: PDB / ID: 3uro
TitlePoliovirus receptor CD155 D1D2
ComponentsPoliovirus receptor
KeywordsVIRAL PROTEIN / poliovirus receptor ectodomain / Immunoglobulin Super Family / Cell adhesion / Cell membrane / Glycoprotein / Host-virus interaction / Immunoglobulin domain / Membrane / Receptor / Secreted / Transmembrane
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 / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / homophilic cell adhesion via plasma membrane adhesion molecules / cell adhesion molecule binding / adherens junction / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell ...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 / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / homophilic cell adhesion via plasma membrane adhesion molecules / cell adhesion molecule binding / adherens junction / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / signaling receptor activity / virus receptor activity / focal adhesion / cell surface / extracellular space / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...: / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.5005 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
DepositionNov 22, 2011Deposition site: RCSB / Processing site: RCSB
SupersessionDec 7, 2011ID: 3EOW
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
R: Poliovirus receptor


Theoretical massNumber of molelcules
Total (without water)24,3561
Polymers24,3561
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
R: Poliovirus receptor

R: Poliovirus receptor


Theoretical massNumber of molelcules
Total (without water)48,7112
Polymers48,7112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area1250 Å2
ΔGint-13 kcal/mol
Surface area23790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.307, 84.307, 117.219
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Poliovirus receptor / Nectin-like protein 5 / NECL-5


Mass: 24355.645 Da / Num. of mol.: 1
Fragment: poliovirus receptor CD155 D1D2 (UNP Residues 29-243)
Mutation: N105D, N120S, N188Q, N218Q, N237S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PVR, PVS / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: P15151

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 4.28 Å3/Da / Density % sol: 71.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM MgSO4, 6.8 M NH4NO3, 100 mM Tris buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.07 Å
DetectorType: KODAK / Detector: CCD / Date: Feb 23, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 3.5→40 Å / Num. all: 5800 / Num. obs: 5700 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 3.5005→35.892 Å / SU ML: 0.76 / σ(F): 1.48 / Phase error: 36.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3414 277 4.88 %Random
Rwork0.3048 ---
obs0.3066 5675 99.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 292.848 Å2 / ksol: 0.373 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.4939 Å20 Å2-0 Å2
2--0.4939 Å20 Å2
3----3.212 Å2
Refinement stepCycle: LAST / Resolution: 3.5005→35.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1638 0 0 0 1638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121680
X-RAY DIFFRACTIONf_angle_d2.5822289
X-RAY DIFFRACTIONf_dihedral_angle_d22.808609
X-RAY DIFFRACTIONf_chiral_restr0.168263
X-RAY DIFFRACTIONf_plane_restr0.009295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5005-4.4090.37631290.34192621X-RAY DIFFRACTION99
4.409-35.89410.32461480.29042777X-RAY DIFFRACTION100

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