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- PDB-3r0n: Crystal Structure of the Immunoglobulin variable domain of Nectin-2 -

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Basic information

Entry
Database: PDB / ID: 3r0n
TitleCrystal Structure of the Immunoglobulin variable domain of Nectin-2
ComponentsPoliovirus receptor-related protein 2
KeywordsCELL ADHESION / Ig-domain / cell-adhesion molecule / Virus entry receptor / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / Atoms-to-Animals: The Immune Function Network / IFN
Function / homology
Function and homology information


sperm mitochondrion organization / susceptibility to T cell mediated cytotoxicity / coreceptor-mediated virion attachment to host cell / establishment of mitochondrion localization / susceptibility to natural killer cell mediated cytotoxicity / spermatid nucleus differentiation / positive regulation of immunoglobulin mediated immune response / Nectin/Necl trans heterodimerization / positive regulation of mast cell activation / regulation of viral entry into host cell ...sperm mitochondrion organization / susceptibility to T cell mediated cytotoxicity / coreceptor-mediated virion attachment to host cell / establishment of mitochondrion localization / susceptibility to natural killer cell mediated cytotoxicity / spermatid nucleus differentiation / positive regulation of immunoglobulin mediated immune response / Nectin/Necl trans heterodimerization / positive regulation of mast cell activation / regulation of viral entry into host cell / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / acrosome assembly / cilium organization / zonula adherens / adhesion of symbiont to host / positive regulation of natural killer cell mediated cytotoxicity / cell-cell contact zone / Adherens junctions interactions / fertilization / apical junction complex / positive regulation of T cell receptor signaling pathway / homophilic cell adhesion via plasma membrane adhesion molecules / spermatid development / coreceptor activity / cell adhesion molecule binding / cytoskeleton organization / establishment of localization in cell / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell-cell junction / virus receptor activity / fusion of virus membrane with host plasma membrane / focal adhesion / cell surface / protein homodimerization activity / extracellular exosome / identical protein binding / membrane / plasma membrane
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 / Immunoglobulin-like domain superfamily ...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 / 1NEU / Resolution: 1.3 Å
AuthorsRamagopal, U.A. / Samanta, D. / Nathenson, S.G. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) / Atoms-to-Animals: The Immune Function Network (IFN)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structure of Nectin-2 reveals determinants of homophilic and heterophilic interactions that control cell-cell adhesion.
Authors: Samanta, D. / Ramagopal, U.A. / Rubinstein, R. / Vigdorovich, V. / Nathenson, S.G. / Almo, S.C.
History
DepositionMar 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 5, 2012Group: Database references
Revision 1.3Sep 12, 2012Group: Structure summary
Revision 1.4Oct 3, 2012Group: Database references
Revision 1.5Nov 7, 2012Group: Data collection

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poliovirus receptor-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0113
Polymers13,9511
Non-polymers602
Water2,414134
1
A: Poliovirus receptor-related protein 2
hetero molecules

A: Poliovirus receptor-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0216
Polymers27,9022
Non-polymers1204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area2260 Å2
ΔGint-36 kcal/mol
Surface area12400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.964, 57.964, 67.544
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-155-

TRP

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Components

#1: Protein Poliovirus receptor-related protein 2 / Herpes virus entry mediator B / Herpesvirus entry mediator B / HveB / Nectin-2


Mass: 13950.778 Da / Num. of mol.: 1 / Fragment: Ig-like V-type domain residues 32-158
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HVEB, PRR2, PVRL2 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q92692
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M MgCl2.6H20, 0.1M TRIS hydrochloride pH 8.5, 30% PEG 4000, Vapor diffusion, Sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.3→28.9 Å / Num. obs: 28989 / % possible obs: 100 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.049 / Χ2: 0.996 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.3-1.327.30.53514110.915199.9
1.32-1.358.60.49414200.8991100
1.35-1.3710.20.4314110.9221100
1.37-1.412.60.36514090.9331100
1.4-1.4315.40.33914340.9521100
1.43-1.4615.40.28714220.9681100
1.46-1.515.50.23514271.0091100
1.5-1.5415.50.19514351.0151100
1.54-1.5915.50.15714231.0381100
1.59-1.6415.60.14214371.0431100
1.64-1.715.60.11814241.0071100
1.7-1.7615.60.092144611100
1.76-1.8415.60.07214420.9661100
1.84-1.9415.50.05414550.9221100
1.94-2.0615.50.04314530.8891100
2.06-2.2215.50.04114630.9351100
2.22-2.4515.40.04814591.3411100
2.45-2.815.20.04814871.5841100
2.8-3.5314.60.02915070.8591100
3.53-5014.30.02316240.59199.6

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: 1NEU / Resolution: 1.3→28.9 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.972 / WRfactor Rfree: 0.172 / WRfactor Rwork: 0.1519 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.9184 / SU B: 1.233 / SU ML: 0.025 / SU R Cruickshank DPI: 0.0576 / SU Rfree: 0.0499 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.05 / Phase error: 26.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY : SYMMETRY VIOLATING CLASH FOUND BETWEEN ONE OF THE ROTAMERS (~ 50% OCCUPANCY) OF TRP-155.
RfactorNum. reflection% reflectionSelection details
Rfree0.1733 1423 5.1 %RANDOM
Rwork0.1523 ---
obs0.1534 28078 97.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 93.64 Å2 / Biso mean: 18.2627 Å2 / Biso min: 7.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2--0.16 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.3→28.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms980 0 2 134 1116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221148
X-RAY DIFFRACTIONr_angle_refined_deg1.311.961588
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6645156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.69824.450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04715183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.32157
X-RAY DIFFRACTIONr_chiral_restr0.0790.2170
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022928
X-RAY DIFFRACTIONr_mcbond_it1.271.5727
X-RAY DIFFRACTIONr_mcangle_it2.1221199
X-RAY DIFFRACTIONr_scbond_it2.7573421
X-RAY DIFFRACTIONr_scangle_it4.3644.5388
X-RAY DIFFRACTIONr_rigid_bond_restr1.20431148
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 73 -
Rwork0.208 1279 -
all-1352 -
obs--65.09 %

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