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- PDB-4dfi: Crystal structure of cell adhesion molecule nectin-2/CD112 mutant FAMP -

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Basic information

Entry
Database: PDB / ID: 4dfi
TitleCrystal structure of cell adhesion molecule nectin-2/CD112 mutant FAMP
ComponentsPoliovirus receptor-related protein 2
KeywordsCELL ADHESION / CD226 / cell surface
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLiu, J. / Qian, X. / Chen, Z. / Xu, X. / Gao, F. / Zhang, S. / Zhang, R. / Qi, J. / Gao, G.F. / Yan, J.
CitationJournal: J.Immunol. / Year: 2012
Title: Crystal Structure of Cell Adhesion Molecule Nectin-2/CD112 and Its Binding to Immune Receptor DNAM-1/CD226
Authors: Liu, J. / Qian, X. / Chen, Z. / Xu, X. / Gao, F. / Zhang, S. / Zhang, R. / Qi, J. / Gao, G.F. / Yan, J.
History
DepositionJan 23, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poliovirus receptor-related protein 2


Theoretical massNumber of molelcules
Total (without water)13,8531
Polymers13,8531
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.272, 45.780, 52.641
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 13852.526 Da / Num. of mol.: 1 / Fragment: Ig-like V-type domain, UNP residues 32-158 / Mutation: M59S, P64S, A113S, F115S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PVRL2, HVEB, PRR2 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q92692
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 1.88 Å3/Da / Density % sol: 34.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M ammonium sulfate, 0.1M Tris (pH 8.5), 25% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9783 Å
DetectorType: ENRAF-NONIUS / Detector: IMAGE PLATE / Date: Jan 1, 2011 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9783 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 9858 / % possible obs: 96.1 % / Observed criterion σ(F): 100 / Observed criterion σ(I): 35.419
Reflection shellResolution: 1.8→1.86 Å / % possible all: 88.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4DFH

4dfh


Resolution: 1.8→34.544 Å / FOM work R set: 0.8275 / SU ML: 0.12 / σ(F): 0.07 / Phase error: 23.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2368 447 4.83 %RANDOM
Rwork0.1974 ---
all0.2368 ---
obs0.1993 9250 91.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.908 Å2 / ksol: 0.379 e/Å3
Displacement parametersBiso mean: 23.4334 Å2
Baniso -1Baniso -2Baniso -3
1-8.5006 Å2-0 Å2-0 Å2
2---4.1011 Å20 Å2
3----4.3995 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.544 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms946 0 0 124 1070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016978
X-RAY DIFFRACTIONf_angle_d1.0671334
X-RAY DIFFRACTIONf_dihedral_angle_d19.051359
X-RAY DIFFRACTIONf_chiral_restr0.065149
X-RAY DIFFRACTIONf_plane_restr0.007177
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7993-2.05970.28791180.2122256581
2.0597-2.59480.24331710.2051295294
2.5948-34.55050.21921580.1896328698
Refinement TLS params.Method: refined / Origin x: -9.2438 Å / Origin y: 2.6187 Å / Origin z: -8.0156 Å
111213212223313233
T0.0882 Å20.0072 Å20.0089 Å2-0.0914 Å20.0004 Å2--0.0868 Å2
L0.5468 °20.0061 °2-0.3384 °2-0.5132 °20.3067 °2--0.713 °2
S0.003 Å °0.019 Å °0.0193 Å °0.0068 Å °-0.0054 Å °0.0265 Å °0.012 Å °-0.0334 Å °-0.009 Å °
Refinement TLS groupSelection details: all

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