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- PDB-4dfh: Crystal structure of cell adhesion molecule nectin-2/CD112 variab... -

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Basic information

Entry
Database: PDB / ID: 4dfh
TitleCrystal structure of cell adhesion molecule nectin-2/CD112 variable domain
ComponentsPoliovirus receptor-related protein 2
KeywordsCELL ADHESION / DNAM-1 / cell surface
Function / homology
Function and homology information


coreceptor-mediated virion attachment to host cell / establishment of mitochondrion localization / sperm mitochondrion organization / positive regulation of immunoglobulin mediated immune response / susceptibility to T cell mediated cytotoxicity / positive regulation of mast cell activation / susceptibility to natural killer cell mediated cytotoxicity / spermatid nucleus differentiation / Nectin/Necl trans heterodimerization / regulation of viral entry into host cell ...coreceptor-mediated virion attachment to host cell / establishment of mitochondrion localization / sperm mitochondrion organization / positive regulation of immunoglobulin mediated immune response / susceptibility to T cell mediated cytotoxicity / positive regulation of mast cell activation / susceptibility to natural killer cell mediated cytotoxicity / spermatid nucleus differentiation / Nectin/Necl trans heterodimerization / regulation of viral entry into host cell / acrosome assembly / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / cilium organization / adhesion of symbiont to host / zonula adherens / positive regulation of natural killer cell mediated cytotoxicity / cell-cell contact zone / fertilization / Adherens junctions interactions / 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 ...: / 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 / AB INITIO PHASING / Resolution: 1.85 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 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

Downloads & links

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Assembly

Deposited unit
A: Poliovirus receptor-related protein 2
B: Poliovirus receptor-related protein 2


Theoretical massNumber of molelcules
Total (without water)27,9022
Polymers27,9022
Non-polymers00
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-11 kcal/mol
Surface area11750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.673, 43.850, 56.075
Angle α, β, γ (deg.)90.00, 118.24, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 2 / Fragment: Ig-like V-type domain, UNP residues 32-158
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HVEB, PRR2, PVRL2 / 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.: 300 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.04 Å3/Da / Density % sol: 39.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2M ammonium acetate, 0.1M Bis-Tris (pH 5.5), 25% 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: Jun 1, 2007 / 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: 19484 / % possible obs: 92.1 % / Observed criterion σ(F): 100 / Observed criterion σ(I): 35.419 / Biso Wilson estimate: 18.48 Å2
Reflection shellResolution: 1.8→1.86 Å / % possible all: 91.7

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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: AB INITIO PHASING / Resolution: 1.85→27.974 Å / FOM work R set: 0.8889 / SU ML: 0.19 / σ(F): 1.34 / Phase error: 17.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1942 995 5.11 %RANDOM
Rwork0.171 ---
all0.1942 ---
obs0.1722 19468 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.177 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 25.2073 Å2
Baniso -1Baniso -2Baniso -3
1-0.8439 Å2-0 Å22.635 Å2
2---1.0297 Å2-0 Å2
3---0.1857 Å2
Refinement stepCycle: LAST / Resolution: 1.85→27.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 0 300 2202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111969
X-RAY DIFFRACTIONf_angle_d0.9762688
X-RAY DIFFRACTIONf_dihedral_angle_d16.86722
X-RAY DIFFRACTIONf_chiral_restr0.074297
X-RAY DIFFRACTIONf_plane_restr0.005357
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8499-1.94740.22641520.1804258699
1.9474-2.06930.21131440.16922654100
2.0693-2.22910.1881270.16192615100
2.2291-2.45330.20591250.16772659100
2.4533-2.8080.20571540.1792600100
2.808-3.53660.18791550.15952640100
3.5366-27.97760.17361380.17332719100
Refinement TLS params.Method: refined / Origin x: -17.9454 Å / Origin y: 4.4239 Å / Origin z: 11.9557 Å
111213212223313233
T0.0624 Å2-0.0077 Å2-0.0077 Å2-0.0822 Å2-0.0146 Å2--0.0826 Å2
L0.5777 °2-0.3603 °2-0.4239 °2-0.5379 °20.4374 °2--0.9883 °2
S-0.0257 Å °0.0038 Å °-0.0755 Å °0.0322 Å °-0.0688 Å °0.113 Å °0.0144 Å °-0.1297 Å °0.0753 Å °
Refinement TLS groupSelection details: all

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