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- PDB-4hza: Crystal Structure of the Immunoglobulin variable domain of Nectin... -

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Basic information

Entry
Database: PDB / ID: 4hza
TitleCrystal Structure of the Immunoglobulin variable domain of Nectin-2 in monoclinic form
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 / MOLECULAR REPLACEMENT / Resolution: 1.7 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: To be published
Title: Crystal Structure of the Immunoglobulin variable domain of Nectin-2 in monoclinic form
Authors: Ramagopal, U.A. / Samanta, D. / Nathenson, S.G. / Almo, S.C.
History
DepositionNov 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Structure summary
Revision 1.2Sep 20, 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

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
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-8 kcal/mol
Surface area11570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.907, 49.261, 51.867
Angle α, β, γ (deg.)90.000, 116.980, 90.000
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 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.12 Å3/Da / Density % sol: 41.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M NaCl, 0.1M BIS-TRIS pH 5.5, 25% PEG 4K, 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: Jun 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. all: 25886 / Num. obs: 25886 / % possible obs: 100 % / Redundancy: 4.3 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.045 / Χ2: 0.922 / Net I/σ(I): 22
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.734.20.52512670.8561100
1.73-1.764.20.47812850.8651100
1.76-1.794.30.36913020.9061100
1.79-1.834.30.35912750.9071100
1.83-1.874.30.2812920.891100
1.87-1.914.30.22512740.9621100
1.91-1.964.30.18812760.97199.9
1.96-2.024.30.15313110.9571100
2.02-2.074.30.12612751.0081100
2.07-2.144.30.1112980.9751100
2.14-2.224.30.09412830.9611100
2.22-2.314.30.08512850.9361100
2.31-2.414.30.07312880.8841100
2.41-2.544.30.06413030.8511100
2.54-2.74.30.05913040.8841100
2.7-2.914.30.05513010.9791100
2.91-3.24.30.05113001.1561100
3.2-3.664.30.04413001.1071100
3.66-4.614.10.0313170.724199.9
4.61-404.20.0313500.651199.6

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RON

3ron


Resolution: 1.7→40 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.2189 / WRfactor Rwork: 0.1864 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.858 / SU B: 2.95 / SU ML: 0.076 / SU R Cruickshank DPI: 0.1357 / SU Rfree: 0.1279 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2259 1140 5 %RANDOM
Rwork0.1864 ---
obs0.1884 22736 87.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 57.9 Å2 / Biso mean: 18.7203 Å2 / Biso min: 3.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å2-0.26 Å2
2---0.17 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1906 0 0 119 2025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222077
X-RAY DIFFRACTIONr_angle_refined_deg2.0871.9752855
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3265270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.91623.6984
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.82915325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6161513
X-RAY DIFFRACTIONr_chiral_restr0.1580.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0221631
X-RAY DIFFRACTIONr_mcbond_it1.5071.51322
X-RAY DIFFRACTIONr_mcangle_it2.68722164
X-RAY DIFFRACTIONr_scbond_it3.9513755
X-RAY DIFFRACTIONr_scangle_it6.574.5691
LS refinement shellResolution: 1.696→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 39 -
Rwork0.224 778 -
all-817 -
obs--42.64 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3163-0.20710.12031.09270.560.76320.0458-0.01880.0129-0.0644-0.01650.00790.0056-0.0524-0.02930.00330.00420.00330.0415-0.00670.0545-3.1460.02513.681
22.9243-0.27120.53150.1949-0.05990.48210.09260.0016-0.05-0.0178-0.02080.01130.04930.0228-0.07180.0227-0.0038-0.00050.0164-0.00220.068216.866-11.46612.5
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 158
2X-RAY DIFFRACTION2B31 - 158

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