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- PDB-4fs0: Crystal structure of mutant F136D of mouse nectin-2 extracellular... -

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Basic information

Entry
Database: PDB / ID: 4fs0
TitleCrystal structure of mutant F136D of mouse nectin-2 extracellular fragment D1-D2
ComponentsPoliovirus receptor-related protein 2
KeywordsCELL ADHESION / Immunoglobulin-like domain / Ig domain / viral entry receptor
Function / homology
Function and homology information


cellular anatomical entity morphogenesis / Nectin/Necl trans heterodimerization / coreceptor-mediated virion attachment to host cell / establishment of mitochondrion localization / sperm mitochondrion organization / positive regulation of immunoglobulin mediated immune response / positive regulation of mast cell activation / susceptibility to T cell mediated cytotoxicity / susceptibility to natural killer cell mediated cytotoxicity / regulation of viral entry into host cell ...cellular anatomical entity morphogenesis / Nectin/Necl trans heterodimerization / coreceptor-mediated virion attachment to host cell / establishment of mitochondrion localization / sperm mitochondrion organization / positive regulation of immunoglobulin mediated immune response / positive regulation of mast cell activation / susceptibility to T cell mediated cytotoxicity / susceptibility to natural killer cell mediated cytotoxicity / regulation of viral entry into host cell / spermatid nucleus differentiation / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / acrosome assembly / Adherens junctions interactions / zonula adherens / cilium organization / cell-cell contact zone / negative regulation of natural killer cell mediated cytotoxicity / fertilization / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / natural killer cell mediated cytotoxicity / apical junction complex / positive regulation of T cell receptor signaling pathway / homophilic cell-cell adhesion / spermatid development / cell adhesion molecule binding / cytoskeleton organization / establishment of localization in cell / cell-cell junction / receptor ligand activity / fusion of virus membrane with host plasma membrane / cell surface / protein homodimerization activity / identical protein binding / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsHarrison, O.J. / Brasch, J. / Shapiro, L.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Nectin ectodomain structures reveal a canonical adhesive interface.
Authors: Harrison, O.J. / Vendome, J. / Brasch, J. / Jin, X. / Hong, S. / Katsamba, P.S. / Ahlsen, G. / Troyanovsky, R.B. / Troyanovsky, S.M. / Honig, B. / Shapiro, L.
History
DepositionJun 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: Database references
Revision 1.2Sep 26, 2012Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5553
Polymers24,8881
Non-polymers6672
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.857, 59.857, 210.013
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-403-

HOH

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Components

#1: Protein Poliovirus receptor-related protein 2 / Nectin-2 / Herpes virus entry mediator B / Herpesvirus entry mediator B / HveB / Murine herpes ...Nectin-2 / Herpes virus entry mediator B / Herpesvirus entry mediator B / HveB / Murine herpes virus entry protein B / mHveB / Poliovirus receptor homolog


Mass: 24887.990 Da / Num. of mol.: 1 / Fragment: extracellular domain (D1-D2, UNP residues 32-250) / Mutation: F136D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pvrl2, Mph, Pvr, Pvs / Plasmid: pCEP4 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: P32507
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.18 Å3/Da / Density % sol: 43.63 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1 M lithium sulfate, 0.6 M ammonium sulfate, 0.1 M tri-sodium citrate, pH 5.5, cryoprotectant: 30% w/v glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9792 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 3, 2012
RadiationMonochromator: Bent single Si(111) crystal (horizontal focusing and deflection)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.25→30 Å / Num. all: 19387 / Num. obs: 19387 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Rsym value: 0.11 / Net I/σ(I): 13.7
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsRsym valueDiffraction-ID% possible all
3.25-3.375.72.50.35193.2
3.37-3.5199.5
3.5-3.661100
3.66-3.85199.7
3.85-4.091100
4.09-4.41199.7
4.41-4.851100
4.85-5.55199.8
5.55-6.981100
6.98-30199.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FMK

4fmk


Resolution: 3.25→20 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.789 / SU B: 77.143 / SU ML: 0.641 / Cross valid method: THROUGHOUT / ESU R Free: 0.794 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33476 375 9.6 %RANDOM
Rwork0.24033 ---
all0.24979 19387 --
obs0.24979 3532 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.836 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å20.89 Å20 Å2
2--1.78 Å20 Å2
3----2.68 Å2
Refinement stepCycle: LAST / Resolution: 3.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1684 0 43 12 1739
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191767
X-RAY DIFFRACTIONr_bond_other_d0.0030.021215
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.9872416
X-RAY DIFFRACTIONr_angle_other_deg1.133.0032919
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8275217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.5222.15279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.06315269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0821522
X-RAY DIFFRACTIONr_chiral_restr0.0770.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211950
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02369
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.25→3.335 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 14 -
Rwork0.297 165 -
obs--84.43 %
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)
17.4289-2.35393.89193.2353-1.728410.3550.2182-0.8988-0.53070.4236-0.0201-0.22630.55510.0828-0.19810.3317-0.03930.01790.27040.0570.209223.7906-30.926115.8571
21.3367-0.382-0.87664.6442-5.43918.6669-0.02520.20060.16880.15270.22610.2685-0.3164-0.4595-0.20090.1142-0.0447-0.01250.2208-0.04370.19716.3013-9.899-19.4661
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 149
2X-RAY DIFFRACTION2A150 - 249

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