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- PDB-4fmk: Crystal structure of mouse nectin-2 extracellular fragment D1-D2 -

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Basic information

Entry
Database: PDB / ID: 4fmk
TitleCrystal structure 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: 2.56 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 17, 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_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _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_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_atom_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 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)27,3227
Polymers24,9201
Non-polymers2,4016
Water64936
1
A: Poliovirus receptor-related protein 2
hetero molecules

A: Poliovirus receptor-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,64314
Polymers49,8402
Non-polymers4,80312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,x-y,-z1
Unit cell
Length a, b, c (Å)68.666, 68.666, 159.605
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112

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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: 24920.076 Da / Num. of mol.: 1 / Fragment: extracellular domain (D1-D2, UNP residues 32-250)
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 alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 4.36 Å3/Da / Density % sol: 71.78 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 6% w/v PEG6000, 0.05 M cadmium sulfate, 0.2 M sodium acetate, 0.1 M MES, pH 6.0, cryoprotectant: 15% 2R,3R-butane-di-ol, 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: Jul 6, 2011
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: 2.54→40 Å / Num. all: 14118 / Num. obs: 14118 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Rsym value: 0.06 / Net I/σ(I): 20.5
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.54-2.636.23.90.54199.4
2.63-2.74199.7
2.74-2.86199.7
2.86-3.01199.9
3.01-3.2199.9
3.2-3.45199.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ALP

3alp


Resolution: 2.56→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / SU B: 19.933 / SU ML: 0.225 / Cross valid method: THROUGHOUT / ESU R: 0.328 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26755 708 5 %RANDOM
Rwork0.22117 ---
all0.22332 14118 --
obs0.22332 14118 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 88.031 Å2
Baniso -1Baniso -2Baniso -3
1-4.63 Å22.32 Å2-0 Å2
2--4.63 Å2-0 Å2
3----6.95 Å2
Refinement stepCycle: LAST / Resolution: 2.56→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1717 0 135 36 1888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191902
X-RAY DIFFRACTIONr_bond_other_d0.0020.021294
X-RAY DIFFRACTIONr_angle_refined_deg1.6672.0352612
X-RAY DIFFRACTIONr_angle_other_deg1.0943.0033100
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3115220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.71221.95182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.67715272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5211522
X-RAY DIFFRACTIONr_chiral_restr0.0910.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212011
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02385
LS refinement shellResolution: 2.56→2.627 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.506 53 -
Rwork0.372 898 -
obs--98.04 %
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)
13.6904-0.4166-3.5026.119-1.715812.12480.13670.0601-0.3477-0.18560.1807-0.16440.28310.008-0.31740.1830.0071-0.04210.150.00950.1112-2.1263-6.594212.4698
24.93343.6785-2.27579.4149-5.24916.4137-0.00120.4302-0.2286-0.45580.3360.4310.6556-0.7015-0.33480.3535-0.0340.0580.5670.29140.3846-25.7599-26.635941.3354
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 149
2X-RAY DIFFRACTION2A150 - 253

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