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- PDB-5b22: Dimer structure of murine Nectin-3 D1D2 -

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Basic information

Entry
Database: PDB / ID: 5b22
TitleDimer structure of murine Nectin-3 D1D2
ComponentsNectin-3
KeywordsCELL ADHESION / cell-adhesion / immuboglobulin-like domain / adherens janction
Function / homology
Function and homology information


Nectin/Necl trans heterodimerization / retina morphogenesis in camera-type eye / establishment of protein localization to plasma membrane / regulation of postsynapse assembly / protein localization to cell junction / Adherens junctions interactions / lens morphogenesis in camera-type eye / cell-cell contact zone / fertilization / apical junction complex ...Nectin/Necl trans heterodimerization / retina morphogenesis in camera-type eye / establishment of protein localization to plasma membrane / regulation of postsynapse assembly / protein localization to cell junction / Adherens junctions interactions / lens morphogenesis in camera-type eye / cell-cell contact zone / fertilization / apical junction complex / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / homophilic cell adhesion via plasma membrane adhesion molecules / cell adhesion molecule binding / hippocampal mossy fiber to CA3 synapse / adherens junction / postsynaptic density membrane / cell-cell adhesion / cell-cell junction / cell adhesion / symbiont entry into host cell / axon / dendrite / protein homodimerization activity / plasma membrane
Similarity search - Function
Nectin-3 / Nectin-4 / : / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. ...Nectin-3 / Nectin-4 / : / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsTakebe, K. / Sangawa, T. / Katsutani, T. / Narita, H. / Suzuki, M.
CitationJournal: To Be Published
Title: Dimer structure of murine Nectin-3 D1D2
Authors: Sangawa, T. / Takebe, K. / Katsutani, T. / Narita, H. / Suzuki, M.
History
DepositionDec 28, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Category: chem_comp / diffrn_source
Item: _chem_comp.type / _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / struct_asym / struct_conn / 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 / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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 16, 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: Nectin-3
B: Nectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4284
Polymers46,2542
Non-polymers1,1732
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint8 kcal/mol
Surface area22330 Å2
Unit cell
Length a, b, c (Å)151.650, 72.880, 81.930
Angle α, β, γ (deg.)90.00, 116.36, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Nectin-3 / Nectin cell adhesion molecule 3 / Poliovirus receptor-related protein 3


Mass: 23127.213 Da / Num. of mol.: 2 / Fragment: UNP residues 59-266
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nectin3, Pvrl3 / Plasmid: pFastBac-1 / Cell line (production host): Sf-9 / Organ (production host): ovary / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9JLB9
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 4.39 Å3/Da / Density % sol: 71.95 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 22% PEG 3350, 100mM Imidazole pH7.0, 100mM Ammmonium citrate tribasic
PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.58→50 Å / Num. obs: 25302 / % possible obs: 99.7 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.5
Reflection shellHighest resolution: 2.58 Å / Redundancy: 3.1 % / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FOM

4fom


Resolution: 2.58→29.77 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2884 1277 5.05 %
Rwork0.2291 --
obs0.2321 25289 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.58→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3232 0 78 183 3493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113425
X-RAY DIFFRACTIONf_angle_d1.2684681
X-RAY DIFFRACTIONf_dihedral_angle_d18.5561251
X-RAY DIFFRACTIONf_chiral_restr0.065564
X-RAY DIFFRACTIONf_plane_restr0.007584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5801-2.68340.33431480.27292643X-RAY DIFFRACTION100
2.6834-2.80540.30581320.2592656X-RAY DIFFRACTION99
2.8054-2.95320.31021490.2612620X-RAY DIFFRACTION99
2.9532-3.1380.32541400.25842679X-RAY DIFFRACTION100
3.138-3.380.30711350.24692655X-RAY DIFFRACTION100
3.38-3.71960.30481590.23012654X-RAY DIFFRACTION100
3.7196-4.25650.27921430.21292656X-RAY DIFFRACTION99
4.2565-5.35760.241380.19412695X-RAY DIFFRACTION100
5.3576-29.77210.2751330.22382754X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 20.083 Å / Origin y: 0.381 Å / Origin z: 18.7608 Å
111213212223313233
T0.0724 Å2-0.0112 Å2-0.0062 Å2-0.0958 Å2-0.0228 Å2--0.0832 Å2
L0.0108 °20.0191 °2-0.0627 °2-0.0329 °2-0.0424 °2---0.0139 °2
S-0.1006 Å °0.1412 Å °-0.0211 Å °0.0959 Å °0.0534 Å °-0.0529 Å °-0.0568 Å °-0.0149 Å °-0 Å °
Refinement TLS groupSelection details: all

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