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- PDB-5zo2: Crystal structure of mouse nectin-like molecule 4 (mNecl-4) full ... -

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Basic information

Entry
Database: PDB / ID: 5zo2
TitleCrystal structure of mouse nectin-like molecule 4 (mNecl-4) full ectodomain in complex with mouse nectin-like molecule 1 (mNecl-1) Ig1 domain, 3.3A
Components
  • Cell adhesion molecule 3
  • Cell adhesion molecule 4
KeywordsCELL ADHESION / cell adhesion molecule / glycoprotein / Ig domain / SynCam / CADM / Nectin-like / Necl-4 / Necl-1 / axon / Schwann Cell / Molecular Replacement / myelogenesis / heterogeneous dimer
Function / homology
Function and homology information


negative regulation of peptidyl-tyrosine phosphorylation / Nectin/Necl trans heterodimerization / vascular endothelial growth factor receptor 1 binding / negative regulation of vascular endothelial growth factor signaling pathway / Adherens junctions interactions / regulation of Rac protein signal transduction / cell-cell contact zone / regulation of wound healing / negative regulation of peptidyl-threonine phosphorylation / regulation of cell motility ...negative regulation of peptidyl-tyrosine phosphorylation / Nectin/Necl trans heterodimerization / vascular endothelial growth factor receptor 1 binding / negative regulation of vascular endothelial growth factor signaling pathway / Adherens junctions interactions / regulation of Rac protein signal transduction / cell-cell contact zone / regulation of wound healing / negative regulation of peptidyl-threonine phosphorylation / regulation of cell motility / vascular endothelial growth factor receptor 2 binding / heterophilic cell-cell adhesion / negative regulation of vascular endothelial growth factor receptor signaling pathway / parallel fiber to Purkinje cell synapse / homophilic cell-cell adhesion / negative regulation of protein phosphorylation / cell leading edge / regulation of protein phosphorylation / receptor tyrosine kinase binding / cell-cell junction / intracellular protein localization / regulation of cell population proliferation / presynaptic membrane / protein phosphatase binding / cell adhesion / protein homodimerization activity / membrane
Similarity search - Function
Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype ...Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 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
Cell adhesion molecule 4 / Cell adhesion molecule 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.29 Å
AuthorsLiu, X. / An, T. / Li, D. / Fan, Z. / Xiang, P. / Li, C. / Ju, W. / Li, J. / Hu, G. / Qin, B. ...Liu, X. / An, T. / Li, D. / Fan, Z. / Xiang, P. / Li, C. / Ju, W. / Li, J. / Hu, G. / Qin, B. / Yin, B. / Wojdyla, J.A. / Wang, M. / Yuan, J. / Qiang, B. / Shu, P. / Cui, S. / Peng, X.
Funding support China, 2items
OrganizationGrant numberCountry
National Key Research and Development Program2016YFA0100702,2016YFC0902502 China
National Key Basic Research Program2013CB531304 China
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Structure of the heterophilic interaction between the nectin-like 4 and nectin-like 1 molecules.
Authors: Liu, X. / An, T. / Li, D. / Fan, Z. / Xiang, P. / Li, C. / Ju, W. / Li, J. / Hu, G. / Qin, B. / Yin, B. / Wojdyla, J.A. / Wang, M. / Yuan, J. / Qiang, B. / Shu, P. / Cui, S. / Peng, X.
History
DepositionApr 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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 / struct_asym / struct_conn / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 13, 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: Cell adhesion molecule 4
C: Cell adhesion molecule 4
B: Cell adhesion molecule 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1764
Polymers82,6053
Non-polymers5711
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint4 kcal/mol
Surface area31980 Å2
Unit cell
Length a, b, c (Å)207.483, 207.483, 52.937
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-274-

GLU

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Components

#1: Protein Cell adhesion molecule 4 / Immunoglobulin superfamily member 4C / IgSF4C / Nectin-like protein 4 / NECL-4 / TSLC1-like protein 2


Mass: 33303.145 Da / Num. of mol.: 2 / Fragment: extracellular domains (Ig1-Ig3) / Mutation: N31Q, N262Q, N286Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Tissue: Brain Kidney Spleen / Gene: Cadm4, Igsf4c, Necl4, Tsll2 / Organ: Brain Kidney Spleen / Plasmid: pFast-Bac 1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8R464
#2: Protein Cell adhesion molecule 3 / Nectin-like protein 1 / Immunoglobulin superfamily member 4B / IgSF4B / NECL-1 / Synaptic cell ...Nectin-like protein 1 / Immunoglobulin superfamily member 4B / IgSF4B / NECL-1 / Synaptic cell adhesion molecule 3 / TSLC1-like protein 1


Mass: 15998.754 Da / Num. of mol.: 1 / Fragment: Ig domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Tissue: Brain / Gene: Cadm3, Igsf4b, Necl1, Syncam3, Tsll1 / Organ: Brain / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / References: UniProt: Q99N28
#3: 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
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: 3.98 Å3/Da / Density % sol: 75.78 % / Description: hexagonal prisms-like crystals
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M calcium acetate, 0.1M HEPES Sodium Salt ,pH7.5, 10% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97776 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 3.29→49.836 Å / Num. obs: 19407 / % possible obs: 97.19 % / Observed criterion σ(I): -3 / Redundancy: 5.68 % / Biso Wilson estimate: 64.79 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.224 / Χ2: 0.98 / Net I/σ(I): 6.96
Reflection shellResolution: 3.29→3.49 Å / Redundancy: 5.74 % / Rmerge(I) obs: 1.074 / Mean I/σ(I) obs: 1.64 / Num. unique obs: 3096 / CC1/2: 0.613 / Χ2: 0.89 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z9M

1z9m


Resolution: 3.29→49.84 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.49
RfactorNum. reflection% reflectionSelection details
Rfree0.302 1003 5.17 %Random
Rwork0.243 ---
obs0.246 19399 97.2 %-
Displacement parametersBiso mean: 65.7 Å2
Refinement stepCycle: LAST / Resolution: 3.29→49.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4553 0 38 0 4591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114681
X-RAY DIFFRACTIONf_angle_d1.6216383
X-RAY DIFFRACTIONf_dihedral_angle_d15.0932852
X-RAY DIFFRACTIONf_chiral_restr0.069738
X-RAY DIFFRACTIONf_plane_restr0.007839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2937-3.46730.38061420.30512591X-RAY DIFFRACTION98
3.4673-3.68450.37341250.28272645X-RAY DIFFRACTION98
3.6845-3.96890.35571640.2782624X-RAY DIFFRACTION98
3.9689-4.36810.28231310.22252656X-RAY DIFFRACTION98
4.3681-4.99960.26031430.20352607X-RAY DIFFRACTION97
4.9996-6.2970.24181380.22912636X-RAY DIFFRACTION97
6.297-49.84150.31051600.24442637X-RAY DIFFRACTION95

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