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- PDB-5zo1: Crystal structure of mouse nectin-like molecule 4 (mNecl-4) full ... -

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Basic information

Entry
Database: PDB / ID: 5zo1
TitleCrystal structure of mouse nectin-like molecule 4 (mNecl-4) full ectodomain (Ig1-Ig3), 2.2A
ComponentsCell adhesion molecule 4
KeywordsCELL ADHESION / cell adhesion molecule / glycoprotein / Ig-like domain / Necl4 / Necl / Nectin / Nectin-Like Molecules / CADM / Native-SAD / disulfide bridges / SynCAM4 / Schwann cell / myelogenesis
Function / homology
Function and homology information


negative regulation of peptidyl-tyrosine phosphorylation / vascular endothelial growth factor receptor 1 binding / negative regulation of vascular endothelial growth factor signaling pathway / regulation of Rac protein signal transduction / synaptic membrane adhesion / 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 ...negative regulation of peptidyl-tyrosine phosphorylation / vascular endothelial growth factor receptor 1 binding / negative regulation of vascular endothelial growth factor signaling pathway / regulation of Rac protein signal transduction / synaptic membrane adhesion / 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 / negative regulation of vascular endothelial growth factor receptor signaling pathway / cell leading edge / regulation of protein phosphorylation / negative regulation of protein phosphorylation / synaptic membrane / receptor tyrosine kinase binding / regulation of cell population proliferation / protein phosphatase binding
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
Similarity search - Domain/homology
Cell adhesion molecule 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.201 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, 2016YFC092502 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.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _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 / pdbx_struct_special_symmetry / 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 / _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_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 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell adhesion molecule 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0584
Polymers33,3031
Non-polymers7553
Water3,387188
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint12 kcal/mol
Surface area16720 Å2
Unit cell
Length a, b, c (Å)109.497, 109.497, 182.441
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-617-

HOH

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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.: 1 / Fragment: ectodomain Ig1-Ig3 / Mutation: N31Q, N262Q, N286Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Tissue: Brain, Kidney, and Spleen / Gene: Cadm4, Igsf4c, Necl4, Tsll2 / Organ: Brain, Kidney, and Spleen / Plasmid: pFast-bac1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8R464
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 4.11 Å3/Da / Density % sol: 70.04 % / Description: Rod-like crystals
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.04M Potassium dihydrogen phosphate, 10% PEG 8000, 25% (v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→47.295 Å / Num. obs: 28426 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.93 % / Biso Wilson estimate: 37.01 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.144 / Χ2: 0.99 / Net I/σ(I): 12.15
Reflection shellResolution: 2.2→2.33 Å / Redundancy: 6.79 % / Rmerge(I) obs: 0.943 / Mean I/σ(I) obs: 2.02 / Num. unique obs: 8531 / CC1/2: 0.678 / Χ2: 0.92 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.201→47.295 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.31
RfactorNum. reflection% reflectionSelection details
Rfree0.2199 1386 4.88 %Random
Rwork0.1998 ---
obs0.2007 28426 99.74 %-
Displacement parametersBiso mean: 48.64 Å2
Refinement stepCycle: LAST / Resolution: 2.201→47.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 50 188 2482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082372
X-RAY DIFFRACTIONf_angle_d1.7833239
X-RAY DIFFRACTIONf_dihedral_angle_d13.2031452
X-RAY DIFFRACTIONf_chiral_restr0.063372
X-RAY DIFFRACTIONf_plane_restr0.006427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2008-2.27950.29471420.25172599X-RAY DIFFRACTION97
2.2795-2.37070.26241480.23972640X-RAY DIFFRACTION100
2.3707-2.47860.24521390.22312674X-RAY DIFFRACTION100
2.4786-2.60930.25281540.20742676X-RAY DIFFRACTION100
2.6093-2.77280.23411400.19922661X-RAY DIFFRACTION100
2.7728-2.98680.21491260.19492701X-RAY DIFFRACTION100
2.9868-3.28730.19811460.18182684X-RAY DIFFRACTION100
3.2873-3.76290.19431250.18752745X-RAY DIFFRACTION100
3.7629-4.74010.1841230.16912766X-RAY DIFFRACTION100
4.7401-47.30550.23931430.22522894X-RAY DIFFRACTION100

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