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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 vascular endothelial growth factor signaling pathway / negative regulation of peptidyl-tyrosine phosphorylation / vascular endothelial growth factor receptor 1 binding / cell-cell contact zone / regulation of Rac protein signal transduction / vascular endothelial growth factor receptor 2 binding / regulation of wound healing / negative regulation of peptidyl-threonine phosphorylation / negative regulation of vascular endothelial growth factor receptor signaling pathway / cell leading edge ...negative regulation of vascular endothelial growth factor signaling pathway / negative regulation of peptidyl-tyrosine phosphorylation / vascular endothelial growth factor receptor 1 binding / cell-cell contact zone / regulation of Rac protein signal transduction / vascular endothelial growth factor receptor 2 binding / regulation of wound healing / negative regulation of peptidyl-threonine phosphorylation / negative regulation of vascular endothelial growth factor receptor signaling pathway / cell leading edge / regulation of cell motility / regulation of protein phosphorylation / negative regulation of protein phosphorylation / receptor tyrosine kinase binding / regulation of cell population proliferation / protein phosphatase binding / cell adhesion / integral component of membrane
Immunoglobulin domain / Neurexin/syndecan/glycophorin C / Ig-like domain profile. / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin-like domain superfamily / Cell adhesion molecule 4 / Immunoglobulin-like fold / CD80-like, immunoglobulin C2-set / Immunoglobulin V-set domain ...Immunoglobulin domain / Neurexin/syndecan/glycophorin C / Ig-like domain profile. / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin-like domain superfamily / Cell adhesion molecule 4 / Immunoglobulin-like fold / CD80-like, immunoglobulin C2-set / Immunoglobulin V-set domain / Immunoglobulin-like domain / Immunoglobulin subtype / Immunoglobulin subtype 2
Cell adhesion molecule 4
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. / Yin, B. / Wojdyla, J.A. / Wang, M. / Yuan, J. / Qiang, B. / Shu, P. / Cui, S. / Peng, X.
Funding supportChina , 2件
OrganizationGrant numberCountry
National Key Research and Development Program2016YFA0100702, 2016YFC092502China
National Key Basic Research Program2013CB531304China
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 12, 2018 / Release: Jan 30, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 30, 2019Structure modelrepositoryInitial release
1.1Feb 6, 2019Structure modelData collection / Database referencescitation / citation_author_citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
1.2Feb 20, 2019Structure modelData collection / Database referencescitation / citation_author_citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell adhesion molecule 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0946
Polymers33,3031
Non-polymers7915
Water3,387188
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint12 kcal/mol
Surface area16720 Å2
Unit cell
γ
α
β
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/peptide 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: Chemical ChemComp-FUC / ALPHA-L-FUCOSE


Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
#3: Chemical ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / N-Acetylglucosamine
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O / Water

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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

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.0082372
f_angle_d1.7833239
f_dihedral_angle_d13.2031452
f_chiral_restr0.063372
f_plane_restr0.006427
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2008-2.27950.29471420.2517259997
2.2795-2.37070.26241480.23972640100
2.3707-2.47860.24521390.22312674100
2.4786-2.60930.25281540.20742676100
2.6093-2.77280.23411400.19922661100
2.7728-2.98680.21491260.19492701100
2.9868-3.28730.19811460.18182684100
3.2873-3.76290.19431250.18752745100
3.7629-4.74010.1841230.16912766100
4.7401-47.30550.23931430.22522894100

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