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- PDB-2l7j: Solution structure of the third Immunoglobulin-like domain of nectin-1 -

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Basic information

Entry
Database: PDB / ID: 2l7j
TitleSolution structure of the third Immunoglobulin-like domain of nectin-1
ComponentsPoliovirus receptor-related 1
KeywordsMEMBRANE PROTEIN / cellular adhesion molecule
Function / homology
Function and homology information


Nectin/Necl trans heterodimerization / desmosome organization / protein localization to cell junction / Adherens junctions interactions / lens morphogenesis in camera-type eye / growth cone membrane / enamel mineralization / camera-type eye morphogenesis / cell-cell contact zone / virion binding ...Nectin/Necl trans heterodimerization / desmosome organization / protein localization to cell junction / Adherens junctions interactions / lens morphogenesis in camera-type eye / growth cone membrane / enamel mineralization / camera-type eye morphogenesis / cell-cell contact zone / virion binding / apical junction complex / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of synapse assembly / homophilic cell adhesion via plasma membrane adhesion molecules / cell adhesion molecule binding / adherens junction / axon guidance / cell-cell adhesion / retina development in camera-type eye / presynaptic membrane / signaling receptor activity / iron ion transport / carbohydrate binding / membrane => GO:0016020 / neuron projection / symbiont entry into host cell / axon / intracellular membrane-bounded organelle / synapse / dendrite / protein-containing complex binding / virion attachment to host cell / protein homodimerization activity / identical protein binding / plasma membrane
Similarity search - Function
Nectin-1 / Nectin-1, first immunoglobulin (Ig) domain / Nectin-1, second immunoglobulin (Ig) domain / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain ...Nectin-1 / Nectin-1, first immunoglobulin (Ig) domain / Nectin-1, second immunoglobulin (Ig) domain / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsClausen, O. / Poulsen, F.M.
CitationJournal: To be Published
Title: Solution structure of the third Immunoglobulin-like domain of nectin-1
Authors: Clausen, O. / Poulsen, F.M.
History
DepositionDec 13, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poliovirus receptor-related 1


Theoretical massNumber of molelcules
Total (without water)10,6001
Polymers10,6001
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Poliovirus receptor-related 1 /


Mass: 10599.743 Da / Num. of mol.: 1 / Fragment: UNP residues 241-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: C57BL/6 / Gene: Pvrl1 / Production host: Pichia pastoris (fungus) / Strain (production host): KM71H / References: UniProt: Q6P9M9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HNCA
1413D HN(CO)CA
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D H(CCO)NH
1813D (H)CCH-TOCSY
1913D 1H-15N TOCSY
11013D 1H-15N NOESY
11113D 1H-13C NOESY

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Sample preparation

DetailsContents: 10 mM sodium phosphate, 50 mM sodium chloride, 0.02 v/v sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
10 mMsodium phosphate-11
50 mMsodium chloride-21
0.02 v/vsodium azide-31
Sample conditionsIonic strength: 0.0 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 750 MHz

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Processing

NMR software
NameDeveloperClassification
VNMRVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ProntoKjur, Andersen and Poulsenchemical shift assignment
ProntoKjur, Andersen and Poulsenpeak picking
TALOSCornilescu, Delaglio and Baxdata analysis
ARIALinge, O'Donoghue and Nilgesrefinement
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1418 / NOE intraresidue total count: 311 / NOE long range total count: 645 / NOE medium range total count: 119 / NOE sequential total count: 403
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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