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- PDB-2dkr: Solution structure of the PDZ domain from human Lin-7 homolog B -

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Basic information

Entry
Database: PDB / ID: 2dkr
TitleSolution structure of the PDZ domain from human Lin-7 homolog B
ComponentsLIN-7 homolog B
KeywordsPROTEIN TRANSPORT / Lin-7b / PDZ / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


protein localization to basolateral plasma membrane / L27 domain binding / MPP7-DLG1-LIN7 complex / maintenance of epithelial cell apical/basal polarity / Dopamine Neurotransmitter Release Cycle / RHO GTPases Activate Rhotekin and Rhophilins / neurotransmitter secretion / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / exocytosis ...protein localization to basolateral plasma membrane / L27 domain binding / MPP7-DLG1-LIN7 complex / maintenance of epithelial cell apical/basal polarity / Dopamine Neurotransmitter Release Cycle / RHO GTPases Activate Rhotekin and Rhophilins / neurotransmitter secretion / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / exocytosis / bicellular tight junction / PDZ domain binding / postsynaptic density membrane / cell-cell junction / protein transport / presynapse / basolateral plasma membrane / protein domain specific binding / synapse / protein kinase binding / plasma membrane
Similarity search - Function
Protein lin-7 / : / L27 domain, C-terminal / L27 domain / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / PDZ domain / Pdz3 Domain ...Protein lin-7 / : / L27 domain, C-terminal / L27 domain / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Protein lin-7 homolog B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSuetake, T. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the PDZ domain from human Lin-7 homolog B
Authors: Suetake, T. / Hayashi, F. / Yokoyama, S.
History
DepositionApr 14, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LIN-7 homolog B


Theoretical massNumber of molelcules
Total (without water)9,4811
Polymers9,4811
Non-polymers00
Water00
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 least restraint violation, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein LIN-7 homolog B / LIN-7B / hLin7B / Mammalian LIN-seven protein 2 / MALS-2 / Vertebrate LIN 7 homolog 2 / Veli-2 ...LIN-7B / hLin7B / Mammalian LIN-seven protein 2 / MALS-2 / Vertebrate LIN 7 homolog 2 / Veli-2 protein / hVeli2


Mass: 9480.609 Da / Num. of mol.: 1 / Fragment: PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cell free protein synthesis / Gene: LIN7B, MALS2, VELI2, UNQ3116/PRO10200 / Plasmid: P050516-07 / Production host: Cell free synthesis / References: UniProt: Q9HAP6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1.12mM 13C, 15N-labeled protein; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3, 90% H2O; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVARIANcollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.9321Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violation, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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