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- PDB-2eeg: Solution Structure of PDZ domain of PDZ and LIM domain protein -

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Basic information

Entry
Database: PDB / ID: 2eeg
TitleSolution Structure of PDZ domain of PDZ and LIM domain protein
ComponentsPDZ and LIM domain protein 4
KeywordsMETAL BINDING PROTEIN / pdz domain / pdz and lim domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


recycling endosome lumen / muscle structure development / excitatory chemical synaptic transmission / muscle alpha-actinin binding / filamentous actin / alpha-actinin binding / stress fiber / early endosome lumen / adherens junction / Z disc ...recycling endosome lumen / muscle structure development / excitatory chemical synaptic transmission / muscle alpha-actinin binding / filamentous actin / alpha-actinin binding / stress fiber / early endosome lumen / adherens junction / Z disc / recycling endosome membrane / lamellipodium / actin cytoskeleton / actin binding / heart development / actin cytoskeleton organization / early endosome membrane / protein phosphatase binding / dendritic spine / postsynaptic membrane / cytoskeleton / perinuclear region of cytoplasm / protein homodimerization activity / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Domain of unknown function DUF4749 / Domain of unknown function (DUF4749) / : / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / PDZ domain / Pdz3 Domain ...Domain of unknown function DUF4749 / Domain of unknown function (DUF4749) / : / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / 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
PDZ and LIM domain protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsNiraula, T.N. / Tomizawa, T. / Koshiba, K. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be published
Title: Solution Structure of PDZ domain of PDZ and LIM domain protein
Authors: Niraula, T.N. / Tomizawa, T. / Koshiba, K. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionFeb 15, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 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: PDZ and LIM domain protein 4


Theoretical massNumber of molelcules
Total (without water)9,6051
Polymers9,6051
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 violations, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein PDZ and LIM domain protein 4 / LIM protein RIL / Reversion-induced LIM protein


Mass: 9604.780 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: PDLIM4 / Plasmid: P050627-04 / References: UniProt: P50479

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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: 2.64mM PDZ domain U-13C,15N; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D20, 90% H2O
Solvent system: 10% D20, 90% H2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 296 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.982Kobayashi, 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 violations, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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