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- PDB-2la8: Solution structure of INAD PDZ5 complexed with Kon-tiki peptide -

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Basic information

Entry
Database: PDB / ID: 2la8
TitleSolution structure of INAD PDZ5 complexed with Kon-tiki peptide
ComponentsInactivation-no-after-potential D protein,kon-tiki peptide
KeywordsPEPTIDE BINDING PROTEIN
Function / homology
Function and homology information


Chondroitin sulfate biosynthesis / Dermatan sulfate biosynthesis / CS/DS degradation / A tetrasaccharide linker sequence is required for GAG synthesis / myosin III binding / detection of light stimulus involved in sensory perception / muscle attachment / inaD signaling complex / muscle tendon junction / negative regulation of opsin-mediated signaling pathway ...Chondroitin sulfate biosynthesis / Dermatan sulfate biosynthesis / CS/DS degradation / A tetrasaccharide linker sequence is required for GAG synthesis / myosin III binding / detection of light stimulus involved in sensory perception / muscle attachment / inaD signaling complex / muscle tendon junction / negative regulation of opsin-mediated signaling pathway / rhabdomere / myofibril assembly / cell tip / cellular response to light stimulus / costamere / muscle organ development / positive regulation of filopodium assembly / sarcomere organization / myosin binding / photoreceptor activity / phototransduction / visual perception / sensory perception of sound / protein localization / Z disc / signaling receptor complex adaptor activity / membrane => GO:0016020 / calmodulin binding
Similarity search - Function
CSPG repeat / CSPG repeat profile. / Laminin G domain / Laminin G domain profile. / Laminin G domain / Laminin G domain / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. ...CSPG repeat / CSPG repeat profile. / Laminin G domain / Laminin G domain profile. / Laminin G domain / Laminin G domain / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Inactivation-no-after-potential D protein / Kon-tiki, isoform B
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsZhang, M. / Wen, W.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: The INAD scaffold is a dynamic, redox-regulated modulator of signaling in the Drosophila eye
Authors: Liu, W. / Wen, W. / Wei, Z. / Yu, J. / Ye, F. / Liu, C.-H. / Hardie, R.C. / Zhang, M.
History
DepositionMar 8, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2020Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_nmr_software / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _pdbx_nmr_software.name ..._entity.pdbx_description / _pdbx_nmr_software.name / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
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: Inactivation-no-after-potential D protein,kon-tiki peptide


Theoretical massNumber of molelcules
Total (without water)11,5981
Polymers11,5981
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 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Inactivation-no-after-potential D protein,kon-tiki peptide


Mass: 11598.378 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Chimera of UNP residues 580-665 of INAD, linker, kon-tiki peptide
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: inaD, CG3504 / Production host: Escherichia coli (E. coli) / References: UniProt: Q24008, UniProt: Q9VJ82

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1242D 1H-1H NOESY
1342D 1H-1H TOCSY
1423D CBCA(CO)NH
1523D HN(CA)CB
1613D 1H-15N NOESY
1733D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] protein-1, 10 mM DTT-2, 50 mM TRIS-3, 50 mM sodium chloride-4, 1 mM EDTA-5, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] protein-6, 10 mM DTT-7, 50 mM TRIS-8, 50 mM sodium chloride-9, 1 mM EDTA-10, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-100% 13C; U-100% 15N] protein-11, 10 mM [U-100% 2H] DTT-12, 50 mM [U-100% 2H] TRIS-13, 50 mM sodium chloride-14, 1 mM EDTA-15, 100% D2O100% D2O
41 mM protein-16, 10 mM [U-100% 2H] DTT-17, 50 mM [U-100% 2H] TRIS-18, 50 mM sodium chloride-19, 1 mM EDTA-20, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMprotein-1[U-100% 15N]1
10 mMDTT-21
50 mMTRIS-31
50 mMsodium chloride-41
1 mMEDTA-51
1 mMprotein-6[U-100% 13C; U-100% 15N]2
10 mMDTT-72
50 mMTRIS-82
50 mMsodium chloride-92
1 mMEDTA-102
1 mMprotein-11[U-100% 13C; U-100% 15N]3
10 mMDTT-12[U-100% 2H]3
50 mMTRIS-13[U-100% 2H]3
50 mMsodium chloride-143
1 mMEDTA-153
1 mMprotein-164
10 mMDTT-17[U-100% 2H]4
50 mMTRIS-18[U-100% 2H]4
50 mMsodium chloride-194
1 mMEDTA-204
Sample conditionsIonic strength: 0.1 / pH: 7 / Pressure: ambient / Temperature: 303 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
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PIPPGarrettpeak picking
SparkyGoddardpeak picking
VnmrJVariancollection
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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