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- PDB-2jsn: Solution structure of the atypical PDZ-like domain of synbindin -

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Basic information

Entry
Database: PDB / ID: 2jsn
TitleSolution structure of the atypical PDZ-like domain of synbindin
ComponentsTrafficking protein particle complex subunit 4
KeywordsPROTEIN TRANSPORT / Protein Interaction
Function / homology
Function and homology information


vesicle coating / vesicle tethering / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / COPII vesicle coating / Golgi stack / RAB GEFs exchange GTP for GDP on RABs / COPII-mediated vesicle transport / Syndecan interactions ...vesicle coating / vesicle tethering / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / COPII vesicle coating / Golgi stack / RAB GEFs exchange GTP for GDP on RABs / COPII-mediated vesicle transport / Syndecan interactions / dendrite development / endoplasmic reticulum to Golgi vesicle-mediated transport / autophagy / synaptic vesicle / postsynaptic membrane / Golgi membrane / dendrite / synapse / endoplasmic reticulum / cytosol / cytoplasm
Similarity search - Function
Pdz3 Domain - #40 / Trafficking protein particle complex subunit / Sybindin-like family / Sybindin-like family / Longin-like domain superfamily / Pdz3 Domain / Roll / Mainly Beta
Similarity search - Domain/homology
Trafficking protein particle complex subunit 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics, simulated annealing
AuthorsFeng, Y. / Fan, S. / Gong, W. / Xia, B.
CitationJournal: PROTEIN AND PEPTIDE LETTERS / Year: 2009
Title: Solution structure of synbindin atypical PDZ domain and interaction with syndecan-2
Authors: Fan, S. / Feng, Y. / Wei, Z. / Xia, B. / Gong, W.
History
DepositionJul 10, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trafficking protein particle complex subunit 4


Theoretical massNumber of molelcules
Total (without water)10,8201
Polymers10,8201
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Trafficking protein particle complex subunit 4 / Synbindin / TRS23 homolog / Hematopoietic stem/progenitor cell protein 172


Mass: 10820.211 Da / Num. of mol.: 1 / Fragment: sequence database residues 19-106
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAPPC4, SBDN / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y296

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HNCA
1613D HNCO
1713D (H)CCH-TOCSY
1813D HBHA(CO)NH
1912D CB(CGCD)HD
11013D HN(CA)CO
11113D 1H-15N TOCSY
11213D 1H-15N NOESY
11313D 1H-13C NOESY
11413D (H)CCH-COSY
11513D CCH-TOCSY

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Sample preparation

DetailsContents: 1-1.5 mM [U-13C; U-15N] apd, 50 mM potassium phosphate, 0.01 % DSS, 0.01 % sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMapd[U-13C; U-15N]1
50 mMpotassium phosphate1
0.01 %DSS1
0.01 %sodium azide1
Sample conditionsIonic strength: 0.05 / pH: 6.0 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
XwinNMRBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
SANEDuggan, Legge, Dyson & Wrightrefinement
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollrefinement
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1
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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