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- PDB-2n04: Solution Structure of the phosphorylated N-terminal region of Hum... -

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Basic information

Entry
Database: PDB / ID: 2n04
TitleSolution Structure of the phosphorylated N-terminal region of Human Cysteine String Protein (CSP)
ComponentsDnaJ homolog subfamily C member 5
KeywordsCHAPERONE / phosphorylation / DnaJ
Function / homology
Function and homology information


clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / chromaffin granule membrane / regulated exocytosis / GABA synthesis, release, reuptake and degradation / regulation of synaptic vesicle cycle / ATP-dependent protein binding / Sensory processing of sound by inner hair cells of the cochlea / azurophil granule membrane / exocytosis / synaptic vesicle exocytosis ...clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / chromaffin granule membrane / regulated exocytosis / GABA synthesis, release, reuptake and degradation / regulation of synaptic vesicle cycle / ATP-dependent protein binding / Sensory processing of sound by inner hair cells of the cochlea / azurophil granule membrane / exocytosis / synaptic vesicle exocytosis / specific granule membrane / chaperone-mediated protein folding / neuromuscular junction / synaptic vesicle membrane / melanosome / presynapse / neuron apoptotic process / negative regulation of neuron apoptotic process / lysosomal membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / Golgi apparatus / mitochondrion / membrane / plasma membrane / cytosol
Similarity search - Function
: / DnaJ domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Helix Hairpins ...: / DnaJ domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DnaJ homolog subfamily C member 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsPatel, P. / Lian, L. / Morgan, A. / Burgoyne, R.
CitationJournal: Structure / Year: 2016
Title: Phosphorylation of Cysteine String Protein Triggers a Major Conformational Switch.
Authors: Patel, P. / Prescott, G.R. / Burgoyne, R.D. / Lian, L.Y. / Morgan, A.
History
DepositionMar 4, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Aug 24, 2016Group: Database references
Revision 1.3Jun 14, 2023Group: 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 / struct_conn / 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 / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DnaJ homolog subfamily C member 5


Theoretical massNumber of molelcules
Total (without water)11,9841
Polymers11,9841
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 lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein DnaJ homolog subfamily C member 5 / Cysteine string protein / CSP


Mass: 11984.200 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNAJC5, CSP / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H3Z4

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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
1312D 1H-13C HSQC aromatic
1413D HNCA
1513D HN(CO)CA
1613D HN(CA)CB
1713D CBCA(CO)NH
1813D HNCO
1913D HCACO
11013D HBHANH
11113D HBHA(CO)NH
11213D (H)CCH-TOCSY
11313D 1H-15N NOESY
11413D 1H-13C NOESY
11513D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 0.5 mM [U-13C; U-15N] Phosphorylated DnaJ domain of cysteine-string protein, 20 mM MES, 150 mM sodium chloride, 1 mM DTT, 10 mM MgCl2, 0.5 mM EDTA, 0.73 nM PKA, 1 mM ATP, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMPhosphorylated DnaJ domain of cysteine-string protein-1[U-13C; U-15N]1
20 mMMES-21
150 mMsodium chloride-31
1 mMDTT-41
10 mMMgCl2-51
0.5 mMEDTA-61
0.00073 uMPKA-71
1 mMATP-81
Sample conditionsIonic strength: 0.15 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CCPN_AnalysisCCPNchemical shift assignment
CCPN_AnalysisCCPNpeak picking
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: 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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