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- PDB-2l6l: Solution structure of human J-protein co-chaperone, Dph4 -

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Basic information

Entry
Database: PDB / ID: 2l6l
TitleSolution structure of human J-protein co-chaperone, Dph4
ComponentsDnaJ homolog subfamily C member 24
KeywordsCHAPERONE / Dph4 / Zn-CSL / J-domain
Function / homology
Function and homology information


Synthesis of diphthamide-EEF2 / protein histidyl modification to diphthamide / : / positive regulation of ATP-dependent activity / ATPase activator activity / chaperone-mediated protein folding / ferrous iron binding / cytoskeleton / zinc ion binding / cytoplasm
Similarity search - Function
DnaJ homolog subfamily C member 24 / Microbial ribonuclease fold / DPH Zinc finger / DPH-type metal-binding domain / DPH-type metal-binding domain superfamily / CSL zinc finger / DPH-type metal-binding (MB) domain profile. / DnaJ domain / DnaJ domain / DnaJ molecular chaperone homology domain ...DnaJ homolog subfamily C member 24 / Microbial ribonuclease fold / DPH Zinc finger / DPH-type metal-binding domain / DPH-type metal-binding domain superfamily / CSL zinc finger / DPH-type metal-binding (MB) domain profile. / DnaJ domain / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Helix Hairpins / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DnaJ homolog subfamily C member 24
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest target function, model 1
AuthorsThakur, A. / Chitoor, B.S. / Atreya, H.S. / Silva, P.D.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structure and mechanistic insights into novel iron-mediated moonlighting functions of human J-protein cochaperone, Dph4.
Authors: Thakur, A. / Chitoor, B. / Goswami, A.V. / Pareek, G. / Atreya, H.S. / D'Silva, P.
History
DepositionNov 23, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_nmr_software
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_software.name
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DnaJ homolog subfamily C member 24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0522
Polymers17,9861
Non-polymers651
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 / 100target function
RepresentativeModel #1lowest target function

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Components

#1: Protein DnaJ homolog subfamily C member 24 / Dph4 / CSL-type zinc finger-containing protein 3 / DPH4 homolog


Mass: 17986.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6P3W2
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Sequence detailsMET1 IS A PART OF ORIGINAL PROTEIN SEQUENCE ACCORDING TO SEQUENCE GIVEN IN NCBI DATABASE(AL137804).

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Superposition is done for whole protein. Since the two domains are not oriented the overall RMSD of protein is high.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-15N HSQC
1312D 1H-13C HSQC
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D 1H-13C NOESY
1713D 1H-15N NOESY
1813D H(CCO)NH-TOCSY
1913D CBCA(CO)NH
11013D (H)C(CO)NH-TOCSY
11113D HNCO
11213D HBHA(CBCACO)NH
1131GFT (3,2)D HA(CA)CO(N)H
1142GFT (4,3)D NOESY-(H)CCH

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM [U-13C; U-15N] Dph4 polypeptide; 1mM Zn; 80mM sodium chloride; 20mM TRIS; 90% H2O/10% D2O90% H2O/10% D2O
21mM Dph4 polypeptide; 1mM Zn; 80mM sodium chloride; 20mM TRIS; 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMDph4 polypeptide-1[U-13C; U-15N]1
1 mMZn-21
80 mMsodium chloride-31
20 mMTRIS-41
1 mMDph4 polypeptide-52
1 mMZn-62
80 mMsodium chloride-72
20 mMTRIS-82
Sample conditionspH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE5002

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Processing

NMR software
NameDeveloperClassification
XEASYBartels et al.peak picking
XEASYBartels et al.chemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
XwinNMRBruker Biospincollection
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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