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- PDB-2m2e: Solution NMR structure of the SANT domain of human DNAJC2, Northe... -

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Basic information

Entry
Database: PDB / ID: 2m2e
TitleSolution NMR structure of the SANT domain of human DNAJC2, Northeast structural genomics consortium target HR8254a
ComponentsDnaJ homolog subfamily C member 2
Keywordstranscription regulator / DNA-binding / NESG / Northeast structural genomics consortium / SGC / Structural Genomics Consortium / PSI-Biology
Function / homology
Function and homology information


'de novo' cotranslational protein folding / ubiquitin-modified histone reader activity / negative regulation of DNA biosynthetic process / ATPase activator activity / Regulation of HSF1-mediated heat shock response / regulation of translational fidelity / regulation of cellular response to heat / Hsp70 protein binding / ribosome binding / histone binding ...'de novo' cotranslational protein folding / ubiquitin-modified histone reader activity / negative regulation of DNA biosynthetic process / ATPase activator activity / Regulation of HSF1-mediated heat shock response / regulation of translational fidelity / regulation of cellular response to heat / Hsp70 protein binding / ribosome binding / histone binding / nuclear membrane / DNA replication / chromatin binding / nucleolus / positive regulation of DNA-templated transcription / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Ribosome-associated complex head domain / Ribosome-associated complex head domain superfamily / J-protein Zuotin/DnaJC2 / : / Ribosome-associated complex head domain / Zuotin-like, zuotin homology domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / SANT domain profile. ...Ribosome-associated complex head domain / Ribosome-associated complex head domain superfamily / J-protein Zuotin/DnaJC2 / : / Ribosome-associated complex head domain / Zuotin-like, zuotin homology domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / SANT domain profile. / DnaJ molecular chaperone homology domain / dnaJ domain profile. / SANT domain / Chaperone J-domain superfamily / DnaJ domain / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DnaJ homolog subfamily C member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / restrained molecular dynamics
Model detailslowest energy, model 1
AuthorsLemak, A. / Yee, A. / Houliston, S. / Garcia, M. / Ong, M. / Montelione, G.T. / Arrowsmith, C. / Northeast Structural Genomics Consortium (NESG) / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: NMR solution structure of the SANT domain of human DnaJC2.
Authors: Lemak, A. / Yee, A. / Houliston, S. / Garcia, M. / Ong, M. / Arrowsmith, C.
History
DepositionDec 18, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Other
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / 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_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DnaJ homolog subfamily C member 2


Theoretical massNumber of molelcules
Total (without water)8,4941
Polymers8,4941
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 2 / M-phase phosphoprotein 11 / Zuotin-related factor 1


Mass: 8493.934 Da / Num. of mol.: 1 / Fragment: SANT 2 domain residues 551-621
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNAJC2, MPHOSPH11, MPP11, ZRF1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99543

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D HNCA
1313D CBCA(CO)NH
1413D HBHA(CO)NH
1513D (H)CCH-TOCSY
1613D (H)CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY aliphatic
1913D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 0.5 mM [U-13C; U-15N] protein, 10 mM TRIS, 300 mM sodium chloride, 10 uM ZnSO4, 10 mM DTT, 0.01 % NaN3, 1 mM benzamidine, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMentity-1[U-13C; U-15N]1
10 mMTRIS-21
300 mMsodium chloride-31
10 uMZnSO4-41
10 mMDTT-51
0.01 %NaN3-61
1 mMbenzamidine-71
Sample conditionsIonic strength: 300 / pH: 7 / Pressure: ambient / Temperature: 298 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
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
FMCLemak,Steren,Llinas, Arrowsmithchemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
PSVSBhattacharya and Montelionevalidation
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: restrained molecular dynamics / 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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