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- PDB-2cto: Solution structure of the HMG box like domain from human hypothet... -

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Basic information

Entry
Database: PDB / ID: 2cto
TitleSolution structure of the HMG box like domain from human hypothetical protein FLJ14904
Componentsnovel protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / high mobility group box domain / helix-turn-helix / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


piP-body / autosome / regulation of miRNA-mediated gene silencing / piRNA processing / transposable element silencing by piRNA-mediated DNA methylation / male meiotic nuclear division / homologous chromosome pairing at meiosis / chromatoid body / regulation of organ growth / XY body ...piP-body / autosome / regulation of miRNA-mediated gene silencing / piRNA processing / transposable element silencing by piRNA-mediated DNA methylation / male meiotic nuclear division / homologous chromosome pairing at meiosis / chromatoid body / regulation of organ growth / XY body / P granule / regulatory ncRNA-mediated gene silencing / fertilization / negative regulation of reproductive process / negative regulation of developmental process / PIWI-interacting RNA (piRNA) biogenesis / ectopic germ cell programmed cell death / male germ cell nucleus / cell morphogenesis / intrinsic apoptotic signaling pathway in response to DNA damage / spermatogenesis / sequence-specific DNA binding / negative regulation of DNA-templated transcription / negative regulation of apoptotic process / chromatin / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
Maelstrom domain / Protein maelstrom / piRNA pathway germ-plasm component / High mobility group box domain / DNA Binding (I), subunit A / HMG-box domain / High mobility group box domain / High mobility group box domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein maelstrom homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, restrained molecular dynamics
AuthorsTomizawa, T. / Kigawa, T. / Sato, M. / Koshiba, S. / Inoue, M. / Kamatari, Y.O. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the HMG box like domain from human hypothetical protein FLJ14904
Authors: Tomizawa, T. / Kigawa, T. / Sato, M. / Koshiba, S. / Inoue, M. / Kamatari, Y.O. / Yokoyama, S.
History
DepositionMay 24, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 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: novel protein


Theoretical massNumber of molelcules
Total (without water)10,3681
Polymers10,3681
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 / 100target function, structures with the lowest energy, structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein novel protein / Hypothetical protein FLJ14904


Mass: 10367.605 Da / Num. of mol.: 1 / Fragment: HMG box like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: FLJ14904 / Plasmid: P050125-12 / References: UniProt: Q96JY0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.06mM HMG box like domain U-15N, 13C; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 296 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
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20030801Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.9295Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics, restrained molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function, structures with the lowest energy, structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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