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- PDB-2d7l: Solution structure of the HMG box domain from human WD repeat and... -

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Entry
Database: PDB / ID: 2d7l
TitleSolution structure of the HMG box domain from human WD repeat and HMG-box DNA binding protein 1
ComponentsWD repeat and HMG-box DNA binding protein 1
KeywordsGENE REGULATION / DNA BINDING PROTEIN / high mobility group box domain / helix-turn-helix / DNA binding / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


nuclear replication fork / DNA-templated DNA replication / mitotic cell cycle / DNA repair / chromatin binding / DNA binding / nucleoplasm / cytoplasm
Similarity search - Function
: / DNA polymerase alpha-binding protein Ctf4, C-terminal domain / Minichromosome loss protein Mcl1, middle region / Minichromosome loss protein, Mcl1, middle region / High mobility group box domain / DNA Binding (I), subunit A / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / HMG boxes A and B DNA-binding domains profile. / high mobility group ...: / DNA polymerase alpha-binding protein Ctf4, C-terminal domain / Minichromosome loss protein Mcl1, middle region / Minichromosome loss protein, Mcl1, middle region / High mobility group box domain / DNA Binding (I), subunit A / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
WD repeat and HMG-box DNA-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, restrained molecular dynamics
AuthorsTomizawa, T. / Kigawa, T. / Saito, K. / 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 domain from human WD repeat and HMG-box DNA binding protein 1
Authors: Tomizawa, T. / Kigawa, T. / Saito, K. / Koshiba, S. / Inoue, M. / Kamatari, Y.O. / Yokoyama, S.
History
DepositionNov 24, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2006Provider: 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: WD repeat and HMG-box DNA binding protein 1


Theoretical massNumber of molelcules
Total (without water)8,8781
Polymers8,8781
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 WD repeat and HMG-box DNA binding protein 1 / Acidic nucleoplasmic DNA- binding protein 1 / And-1


Mass: 8877.777 Da / Num. of mol.: 1 / Fragment: HMG box domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: WDHD1 / Plasmid: P050111-08 / References: UniProt: O75717

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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: 1.13mM HMG box domain U-15N, 13C; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / 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
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe20030801Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.932Kobayashi, 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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