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- PDB-7dta: Solution structure of the C-clamp domain from human HDBP1 in comp... -

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Basic information

Entry
Database: PDB / ID: 7dta
TitleSolution structure of the C-clamp domain from human HDBP1 in complex with DNA
Components
  • DNA (5'-D(*GP*TP*CP*CP*CP*GP*GP*CP*AP*TP*A)-3')
  • DNA (5'-D(*TP*AP*TP*GP*CP*CP*GP*GP*GP*AP*C)-3')
  • SLC2A4 regulator
KeywordsDNA BINDING PROTEIN / C-clamp / zinc finger / unmethylated CpG binding
Function / homology
Function and homology information


nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / metal ion binding / nucleus / cytoplasm
Similarity search - Function
: / c-clamp / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
DNA / DNA (> 10) / SLC2A4 regulator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsDuan, B. / Xia, B.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2016YFA0501203 China
National Natural Science Foundation of China (NSFC)31570734 China
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Selective Nonmethylated CpG DNA Recognition Mechanism of Cysteine Clamp Domains.
Authors: Duan, B. / Fu, D. / Zhang, C. / Ding, P. / Dong, X. / Xia, B.
History
DepositionJan 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SLC2A4 regulator
B: DNA (5'-D(*TP*AP*TP*GP*CP*CP*GP*GP*GP*AP*C)-3')
C: DNA (5'-D(*GP*TP*CP*CP*CP*GP*GP*CP*AP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8074
Polymers10,7413
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2580 Å2
ΔGint-11 kcal/mol
Surface area5850 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide SLC2A4 regulator / GLUT4 enhancer factor / GEF / Huntington disease gene regulatory region-binding protein 1 / HDBP-1


Mass: 4032.811 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC2A4RG, HDBP1 / Plasmid: pET-21b / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q9NR83
#2: DNA chain DNA (5'-D(*TP*AP*TP*GP*CP*CP*GP*GP*GP*AP*C)-3')


Mass: 3374.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*GP*TP*CP*CP*CP*GP*GP*CP*AP*TP*A)-3')


Mass: 3334.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
151isotropic23D HN(CA)CB
161isotropic23D CBCA(CO)NH
191isotropic23D CCH-COSY
181isotropic13D 1H-15N NOESY
171isotropic13D 1H-13C NOESY
1101isotropic12D 1H-13C NOESY aromatic
1111isotropic12D F1, F2-15N/13C-filtered 1H-1H NOESY
1121isotropic13D F1-15N/13C filtered, F2-15N edited NOESY
1131isotropic13D F1-15N/13C filtered, F2-13C edited NOESY

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-13C; U-15N] C-clamp, 0.5 mM HD5-DNA, 95% H2O/5% D2O
Details: Equimolar amounts of C-clamp and HD5-DNA in 10 mM sodium phosphate, 10 mM NaCl, pH 7
Label: 15N,13C / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMC-clamp[U-13C; U-15N]1
0.5 mMHD5-DNAnatural abundance1
Sample conditionsDetails: 10 mM sodium phosphate, 10 mM NaCl, pH = 7 / Ionic strength: 10 mM sodium phosphate, 10 mM NaCl mM / Label: conditions_1 / pH: 7 / Pressure: 1 bar / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE III HDBrukerAVANCE III HD9501
Bruker AVANCE III HDBrukerAVANCE III HD5002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
SANEDuggan, Legge, Dyson & Wrightdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 5
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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