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- PDB-7nf9: N-terminal C2H2 Zn-finger domain of Clamp -

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Basic information

Entry
Database: PDB / ID: 7nf9
TitleN-terminal C2H2 Zn-finger domain of Clamp
ComponentsChromatin-linked adaptor for MSL proteins, isoform A
KeywordsGENE REGULATION / Dosage Compensation zinc finger
Function / homology
Function and homology information


RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of transcription by RNA polymerase II
Similarity search - Function
Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Chromatin-linked adaptor for MSL proteins, isoform A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / simulated annealing
AuthorsMariasina, S.S. / Bonchuk, A.N. / Tikhonova, E.A. / Efimov, S.V. / Maksimenko, O.G. / Georgiev, P.G. / Polshakov, V.I.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Foundation for Basic Research19-04-00933 Russian Federation
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Structural basis for interaction between CLAMP and MSL2 proteins involved in the specific recruitment of the dosage compensation complex in Drosophila.
Authors: Tikhonova, E. / Mariasina, S. / Efimov, S. / Polshakov, V. / Maksimenko, O. / Georgiev, P. / Bonchuk, A.
History
DepositionFeb 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: Database references / Category: citation / citation_author
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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3Jun 19, 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: Chromatin-linked adaptor for MSL proteins, isoform A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4782
Polymers7,4121
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7380 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Chromatin-linked adaptor for MSL proteins, isoform A / SD16766p


Mass: 7412.407 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Clamp, CLAMP, clamp, Dmel\CG1832, CG1832, Dmel_CG1832 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9V9N4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
122isotropic22D 1H-15N HSQC
141isotropic13D 1H-15N NOESY
153isotropic13D 1H-13C NOESY
1132isotropic13D HNCO
1122isotropic13D HN(CA)CO
1112isotropic13D HN(CA)CB
1102isotropic13D CBCA(CO)NH
192isotropic13D 1H-15N TOCSY
173isotropic13D (H)CCH-TOCSY
184isotropic22D 15N HSQC-NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.3 mM [U-95% 15N] Clamp[86...153], 20 mM Na2HPO4/HaH2PO4, 50 mM NaCl, 1 mM DTT, 95% H2O/5% D2O15N_H2O95% H2O/5% D2O
solution40.3 mM [U-95% 15N] Clamp[86...153], 20 mM Na2HPO4/HaH2PO4, 50 mM NaCl, 1 mM DTT, 100% D2O15N_D2O100% D2O
solution20.3 mM [U-99% 13C; U-99% 15N] Clamp[86...153], 20 mM Na2HPO4/HaH2PO4, 50 mM NaCl, 1 mM DTT, 95% H2O/5% D2O15N_13C_H2O95% H2O/5% D2O
solution30.3 mM [U-99% 13C; U-99% 15N] Clamp[86...153], 20 mM Na2HPO4/HaH2PO4, 50 mM NaCl, 1 mM DTT, 100% D2O15N_13C_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMClamp[86...153][U-95% 15N]1
20 mMNa2HPO4/HaH2PO4natural abundance1
50 mMNaClnatural abundance1
1 mMDTTnatural abundance1
0.3 mMClamp[86...153][U-95% 15N]4
20 mMNa2HPO4/HaH2PO4natural abundance4
50 mMNaClnatural abundance4
1 mMDTTnatural abundance4
0.3 mMClamp[86...153][U-99% 13C; U-99% 15N]2
20 mMNa2HPO4/HaH2PO4natural abundance2
50 mMNaClnatural abundance2
1 mMDTTnatural abundance2
0.3 mMClamp[86...153][U-99% 13C; U-99% 15N]3
20 mMNa2HPO4/HaH2PO4natural abundance3
50 mMNaClnatural abundance3
1 mMDTTnatural abundance3
Sample conditionsIonic strength: 70 mM / Label: conditions_1 / pH: 6.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III7001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
TopSpinv3.1Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRFAM-SPARKYWoonghee Leepeak picking
NMRFAM-SPARKYWoonghee Leedata analysis
TALOS+Yang Shen, Frank Delaglio, Gabriel Cornilescu, and Ad Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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