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- PDB-2kmk: Gfi-1 Zinc Fingers 3-5 complexed with DNA -

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Basic information

Entry
Database: PDB / ID: 2kmk
TitleGfi-1 Zinc Fingers 3-5 complexed with DNA
Components
  • DNA (5'-D(*CP*AP*TP*AP*AP*AP*TP*CP*AP*CP*TP*GP*CP*CP*TP*A)-3')
  • DNA (5'-D(*TP*AP*GP*GP*CP*AP*GP*TP*GP*AP*TP*TP*TP*AP*TP*G)-3')
  • Zinc finger protein Gfi-1
KeywordsDNA BINDING PROTEIN/DNA / Tandem Repeat Zinc Finger Domain / Protein-DNA Complex / DNA-binding / Metal-binding / Nucleus / Transcription / Transcription regulation / Zinc / Zinc-finger / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


negative regulation of cell fate specification / positive regulation of cell fate specification / positive regulation of interleukin-6-mediated signaling pathway / mechanosensory behavior / inner ear auditory receptor cell differentiation / cell fate specification / inner ear morphogenesis / DNA-binding transcription repressor activity / regulation of toll-like receptor signaling pathway / cell fate commitment ...negative regulation of cell fate specification / positive regulation of cell fate specification / positive regulation of interleukin-6-mediated signaling pathway / mechanosensory behavior / inner ear auditory receptor cell differentiation / cell fate specification / inner ear morphogenesis / DNA-binding transcription repressor activity / regulation of toll-like receptor signaling pathway / cell fate commitment / enzyme-substrate adaptor activity / transcription repressor complex / DNA-binding transcription repressor activity, RNA polymerase II-specific / nuclear matrix / sequence-specific double-stranded DNA binding / negative regulation of neuron projection development / cellular response to lipopolysaccharide / transcription cis-regulatory region binding / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA damage response / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleus
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
DNA / DNA (> 10) / Zinc finger protein Gfi-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing, distance geometry
AuthorsLee, S. / Wu, Z.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Solution structure of Gfi-1 zinc domain bound to consensus DNA.
Authors: Lee, S. / Doddapaneni, K. / Hogue, A. / McGhee, L. / Meyers, S. / Wu, Z.
History
DepositionJul 30, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zinc finger protein Gfi-1
B: DNA (5'-D(*CP*AP*TP*AP*AP*AP*TP*CP*AP*CP*TP*GP*CP*CP*TP*A)-3')
C: DNA (5'-D(*TP*AP*GP*GP*CP*AP*GP*TP*GP*AP*TP*TP*TP*AP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3946
Polymers19,1983
Non-polymers1963
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)12 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Zinc finger protein Gfi-1 / Growth factor independent protein 1


Mass: 9403.864 Da / Num. of mol.: 1 / Fragment: UNP residues 312-393
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gfi1, Gfi-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: Q07120
#2: DNA chain DNA (5'-D(*CP*AP*TP*AP*AP*AP*TP*CP*AP*CP*TP*GP*CP*CP*TP*A)-3')


Mass: 4826.169 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*TP*AP*GP*GP*CP*AP*GP*TP*GP*AP*TP*TP*TP*AP*TP*G)-3')


Mass: 4968.237 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CA)CB
1413D CBCA(CO)NH
1512D 1H-13C HSQC
1613D 15N-edited TOCSY-HSQC
1713D (H)CCH-TOCSY
1813D 13C-edited NOESY-ctHSQC
1912D 13C,15N-edited TOCSY
11012D 13C,15N-edited NOESY
11113D 15N-edited 1H-15N NOESY-HSQC
11213D 15N-edited 15N-15N NOESY-HSQC
11312D 13C,15N-filtered 13C,15N-selected NOESY
11413D 13C-edited 15N,13C-filtered NOESY-HSQC
11522D 1H-15N TROSY-antiTROSY
11623D (HA)CA(CO)NH
11723D HNCO

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Sample preparation

Details
Solution-IDContentsSolvent system
125 mM [U-2H] sodium acetate-1, 0.1 mM zinc chloride-2, 0.1 mM beta-mercaptoethanol-3, 0.04 % sodium azide-4, 93% H2O/7% D2O93% H2O/7% D2O
225 mM [U-2H] sodium acetate-5, 0.1 mM zinc chloride-6, 0.1 mM beta-mercaptoethanol-7, 0.4 % sodium azide-8, 7.1 % polyacrylamide-9, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
25 mMsodium acetate-1[U-2H]1
0.1 mMzinc chloride-21
0.1 mMbeta-mercaptoethanol-31
0.04 %sodium azide-41
25 mMsodium acetate-5[U-2H]2
0.1 mMzinc chloride-62
0.1 mMbeta-mercaptoethanol-72
0.4 %sodium azide-82
7.1 %polyacrylamide-92
Sample conditionspH: 6 / Pressure: ambient / Temperature: 305 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002
Bruker DMXBrukerDMX6003

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
XwinNMRBruker Biospincollection
RefinementMethod: simulated annealing, distance geometry / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 12

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