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- PDB-6ml2: ZBTB24 Zinc Fingers 4-8 with 19+1mer DNA Oligonucleotide (Sequence 1) -

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Basic information

Entry
Database: PDB / ID: 6ml2
TitleZBTB24 Zinc Fingers 4-8 with 19+1mer DNA Oligonucleotide (Sequence 1)
Components
  • DNA (5'-D(*AP*CP*GP*CP*AP*GP*GP*TP*CP*CP*TP*GP*GP*CP*AP*GP*CP*TP*AP*A)-3')
  • DNA (5'-D(*TP*TP*TP*AP*GP*CP*TP*GP*CP*CP*AP*GP*GP*AP*CP*CP*TP*GP*CP*G)-3')
  • Zinc finger and BTB domain-containing protein 24
KeywordsTRANSCRIPTION/DNA / protein-DNA complex / transcription / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


regulation of immune system process / hematopoietic progenitor cell differentiation / regulation of cytokine production / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding
Similarity search - Function
BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
DNA / DNA (> 10) / Zinc finger and BTB domain-containing protein 24
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.874 Å
AuthorsHorton, J.R. / Cheng, X. / Ren, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-23 United States
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structural basis of specific DNA binding by the transcription factor ZBTB24.
Authors: Ren, R. / Hardikar, S. / Horton, J.R. / Lu, Y. / Zeng, Y. / Singh, A.K. / Lin, K. / Coletta, L.D. / Shen, J. / Lin Kong, C.S. / Hashimoto, H. / Zhang, X. / Chen, T. / Cheng, X.
History
DepositionSep 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Zinc finger and BTB domain-containing protein 24
E: DNA (5'-D(*AP*CP*GP*CP*AP*GP*GP*TP*CP*CP*TP*GP*GP*CP*AP*GP*CP*TP*AP*A)-3')
F: DNA (5'-D(*TP*TP*TP*AP*GP*CP*TP*GP*CP*CP*AP*GP*GP*AP*CP*CP*TP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8718
Polymers29,5443
Non-polymers3275
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-42 kcal/mol
Surface area14610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.065, 68.619, 49.477
Angle α, β, γ (deg.)90.00, 91.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Zinc finger and BTB domain-containing protein 24 / Bone morphogenetic protein-induced factor 1 / Brain-specific protein 1 / Zinc finger protein 450


Mass: 17274.033 Da / Num. of mol.: 1 / Fragment: zinc fingers 4-8 (UNP residues 375-519)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Zbtb24, Bif1, Bsg1, Znf450 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q80X44
#2: DNA chain DNA (5'-D(*AP*CP*GP*CP*AP*GP*GP*TP*CP*CP*TP*GP*GP*CP*AP*GP*CP*TP*AP*A)-3')


Mass: 6143.981 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#3: DNA chain DNA (5'-D(*TP*TP*TP*AP*GP*CP*TP*GP*CP*CP*AP*GP*GP*AP*CP*CP*TP*GP*CP*G)-3')


Mass: 6125.953 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG3350, 0.1 M Bis-Tris, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 3, 2018
RadiationMonochromator: Rosenbaum-Rock double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→40.12 Å / Num. obs: 36754 / % possible obs: 77.7 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.024 / Net I/σ(I): 22.6
Reflection shellResolution: 1.87→1.94 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 699 / CC1/2: 0.864 / Rpim(I) all: 0.264 / % possible all: 27.6

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5V3G (zinc fingers) + 18-mer B-DNA model

5v3g


Resolution: 1.874→38.232 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 45.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2781 956 5.15 %
Rwork0.2509 --
obs0.2523 36616 73.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.874→38.232 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1048 814 5 25 1892
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051986
X-RAY DIFFRACTIONf_angle_d0.6442842
X-RAY DIFFRACTIONf_dihedral_angle_d22.9321032
X-RAY DIFFRACTIONf_chiral_restr0.034308
X-RAY DIFFRACTIONf_plane_restr0.004225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8743-1.92490.4654370.3643778X-RAY DIFFRACTION22
1.9249-1.98160.3669610.39511042X-RAY DIFFRACTION29
1.9816-2.04550.3432820.37021405X-RAY DIFFRACTION39
2.0455-2.11860.38911000.36341902X-RAY DIFFRACTION52
2.1186-2.20350.48951270.37162269X-RAY DIFFRACTION62
2.2035-2.30370.38391680.35563056X-RAY DIFFRACTION84
2.3037-2.42520.37741970.36433421X-RAY DIFFRACTION95
2.4252-2.57710.38581920.35213567X-RAY DIFFRACTION98
2.5771-2.7760.40711980.35353516X-RAY DIFFRACTION98
2.776-3.05530.41511760.34513453X-RAY DIFFRACTION95
3.0553-3.49710.34211720.2913313X-RAY DIFFRACTION91
3.4971-4.4050.21641830.20153592X-RAY DIFFRACTION98
4.405-38.23950.19141920.17923417X-RAY DIFFRACTION95

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