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- PDB-6ml6: ZBTB24 Zinc Fingers 4-8 with 19+1mer DNA Oligonucleotide (Sequenc... -

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Basic information

Entry
Database: PDB / ID: 6ml6
TitleZBTB24 Zinc Fingers 4-8 with 19+1mer DNA Oligonucleotide (Sequence 4 with a CpA 5mC Modification)
Components
  • DNA (5'-D(*AP*CP*GP*(5CM)P*AP*GP*GP*TP*CP*CP*TP*GP*GP*AP*CP*GP*AP*AP*TP*T)-3')
  • DNA (5'-D(*TP*AP*AP*TP*TP*CP*GP*TP*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 / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / 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 / MOLECULAR REPLACEMENT / Resolution: 1.54 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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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*(5CM)P*AP*GP*GP*TP*CP*CP*TP*GP*GP*AP*CP*GP*AP*AP*TP*T)-3')
F: DNA (5'-D(*TP*AP*AP*TP*TP*CP*GP*TP*CP*CP*AP*GP*GP*AP*CP*CP*TP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,19413
Polymers29,5573
Non-polymers63710
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint-28 kcal/mol
Surface area14000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.163, 68.244, 49.259
Angle α, β, γ (deg.)90.00, 92.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#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

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DNA chain , 2 types, 2 molecules EF

#2: DNA chain DNA (5'-D(*AP*CP*GP*(5CM)P*AP*GP*GP*TP*CP*CP*TP*GP*GP*AP*CP*GP*AP*AP*TP*T)-3')


Mass: 6173.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#3: DNA chain DNA (5'-D(*TP*AP*AP*TP*TP*CP*GP*TP*CP*CP*AP*GP*GP*AP*CP*CP*TP*GP*CP*G)-3')


Mass: 6109.954 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)

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Non-polymers , 3 types, 366 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.62 Å3/Da / Density % sol: 53.09 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG3350, 0.1 M Bis-Tris, pH 5.5, 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: PIXEL / Date: Aug 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.54→28.04 Å / Num. obs: 45159 / % possible obs: 100 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.036 / Net I/σ(I): 9.6
Reflection shellResolution: 1.54→1.6 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4490 / CC1/2: 0.392 / Rpim(I) all: 0.724 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
CrysalisProdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6ML5

6ml5


Resolution: 1.54→28.038 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.4
RfactorNum. reflection% reflection
Rfree0.2215 1814 4.02 %
Rwork0.2015 --
obs0.2023 45091 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.54→28.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1123 815 25 356 2319
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032143
X-RAY DIFFRACTIONf_angle_d0.5383054
X-RAY DIFFRACTIONf_dihedral_angle_d17.2611399
X-RAY DIFFRACTIONf_chiral_restr0.032327
X-RAY DIFFRACTIONf_plane_restr0.003240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.58160.35181410.31493309X-RAY DIFFRACTION100
1.5816-1.62820.3511370.30393298X-RAY DIFFRACTION100
1.6282-1.68070.29521420.273294X-RAY DIFFRACTION99
1.6807-1.74080.21891380.24553307X-RAY DIFFRACTION100
1.7408-1.81050.26011230.24153330X-RAY DIFFRACTION100
1.8105-1.89290.25151500.22953336X-RAY DIFFRACTION100
1.8929-1.99260.24421460.22363294X-RAY DIFFRACTION100
1.9926-2.11740.2511460.22243347X-RAY DIFFRACTION100
2.1174-2.28090.24191330.20853332X-RAY DIFFRACTION100
2.2809-2.51030.22561420.20053327X-RAY DIFFRACTION100
2.5103-2.87320.24321370.20133371X-RAY DIFFRACTION100
2.8732-3.61870.21841400.18223326X-RAY DIFFRACTION99
3.6187-28.04250.13641390.14523406X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.73060.2821-1.90187.58544.69868.5124-0.0716-0.04480.2468-0.2606-0.2137-0.17390.30610.05960.27850.22230.08760.0290.1920.00440.19337.295634.645726.0255
25.52162.58560.28176.13681.39527.7172-0.13030.20560.2306-0.31570.1165-0.3277-0.3214-0.0552-0.01920.09020.02680.03350.16310.0040.158439.971420.52598.2468
36.6899-3.4747-0.32012.96650.26420.7032-0.0396-0.2392-0.08030.0790.07860.1280.0513-0.0276-0.03920.1041-0.00770.00920.09130.00010.059416.88228.50078.434
46.4182-1.2042-0.23766.1326-0.33749.1814-0.19320.3206-0.0953-0.47480.14350.16470.139-0.03420.05960.1176-0.0597-0.02670.08950.00850.161412.375227.4749-9.3335
52.1021-0.7183.39140.558-0.57036.5613-0.15240.21830.374-0.31770.14180.3119-0.1717-0.12090.1190.2611-0.0535-0.13610.19070.04620.26395.992218.6258-10.3125
68.125-4.95196.31716.6355-2.65335.3168-0.0192-0.049-0.4042-0.09640.17070.3718-0.1643-0.1062-0.16660.14130.01830.01280.08840.00180.067117.423910.63811.3893
74.32682.4656-1.6634.2939-4.13547.45960.1144-0.42040.3480.1570.17490.1163-0.4261-0.1494-0.23440.1020.0267-0.00160.1907-0.01010.11629.248620.39712.9266
87.3348-3.05293.8759.2075-1.0957.654-0.0733-0.659-0.49840.57860.2524-0.1410.1537-0.5117-0.16040.229-0.0276-0.06290.3055-00.142936.689213.477626.9989
93.73371.61082.41232.87231.44866.2872-0.0021-0.4152-0.11180.34990.1409-0.3063-0.0696-0.0201-0.1410.17320.0293-0.04790.2149-0.01970.131835.871816.485123.1563
105.3931.90955.58937.66611.37268.7483-0.17080.19980.081-0.59750.2814-0.1486-1.132-0.3151-0.07340.18160.00760.01720.14290.02210.117620.882619.6922.3865
114.10590.02884.90996.75610.42616.7562-0.24470.9771-1.6252-0.45770.59630.2770.3690.0205-0.35450.3302-0.065-0.06030.2219-0.04490.26139.015910.401-8.8731
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 373 through 400 )
2X-RAY DIFFRACTION2chain 'A' and (resid 401 through 428 )
3X-RAY DIFFRACTION3chain 'A' and (resid 429 through 484 )
4X-RAY DIFFRACTION4chain 'A' and (resid 485 through 515 )
5X-RAY DIFFRACTION5chain 'E' and (resid 1 through 5 )
6X-RAY DIFFRACTION6chain 'E' and (resid 6 through 10 )
7X-RAY DIFFRACTION7chain 'E' and (resid 11 through 15 )
8X-RAY DIFFRACTION8chain 'E' and (resid 16 through 20 )
9X-RAY DIFFRACTION9chain 'F' and (resid 1 through 10 )
10X-RAY DIFFRACTION10chain 'F' and (resid 11 through 15 )
11X-RAY DIFFRACTION11chain 'F' and (resid 16 through 20 )

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