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- PDB-6ml7: ZBTB24 Zinc Fingers 4-8 with 19+1mer DNA Oligonucleotide (Sequenc... -

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Basic information

Entry
Database: PDB / ID: 6ml7
TitleZBTB24 Zinc Fingers 4-8 with 19+1mer DNA Oligonucleotide (Sequence 4 with a CpG 5mC Modification)
Components
  • DNA (5'-D(*AP*CP*GP*CP*AP*GP*GP*TP*CP*CP*TP*GP*GP*AP*(5CM)P*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
DI(HYDROXYETHYL)ETHER / 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: 1.75 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*CP*AP*GP*GP*TP*CP*CP*TP*GP*GP*AP*(5CM)P*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)30,28213
Polymers29,5573
Non-polymers72510
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7430 Å2
ΔGint-25 kcal/mol
Surface area14000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.130, 68.707, 48.448
Angle α, β, γ (deg.)90.00, 92.58, 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*CP*AP*GP*GP*TP*CP*CP*TP*GP*GP*AP*(5CM)P*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 , 4 types, 319 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.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.59 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 30% PEG2000 MME, 0.1 M potassium thiocyanate

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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 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→28.014 Å / Num. obs: 30550 / % possible obs: 100 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.048 / Net I/σ(I): 8.4
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 3045 / CC1/2: 0.426 / Rpim(I) all: 0.818 / % 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 6ML6

6ml6


Resolution: 1.75→28.014 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.19
RfactorNum. reflection% reflection
Rfree0.2398 1520 4.98 %
Rwork0.1927 --
obs0.195 30506 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→28.014 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1116 815 31 309 2271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052085
X-RAY DIFFRACTIONf_angle_d0.7772961
X-RAY DIFFRACTIONf_dihedral_angle_d21.6681094
X-RAY DIFFRACTIONf_chiral_restr0.041317
X-RAY DIFFRACTIONf_plane_restr0.004236
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7501-1.80650.34391360.31652625X-RAY DIFFRACTION100
1.8065-1.87110.30381440.32605X-RAY DIFFRACTION100
1.8711-1.9460.28711410.27132634X-RAY DIFFRACTION100
1.946-2.03450.30741410.25592613X-RAY DIFFRACTION100
2.0345-2.14180.29151360.23772634X-RAY DIFFRACTION100
2.1418-2.27590.24751370.21222634X-RAY DIFFRACTION100
2.2759-2.45150.25711450.19812627X-RAY DIFFRACTION100
2.4515-2.69810.22511350.1882635X-RAY DIFFRACTION100
2.6981-3.0880.25721360.19282646X-RAY DIFFRACTION100
3.088-3.8890.20791310.15852629X-RAY DIFFRACTION99
3.889-28.01760.19221380.14262704X-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)
14.3061-0.0087-2.98393.25033.68219.5750.120.20610.0907-0.6003-0.2737-0.0630.27350.19470.20620.42120.17890.02130.3046-0.00560.300137.55934.623225.4732
27.46024.10770.88912.0186-6.1624.6793-0.02450.30570.37490.33430.0941-0.6251-0.9165-0.0903-0.18190.45980.03610.08570.3103-0.01110.356941.629624.76378.2921
30.82240.13390.87283.97343.93772.0322-0.12720.18950.06-0.46350.425-0.39530.15320.3871-0.19610.2064-0.06020.09040.3748-0.0880.261738.482215.27627.2507
46.7628-3.4599-1.01273.50141.14241.809-0.0897-0.2297-0.32290.1520.15530.05970.13530.0738-0.06830.14480.0032-0.01880.10080.01190.103621.45094.24778.3531
51.16870.9884-0.22077.0562-4.17212.8463-0.0838-0.00540.21130.08960.18740.3402-0.0804-0.1553-0.07250.1229-0.00130.00440.1616-0.01370.15069.280120.92063.5249
66.5876-1.05450.04196.6327-2.75.7255-0.24310.6944-0.0388-0.85860.16510.11580.6152-0.15110.0340.2808-0.0902-0.01450.19660.00190.200513.144325.7478-10.9222
71.4106-1.15511.8951.8099-1.44812.0222-0.24480.18990.1541-0.34910.2260.2141-0.37720.1833-0.03440.2732-0.0623-0.0810.24470.01340.25126.073418.6703-10.3616
83.5705-3.20332.70134.7557-0.93233.1590.05520.0267-0.2133-0.00620.08770.3724-0.2824-0.0986-0.15660.21310.01830.01980.15540.01610.138917.493110.56081.1139
95.3034-0.40993.7443.9375-1.07078.10730.0244-0.6924-0.02660.33440.2625-0.21650.0225-0.5416-0.28150.1678-0.0388-0.01210.213-0.04850.163332.934816.875119.6355
105.64121.96362.61383.42261.27254.59850.0709-0.0957-0.08530.47010.1682-0.3439-0.10160.2287-0.20520.22550.0303-0.03890.2449-0.04810.169135.943216.483822.7996
112.16411.18193.89287.15586.78542.024-0.09170.14490.206-1.00170.30610.0652-1.71-0.5732-0.25140.32590.02520.01280.21350.04610.176421.018219.4553.0493
127.5743-0.98495.25179.613-0.71597.2181-0.34221.0061-2.2581-0.53080.87060.50510.3255-0.0634-0.46980.282-0.0195-0.04710.2655-0.05760.37669.200610.4088-8.7198
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 416 )
3X-RAY DIFFRACTION3chain 'A' and (resid 417 through 428 )
4X-RAY DIFFRACTION4chain 'A' and (resid 429 through 465 )
5X-RAY DIFFRACTION5chain 'A' and (resid 466 through 494 )
6X-RAY DIFFRACTION6chain 'A' and (resid 495 through 515 )
7X-RAY DIFFRACTION7chain 'E' and (resid 1 through 5 )
8X-RAY DIFFRACTION8chain 'E' and (resid 6 through 10 )
9X-RAY DIFFRACTION9chain 'E' and (resid 11 through 20 )
10X-RAY DIFFRACTION10chain 'F' and (resid 1 through 10 )
11X-RAY DIFFRACTION11chain 'F' and (resid 11 through 15 )
12X-RAY DIFFRACTION12chain 'F' and (resid 16 through 20 )

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