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- PDB-8ymz: Structure of ZBTB43 in complex with CACA containing B-form DNA -

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Basic information

Entry
Database: PDB / ID: 8ymz
TitleStructure of ZBTB43 in complex with CACA containing B-form DNA
Components
  • DNA (5'-D(*AP*AP*GP*TP*GP*TP*GP*TP*AP*TP*GP*TP*GP*TP*G)-3')
  • DNA (5'-D(*TP*CP*AP*CP*AP*CP*AP*TP*AP*CP*AP*CP*AP*CP*T)-3')
  • Zinc finger and BTB domain-containing protein 43
KeywordsDNA/DNA BINDING PROTEIN / ZBTB43 / DNA / CACA / B-DNA / DNA BINDING PROTEIN / DNA-DNA BINDING PROTEIN complex
Function / homology
Function and homology information


RNA polymerase III general transcription initiation factor binding / sequence-specific double-stranded DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / chromatin / zinc ion binding / nucleus
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 / Zinc finger C2H2 type domain signature. ...: / 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 / Zinc finger C2H2 type domain signature. / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2-type
Similarity search - Domain/homology
DNA / DNA (> 10) / Zinc finger and BTB domain-containing protein 43
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsLi, X. / Yang, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Febs J. / Year: 2024
Title: Structural insights into the recognition of purine-pyrimidine dinucleotide repeats by zinc finger protein ZBTB43.
Authors: Yang, Y. / Zhang, S. / Xu, L. / Pan, Y. / Xuan, Y. / Kai, Y. / Chen, X.
History
DepositionMar 10, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*TP*CP*AP*CP*AP*CP*AP*TP*AP*CP*AP*CP*AP*CP*T)-3')
D: DNA (5'-D(*AP*AP*GP*TP*GP*TP*GP*TP*AP*TP*GP*TP*GP*TP*G)-3')
E: Zinc finger and BTB domain-containing protein 43
A: DNA (5'-D(*TP*CP*AP*CP*AP*CP*AP*TP*AP*CP*AP*CP*AP*CP*T)-3')
B: DNA (5'-D(*AP*AP*GP*TP*GP*TP*GP*TP*AP*TP*GP*TP*GP*TP*G)-3')
F: Zinc finger and BTB domain-containing protein 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,03912
Polymers37,6476
Non-polymers3926
Water00
1
C: DNA (5'-D(*TP*CP*AP*CP*AP*CP*AP*TP*AP*CP*AP*CP*AP*CP*T)-3')
D: DNA (5'-D(*AP*AP*GP*TP*GP*TP*GP*TP*AP*TP*GP*TP*GP*TP*G)-3')
E: Zinc finger and BTB domain-containing protein 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0206
Polymers18,8243
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-57 kcal/mol
Surface area9690 Å2
MethodPISA
2
A: DNA (5'-D(*TP*CP*AP*CP*AP*CP*AP*TP*AP*CP*AP*CP*AP*CP*T)-3')
B: DNA (5'-D(*AP*AP*GP*TP*GP*TP*GP*TP*AP*TP*GP*TP*GP*TP*G)-3')
F: Zinc finger and BTB domain-containing protein 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0206
Polymers18,8243
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-17 kcal/mol
Surface area9570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.979, 67.535, 99.466
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain DNA (5'-D(*TP*CP*AP*CP*AP*CP*AP*TP*AP*CP*AP*CP*AP*CP*T)-3')


Mass: 4481.952 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: DNA chain DNA (5'-D(*AP*AP*GP*TP*GP*TP*GP*TP*AP*TP*GP*TP*GP*TP*G)-3')


Mass: 4695.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein Zinc finger and BTB domain-containing protein 43 / Zinc finger and BTB domain-containing protein 22B / Zinc finger protein 297B / ZnF-x


Mass: 9646.515 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZBTB43, KIAA0414, ZBTB22B, ZNF297B / Production host: Escherichia coli (E. coli) / References: UniProt: O43298
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN
Has protein modificationN

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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: 2.68 Å3/Da / Density % sol: 54.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M sodium chloride, 0.1 M Bis-Tris, pH 5.5, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 8996 / % possible obs: 99.5 % / Redundancy: 12.1 % / CC1/2: 0.969 / CC star: 0.992 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.031 / Rrim(I) all: 0.106 / Χ2: 0.931 / Net I/σ(I): 4.8 / Num. measured all: 109139
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.95-310.41.0884210.9820.9950.3361.1410.88492.5
3-3.0610.11.0424190.9880.9970.3361.0970.9199.1
3.06-3.1110.80.4824430.9960.9990.1510.5060.93499.6
3.11-3.1812.10.3954410.9950.9990.1150.4120.91199.5
3.18-3.2512.30.2174360.9970.9990.0640.2270.882100
3.25-3.3212.10.0924470.99810.0310.0970.948100
3.32-3.4113.20.152429110.0480.1590.95499.8
3.41-3.513.50.2084490.99810.0590.2160.961100
3.5-3.613.30.244400.99810.0680.250.99100
3.6-3.7213.30.1844560.9970.9990.0520.1910.947100
3.72-3.8513.10.1494390.99810.0430.1550.978100
3.85-412.60.1394610.9970.9990.0410.1450.955100
4-4.19120.1334410.99810.040.1390.997100
4.19-4.4112.90.1224390.99810.0350.1270.989100
4.41-4.68120.1034580.9970.9990.0310.1080.966100
4.68-5.04130.0944660.99910.0270.0980.873100
5.04-5.5512.80.0794550.99910.0230.0820.884100
5.55-6.3512.10.0764620.99810.0230.0790.911100
6.35-811.20.0634710.99910.020.0660.859100
8-5010.30.0665230.9970.9990.0230.070.85799.4

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→29.02 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2971 700 10.12 %
Rwork0.269 --
obs0.2719 6919 77.35 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.95→29.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1280 1218 6 0 2504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072684
X-RAY DIFFRACTIONf_angle_d1.1393856
X-RAY DIFFRACTIONf_dihedral_angle_d33.972756
X-RAY DIFFRACTIONf_chiral_restr0.046406
X-RAY DIFFRACTIONf_plane_restr0.025278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.180.4565610.4041616X-RAY DIFFRACTION39
3.18-3.50.384950.3256884X-RAY DIFFRACTION56
3.5-40.32321590.27831469X-RAY DIFFRACTION91
4-5.040.341870.26791592X-RAY DIFFRACTION100
5.04-29.020.23671980.24371658X-RAY DIFFRACTION99
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)
11.3161-0.58880.53224.2275-1.91626.0650.27250.7354-0.5717-0.978-0.22411.7451.7987-1.1381-0.78780.70330.2588-0.16421.21510.15460.444112.3466-2.3371-31.0934
22.7733-0.8798-0.18024.26452.74818.1367-0.08130.8920.1895-0.2151-0.33191.03150.3129-0.82960.2210.48590.0283-0.06490.7896-0.07440.50715.1298-1.3436-27.4546
34.9106-2.2606-2.10115.7721-0.13965.2622-0.2865-0.89860.828-0.16280.88750.7664-0.35940.0069-0.21270.16410.05340.16570.4435-0.05190.925817.89021.4119-17.4526
41.74620.8942-0.72232.7793-0.60886.8818-0.10250.0908-0.5525-0.3155-0.0782-0.02122.1622-0.33510.07220.94580.26970.0031.0649-0.0440.621147.5306-1.8007-18.4701
52.35010.8550.64114.4136-3.15318.7345-0.40380.0537-0.6848-0.0750.47-1.3902-0.48560.9650.28810.75180.1120.11040.843-0.12750.517844.9868-1.0026-22.1882
63.0063-2.3130.33565.4159-2.69615.8215-0.35720.09120.3489-1.09360.5441-1.55470.55530.131-0.25560.6192-0.04820.150.6594-0.30890.639142.65161.1674-32.2681
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'C' and resid 1 through 15)
2X-RAY DIFFRACTION2(chain 'D' and resid 1 through 15)
3X-RAY DIFFRACTION3(chain 'E' and resid 372 through 450)
4X-RAY DIFFRACTION4(chain 'A' and resid 1 through 15)
5X-RAY DIFFRACTION5(chain 'B' and resid 1 through 15)
6X-RAY DIFFRACTION6(chain 'F' and resid 372 through 450)

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