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- PDB-9jzt: Crystal structure of ZBTB20 in complex with mouse AFP promoter -

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Basic information

Entry
Database: PDB / ID: 9jzt
TitleCrystal structure of ZBTB20 in complex with mouse AFP promoter
Components
  • DNA (5'-D(*CP*TP*TP*CP*CP*TP*TP*AP*CP*GP*TP*TP*GP*AP*AP*G)-3')
  • DNA (5'-D(*GP*CP*TP*TP*CP*AP*AP*CP*GP*TP*AP*AP*GP*GP*AP*A)-3')
  • Zinc finger and BTB domain-containing protein 20
KeywordsTRANSCRIPTION / Transcription factor
Function / homology
Function and homology information


regulation of immune system process / lipid homeostasis / positive regulation of lipid biosynthetic process / regulation of cytokine production / positive regulation of interferon-beta production / positive regulation of glycolytic process / cellular response to glucose stimulus / positive regulation of interleukin-6 production / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding ...regulation of immune system process / lipid homeostasis / positive regulation of lipid biosynthetic process / regulation of cytokine production / positive regulation of interferon-beta production / positive regulation of glycolytic process / cellular response to glucose stimulus / positive regulation of interleukin-6 production / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / positive regulation of tumor necrosis factor production / transcription cis-regulatory region binding / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytoplasm
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 20
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsLi, F.D. / Yang, L.N. / Xie, H.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371282 China
CitationJournal: Structure / Year: 2025
Title: Structural insights into ZBTB20 action at the AFP promoter.
Authors: Yang, L. / Xie, H. / Wan, X. / Li, M. / Lv, M. / Duan, Y. / Shi, Y. / Zhang, W.J. / Li, F.
History
DepositionOct 14, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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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 20
B: DNA (5'-D(*CP*TP*TP*CP*CP*TP*TP*AP*CP*GP*TP*TP*GP*AP*AP*G)-3')
C: DNA (5'-D(*GP*CP*TP*TP*CP*AP*AP*CP*GP*TP*AP*AP*GP*GP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9347
Polymers23,6733
Non-polymers2624
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-37 kcal/mol
Surface area12710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.944, 103.944, 77.216
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Zinc finger and BTB domain-containing protein 20 / Dendritic-derived BTB/POZ zinc finger protein / Zinc finger protein 288


Mass: 13877.247 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZBTB20, DPZF, ZNF288 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HC78
#2: DNA chain DNA (5'-D(*CP*TP*TP*CP*CP*TP*TP*AP*CP*GP*TP*TP*GP*AP*AP*G)-3')


Mass: 4864.165 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#3: DNA chain DNA (5'-D(*GP*CP*TP*TP*CP*AP*AP*CP*GP*TP*AP*AP*GP*GP*AP*A)-3')


Mass: 4931.231 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.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 4.41 Å3/Da / Density % sol: 72.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.12 M Ethylene glycols, 0.1 M Tris (base), Bicine pH 8.5, 18% Ethylene glycol, PEG 4K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97923 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 31, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 3.1→61.98 Å / Num. obs: 8098 / % possible obs: 99.7 % / Redundancy: 16.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.32 / Rpim(I) all: 0.078 / Rrim(I) all: 0.33 / Χ2: 0.99 / Net I/σ(I): 9.7
Reflection shellResolution: 3.1→3.31 Å / % possible obs: 99.3 % / Redundancy: 17.4 % / Rmerge(I) obs: 1.94 / Num. measured all: 24682 / Num. unique obs: 1415 / CC1/2: 0.98 / Rpim(I) all: 0.467 / Rrim(I) all: 1.997 / Χ2: 0.96 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 3.1→53.24 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2489 395 4.9 %
Rwork0.2046 --
obs0.2065 8055 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→53.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms925 650 4 7 1586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031677
X-RAY DIFFRACTIONf_angle_d0.5072391
X-RAY DIFFRACTIONf_dihedral_angle_d21.891665
X-RAY DIFFRACTIONf_chiral_restr0.031261
X-RAY DIFFRACTIONf_plane_restr0.002187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.550.35181370.28242451X-RAY DIFFRACTION99
3.55-4.470.24851310.22422539X-RAY DIFFRACTION100
4.47-53.240.20731270.16722670X-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)
1-0.2337-0.2182-0.45010.3787-0.8713-0.08220.0845-0.0517-0.00630.1065-0.14740.0097-0.00230.0147-0.00720.4826-0.0406-0.03880.7478-0.06860.5352-29.5044-27.1313-13.4251
20.21360.17110.29060.7081-0.13710.4884-0.4381-0.7847-0.524-0.01360.1496-0.26510.10880.05330.00020.64490.01070.0691.3530.02150.9474-18.6158-25.0254-18.9166
30.0237-0.04320.0853-0.05010.0080.8804-0.4517-1.03390.13390.34190.16190.03980.11450.13790.00020.60860.0770.00561.33360.02120.8873-16.8047-22.9115-18.4898
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 577 through 688)
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 16)
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 16)

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