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- PDB-8jq0: Crystal structure of ZBTB48 ZF10-11-C in complex with CIITA promoter -

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Basic information

Entry
Database: PDB / ID: 8jq0
TitleCrystal structure of ZBTB48 ZF10-11-C in complex with CIITA promoter
Components
  • DNA (5'-D(*CP*AP*CP*AP*AP*GP*TP*GP*AP*GP*GP*GP*AP*TP*CP*A)-3')
  • DNA (5'-D(*GP*TP*GP*AP*TP*CP*CP*CP*TP*CP*AP*CP*TP*TP*GP*T)-3')
  • HKR3 protein
KeywordsDNA BINDING PROTEIN / Transcription factor
Function / homology
Function and homology information


: / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
DNA / DNA (> 10) / HKR3 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLi, F.D. / Wang, S.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of ZBTB48 ZF10-11-C in complex with CIITA promoter
Authors: Li, F.D. / Wang, S.M.
History
DepositionJun 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HKR3 protein
B: DNA (5'-D(*CP*AP*CP*AP*AP*GP*TP*GP*AP*GP*GP*GP*AP*TP*CP*A)-3')
C: DNA (5'-D(*GP*TP*GP*AP*TP*CP*CP*CP*TP*CP*AP*CP*TP*TP*GP*T)-3')
D: HKR3 protein
E: DNA (5'-D(*CP*AP*CP*AP*AP*GP*TP*GP*AP*GP*GP*GP*AP*TP*CP*A)-3')
F: DNA (5'-D(*GP*TP*GP*AP*TP*CP*CP*CP*TP*CP*AP*CP*TP*TP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,93210
Polymers37,6706
Non-polymers2624
Water00
1
A: HKR3 protein
B: DNA (5'-D(*CP*AP*CP*AP*AP*GP*TP*GP*AP*GP*GP*GP*AP*TP*CP*A)-3')
C: DNA (5'-D(*GP*TP*GP*AP*TP*CP*CP*CP*TP*CP*AP*CP*TP*TP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9665
Polymers18,8353
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-21 kcal/mol
Surface area9240 Å2
MethodPISA
2
D: HKR3 protein
E: DNA (5'-D(*CP*AP*CP*AP*AP*GP*TP*GP*AP*GP*GP*GP*AP*TP*CP*A)-3')
F: DNA (5'-D(*GP*TP*GP*AP*TP*CP*CP*CP*TP*CP*AP*CP*TP*TP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9665
Polymers18,8353
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-23 kcal/mol
Surface area9150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.563, 46.864, 79.047
Angle α, β, γ (deg.)90.00, 124.89, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein HKR3 protein / ZBTB48


Mass: 9038.560 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HKR3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6LCP1
#2: DNA chain DNA (5'-D(*CP*AP*CP*AP*AP*GP*TP*GP*AP*GP*GP*GP*AP*TP*CP*A)-3')


Mass: 4956.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*GP*TP*GP*AP*TP*CP*CP*CP*TP*CP*AP*CP*TP*TP*GP*T)-3')


Mass: 4840.140 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / 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: 2.55 Å3/Da / Density % sol: 51.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium acetate, 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: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. obs: 8503 / % possible obs: 98.9 % / Redundancy: 6.2 % / CC1/2: 0.989 / CC star: 0.997 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.05 / Rrim(I) all: 0.128 / Χ2: 0.857 / Net I/σ(I): 4.9 / Num. measured all: 52860
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.9-2.9550.8674060.8150.9480.3880.9540.61991.4
2.95-35.30.7353810.8930.9710.3220.8050.56495.7
3-3.065.50.8364350.8280.9520.3720.9180.57598
3.06-3.1260.6034140.920.9790.2570.6570.56997.6
3.12-3.195.80.4354100.9660.9910.1880.4750.62599
3.19-3.276.20.364220.9750.9940.1530.3920.83198.8
3.27-3.356.10.2724410.9870.9970.1170.2970.60699.5
3.35-3.445.60.3663920.9390.9840.1740.4071.22598.7
3.44-3.546.30.274480.9780.9940.1180.2960.96399.8
3.54-3.656.70.2674120.9710.9930.1170.2930.946100
3.65-3.786.70.2174240.9860.9960.090.2351.073100
3.78-3.946.50.2154510.9610.990.0960.2361.5399.8
3.94-4.116.80.1334020.9930.9980.0530.1430.876100
4.11-4.336.60.1124340.9940.9980.0460.1210.816100
4.33-4.66.10.114230.9930.9980.0470.120.85199.3
4.6-4.9670.0954360.9960.9990.0380.1020.888100
4.96-5.456.90.0824320.9960.9990.0330.0890.822100
5.45-6.246.60.0814310.9940.9990.0330.0880.864100
6.24-7.856.30.0734540.9970.9990.0310.0790.76199.8
7.85-406.10.0694550.9920.9980.0310.0760.88699.6

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YJ3

5yj3


Resolution: 2.9→39.44 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2912 330 4.66 %
Rwork0.2334 --
obs0.2361 7083 82.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→39.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1172 1300 4 0 2476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032653
X-RAY DIFFRACTIONf_angle_d0.4733832
X-RAY DIFFRACTIONf_dihedral_angle_d28.231783
X-RAY DIFFRACTIONf_chiral_restr0.025411
X-RAY DIFFRACTIONf_plane_restr0.004271
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.660.36541410.28422620X-RAY DIFFRACTION65
3.66-39.440.26461890.21584133X-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)
10.7120.03810.3670.82730.5971.2334-0.09230.0069-0.13250.08270.18360.0105-0.15670.10660.90880.31790.0598-0.10870.05110.08480.4462-8.9676-21.179626.8305
22.82240.31961.18261.00540.43542.8760.11221.1348-0.0812-0.49330.32490.38640.33380.52430.35360.7672-0.18160.05120.70720.10480.5274-8.127-22.217215.323
31.3388-0.73321.40381.7492-1.27181.6567-0.3442-0.2659-0.2589-0.22060.6970.0152-0.0631-0.6176-0.18551.0057-0.0774-0.05420.80270.14840.7083-6.1356-21.427818.6097
40.267-0.20250.15630.8171-0.11092.0389-0.0518-0.05240.10670.3539-0.0226-0.27810.03220.5516-0.56750.1496-0.0107-0.14450.0973-0.09750.126118.6107-38.925511.7471
52.796-1.7557-1.84824.12641.55383.63810.4021-0.25730.6810.29310.2081-0.6712-0.48560.33890.48560.4153-0.0564-0.06990.43340.17490.455821.9323-28.0439.4968
62.31530.7854-0.11481.79551.37421.9673-0.11440.41080.61410.37120.0211-0.3028-0.61471.0799-0.28520.6607-0.1092-0.21490.62260.14810.702223.3882-31.630610.0488
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 550 through 616)
2X-RAY DIFFRACTION2(chain 'B' and resid 3 through 18)
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 16)
4X-RAY DIFFRACTION4(chain 'D' and resid 549 through 617)
5X-RAY DIFFRACTION5(chain 'E' and resid 3 through 18)
6X-RAY DIFFRACTION6(chain 'F' and resid 1 through 16)

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