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- PDB-5yj3: Crystal structure of TZAP and telomeric DNA complex -

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Basic information

Entry
Database: PDB / ID: 5yj3
TitleCrystal structure of TZAP and telomeric DNA complex
Components
  • DNA (5'-D(*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*C)-3')
  • DNA (5'-D(*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')
  • Telomere zinc finger-associated protein
KeywordsDNA BINDING PROTEIN/DNA / telomeric DNA binding protein / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


telomere maintenance via telomere lengthening / double-stranded telomeric DNA binding / chromosome, telomeric region / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / identical protein binding ...telomere maintenance via telomere lengthening / double-stranded telomeric DNA binding / chromosome, telomeric region / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / identical protein binding / nucleus / 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) / Telomere zinc finger-associated protein
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.845 Å
AuthorsLi, F. / Zhao, Y.
CitationJournal: Cell Res. / Year: 2018
Title: The 11th C2H2 zinc finger and an adjacent C-terminal arm are responsible for TZAP recognition of telomeric DNA.
Authors: Zhao, Y. / Zhang, G. / He, C. / Mei, Y. / Shi, Y. / Li, F.
History
DepositionOct 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*C)-3')
B: DNA (5'-D(*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')
C: Telomere zinc finger-associated protein
D: Telomere zinc finger-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3548
Polymers37,0924
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-57 kcal/mol
Surface area15020 Å2
Unit cell
Length a, b, c (Å)56.713, 56.713, 226.229
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: DNA chain DNA (5'-D(*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*C)-3')


Mass: 5349.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')


Mass: 5682.672 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein Telomere zinc finger-associated protein / TZAP / Krueppel-related zinc finger protein 3 / hKR3 / Zinc finger and BTB domain-containing ...TZAP / Krueppel-related zinc finger protein 3 / hKR3 / Zinc finger and BTB domain-containing protein 48 / Zinc finger protein 855


Mass: 13030.060 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 516-620
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZBTB48, HKR3, TZAP, ZNF855 / Production host: Escherichia coli (E. coli) / References: UniProt: P10074
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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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: 2.45 Å3/Da / Density % sol: 49.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 M Imidazole-Malate pH 8.5, 20% PEG 4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.845→40 Å / Num. obs: 9428 / % possible obs: 100 % / Redundancy: 23.7 % / Biso Wilson estimate: 76.05 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.015 / Rrim(I) all: 0.073 / Χ2: 0.477 / Net I/σ(I): 4.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.85-2.9221.20.9835820.9040.2141.0070.427100
2.92-2.9923.90.8136290.970.1670.830.434100
2.99-3.0725.20.6285780.9880.1260.640.442100
3.07-3.16250.4536360.9960.0910.4620.427100
3.16-3.2625.10.14358410.0290.1460.445100
3.26-3.3823.90.1056270.9990.0220.1070.474100
3.38-3.5123.10.09561110.020.0970.461100
3.51-3.6725.50.10160910.020.1030.462100
3.67-3.8725.60.16260.9990.020.1020.464100
3.87-4.1124.80.0776260.9990.0160.0790.467100
4.11-4.43240.0626280.9990.0130.0640.489100
4.43-4.8723.60.05563810.0110.0560.497100
4.87-5.5724.70.0564410.010.0510.504100
5.57-7.02220.04866310.010.0490.526100
7.02-4019.30.04174710.0090.0420.63499.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W0T

1w0t


Resolution: 2.845→28.279 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.78
RfactorNum. reflection% reflection
Rfree0.2678 446 4.85 %
Rwork0.2261 --
obs0.2281 9190 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 198.14 Å2 / Biso mean: 98.4463 Å2 / Biso min: 45.27 Å2
Refinement stepCycle: final / Resolution: 2.845→28.279 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1093 732 4 0 1829
Biso mean--88.43 --
Num. residues----172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041936
X-RAY DIFFRACTIONf_angle_d0.592754
X-RAY DIFFRACTIONf_chiral_restr0.035292
X-RAY DIFFRACTIONf_plane_restr0.003235
X-RAY DIFFRACTIONf_dihedral_angle_d26.0581034
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8449-3.25610.3461510.30462806295799
3.2561-4.10030.29421510.24112877302898
4.1003-28.280.23771440.20543061320598
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)
10.0636-0.48062.67621.9752-1.89116.81770.1683-0.2455-0.41930.62740.05790.38270.5751-0.4614-0.11250.78020.1540.04271.40990.07860.59465.490137.8272-11.2463
2-0.2072-0.64543.8291.9411-3.77786.3228-0.2791-0.3663-0.36150.98790.45380.1978-1.2356-0.9298-0.12380.90920.2195-0.04651.2620.11520.59614.135637.1791-8.6219
35.34860.4469-2.5636.2221.57565.3991-0.11130.18020.234-0.2570.05420.26610.0851-0.1968-0.01830.37750.1225-0.18990.9417-0.04870.5346-3.839350.7953-35.7282
43.47612.32584.53562.91511.23028.8580.2619-0.28890.9787-0.36260.1184-0.13240.5548-0.1678-0.59440.6193-0.16290.05811.715-0.10621.3391-5.761517.6903-31.2166
55.6517-4.4117-1.17547.7281-1.00579.18410.046-0.0583-0.22340.7796-0.2589-0.5016-0.5203-0.390.14720.4832-0.1822-0.13080.8930.05180.507713.323131.2151-17.8238
61.88920.96731.9453.5008-0.68892.9050.72931.1140.52560.5775-0.8091-0.3124-1.74270.62720.31451.44260.0610.24331.19680.02271.055618.427447.9019-52.1812
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 18)A1 - 18
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 18)B1 - 18
3X-RAY DIFFRACTION3chain 'C' and (resid 575 through 618 )C575 - 618
4X-RAY DIFFRACTION4chain 'D' and (resid 549 through 574 )D549 - 574
5X-RAY DIFFRACTION5chain 'D' and (resid 575 through 614 )D575 - 614
6X-RAY DIFFRACTION6chain 'C' and (resid 549 through 574 )C549 - 574

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