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- PDB-7c4q: Crystal structure of DBD plasma treated zebrafish TRF2 myb-domain... -

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Basic information

Entry
Database: PDB / ID: 7c4q
TitleCrystal structure of DBD plasma treated zebrafish TRF2 myb-domain complexed with DNA
Components
  • (Terfa protein) x 2
  • DNA (5'-D(*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*A)-3')
  • DNA (5'-D(*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')
  • DNA (5'-D(*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')
KeywordsDNA BINDING PROTEIN / zebrafish TRF2 / telomeric DNA / complex.
Function / homology
Function and homology information


negative regulation of telomere maintenance via recombination / telomeric loop formation / cell cycle / negative regulation of telomeric D-loop disassembly / protection from non-homologous end joining at telomere / RNA-templated DNA biosynthetic process / telomeric D-loop disassembly / shelterin complex / regulation of telomere maintenance via telomerase / double-stranded telomeric DNA binding ...negative regulation of telomere maintenance via recombination / telomeric loop formation / cell cycle / negative regulation of telomeric D-loop disassembly / protection from non-homologous end joining at telomere / RNA-templated DNA biosynthetic process / telomeric D-loop disassembly / shelterin complex / regulation of telomere maintenance via telomerase / double-stranded telomeric DNA binding / G-rich strand telomeric DNA binding / protein localization to chromosome, telomeric region / protein homodimerization activity
Similarity search - Function
Telomeric repeat-binding factor 2 / Telomere repeat-binding factor, dimerisation domain superfamily / Telomere repeat-binding factor, dimerisation domain / Telomere repeat binding factor (TRF) / Myb-like domain profile. / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Terfa protein
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsJin, Z. / Park, J.H. / Yun, J.H. / Park, S.Y. / Lee, W.
CitationJournal: To Be Published
Title: Crystal structure of DBD plasma treated zebrafish TRF2 myb-domain complexed with DNA
Authors: Jin, Y. / Park, J.H. / Yun, J.H. / Park, S.Y. / Lee, W.
History
DepositionMay 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

Downloads & links

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Assembly

Deposited unit
A: Terfa protein
C: DNA (5'-D(*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')
D: DNA (5'-D(*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*A)-3')
B: Terfa protein
E: DNA (5'-D(*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')
F: DNA (5'-D(*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)27,1346
Polymers27,1346
Non-polymers00
Water23413
1
A: Terfa protein
C: DNA (5'-D(*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')
D: DNA (5'-D(*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)13,8463
Polymers13,8463
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-16 kcal/mol
Surface area6780 Å2
MethodPISA
2
B: Terfa protein
E: DNA (5'-D(*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')
F: DNA (5'-D(*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)13,2873
Polymers13,2873
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-15 kcal/mol
Surface area6660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.211, 64.211, 143.706
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Terfa protein / Zebrafish TELOMERIC REPEAT BINDING FACTOR2


Mass: 6521.669 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: terfa / Production host: Escherichia coli (E. coli) / References: UniProt: Q4QRH9
#4: Protein Terfa protein / Zebrafish TELOMERIC REPEAT BINDING FACTOR2


Mass: 6620.800 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: terfa / Production host: Escherichia coli (E. coli) / References: UniProt: Q4QRH9

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DNA chain , 3 types, 4 molecules CDFE

#2: DNA chain DNA (5'-D(*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')


Mass: 3773.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*A)-3')


Mass: 3551.346 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#5: DNA chain DNA (5'-D(*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')


Mass: 3115.050 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 1 types, 13 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.15 Å3/Da / Density % sol: 60.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 20-25% (w/v) polyethylene glycol 3000, 100 mM Sodium acetate/acetic acid, pH 4.5

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→36.297 Å / Num. obs: 12151 / % possible obs: 97.67 % / Redundancy: 7.8 % / Biso Wilson estimate: 57.03 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 16.11
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.783 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1097

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1w0u

1w0u


Resolution: 2.5→36.293 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.97
RfactorNum. reflection% reflection
Rfree0.2444 1204 9.91 %
Rwork0.2246 --
obs0.2266 12151 97.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.65 Å2 / Biso mean: 51.7307 Å2 / Biso min: 32.6 Å2
Refinement stepCycle: final / Resolution: 2.5→36.293 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms923 928 0 13 1864
Biso mean---48.34 -
Num. residues----155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031985
X-RAY DIFFRACTIONf_angle_d0.4842864
X-RAY DIFFRACTIONf_chiral_restr0.029308
X-RAY DIFFRACTIONf_plane_restr0.002199
X-RAY DIFFRACTIONf_dihedral_angle_d22.0941000
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5001-2.60020.48451090.413598882
2.6002-2.71850.34181290.3234117196
2.7185-2.86180.35491330.29151231100
2.8618-3.0410.3081320.28091228100
3.041-3.27570.27661400.23791241100
3.2757-3.6050.25371360.22341217100
3.605-4.12610.21611360.22151254100
4.1261-5.1960.19771390.19691274100
5.196-36.2930.21351500.18091343100

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