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- PDB-4gfb: Rap1/DNA complex -

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Basic information

Entry
Database: PDB / ID: 4gfb
TitleRap1/DNA complex
Components
  • (telomeric DNA) x 2
  • DNA-binding protein RAP1
KeywordsTranscription/DNA / double-Myb / Transcription-DNA complex
Function / homology
Function and homology information


positive regulation of ribosomal protein gene transcription by RNA polymerase II / G-quadruplex DNA formation / telomeric G-quadruplex DNA binding / protection from non-homologous end joining at telomere / establishment of protein localization to telomere / establishment of protein localization to chromatin / telomere maintenance via telomere lengthening / shelterin complex / double-stranded telomeric DNA binding / G-quadruplex DNA binding ...positive regulation of ribosomal protein gene transcription by RNA polymerase II / G-quadruplex DNA formation / telomeric G-quadruplex DNA binding / protection from non-homologous end joining at telomere / establishment of protein localization to telomere / establishment of protein localization to chromatin / telomere maintenance via telomere lengthening / shelterin complex / double-stranded telomeric DNA binding / G-quadruplex DNA binding / silent mating-type cassette heterochromatin formation / regulation of glycolytic process / DNA binding, bending / nucleosomal DNA binding / nuclear chromosome / telomeric DNA binding / TFIID-class transcription factor complex binding / subtelomeric heterochromatin formation / cis-regulatory region sequence-specific DNA binding / telomere maintenance / TBP-class protein binding / protein-DNA complex / histone binding / transcription regulator complex / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromosome, telomeric region / DNA-binding transcription factor activity / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus / cytosol
Similarity search - Function
Rap1, DNA-binding domain / Rap1, DNA-binding / TRF2-interacting telomeric protein/Rap1, C-terminal / TRF2-interacting telomeric protein/Rap1, C-terminal domain superfamily / TRF2-interacting telomeric protein/Rap1 - C terminal domain / TE2IP/Rap1 / BRCT domain / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain ...Rap1, DNA-binding domain / Rap1, DNA-binding / TRF2-interacting telomeric protein/Rap1, C-terminal / TRF2-interacting telomeric protein/Rap1, C-terminal domain superfamily / TRF2-interacting telomeric protein/Rap1 - C terminal domain / TE2IP/Rap1 / BRCT domain / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / breast cancer carboxy-terminal domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / Homeodomain-like / SANT/Myb domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA-binding protein RAP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsLe Bihan, Y.-V. / Matot, B. / Le Du, M.-H.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Effect of Rap1 binding on DNA distortion and potassium permanganate hypersensitivity.
Authors: Le Bihan, Y.V. / Matot, B. / Pietrement, O. / Giraud-Panis, M.J. / Gasparini, S. / Le Cam, E. / Gilson, E. / Sclavi, B. / Miron, S. / Le Du, M.H.
#1: Journal: Nucleic Acids Res. / Year: 2012
Title: The orientation of the C-terminal domain of the Saccharomyces cerevisiae Rap1 protein is determined by its binding to DNA.
Authors: Matot, B. / Le Bihan, Y.-V. / Lescasse, R. / Perez, J. / Miron, S. / David, G. / Castaing, B. / Weber, P. / Raynal, B. / Zinn-Justin, S. / Gasparini, S. / Le Du, M.-H.
History
DepositionAug 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-binding protein RAP1
C: telomeric DNA
D: telomeric DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0954
Polymers51,0553
Non-polymers401
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7790 Å2
ΔGint-41 kcal/mol
Surface area21900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.830, 122.650, 149.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein DNA-binding protein RAP1 / Repressor/activator site-binding protein / SBF-E / TUF


Mass: 31988.744 Da / Num. of mol.: 1 / Fragment: 358-596
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RAP1, GRF1, TUF1, YNL216W, N1310 / Production host: Escherichia coli (E. coli) / References: UniProt: P11938
#2: DNA chain telomeric DNA


Mass: 9398.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#3: DNA chain telomeric DNA


Mass: 9668.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.86 Å3/Da / Density % sol: 57.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100mM Tris-HCl pH 8.0, 20% PEGmme-550, 100mM CaCl2, 5% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.99→36.27 Å / Num. all: 12206 / Num. obs: 11279 / % possible obs: 92.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 66.52 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 16.61
Reflection shellResolution: 2.99→3.13 Å / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 3.1 / % possible all: 78.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
BUSTER2.8.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UKG

3ukg


Resolution: 2.99→36.27 Å / Cor.coef. Fo:Fc: 0.9152 / Cor.coef. Fo:Fc free: 0.8513 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.269 603 5 %RANDOM
Rwork0.2044 ---
obs0.2076 11279 --
all-12206 --
Displacement parametersBiso mean: 68.15 Å2
Baniso -1Baniso -2Baniso -3
1--16.2102 Å20 Å20 Å2
2--7.5661 Å20 Å2
3---8.6441 Å2
Refine analyzeLuzzati coordinate error obs: 0.415 Å
Refinement stepCycle: LAST / Resolution: 2.99→36.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1813 1231 1 12 3057
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013238HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.414633HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1364SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes48HARMONIC2
X-RAY DIFFRACTIONt_gen_planes331HARMONIC5
X-RAY DIFFRACTIONt_it3238HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.81
X-RAY DIFFRACTIONt_other_torsion22.54
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion414SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3375SEMIHARMONIC4
LS refinement shellResolution: 2.99→3.27 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3652 136 5.01 %
Rwork0.247 2578 -
all0.2529 2714 -

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