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- PDB-3owt: Crystal structure of S. cerevisiae RAP1-Sir3 complex -

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Basic information

Entry
Database: PDB / ID: 3owt
TitleCrystal structure of S. cerevisiae RAP1-Sir3 complex
Components
  • DNA-binding protein RAP1
  • Regulatory protein SIR3
KeywordsPROTEIN BINDING / RCT domain
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 / establishment of protein-containing complex localization to telomere / protection from non-homologous end joining at telomere / nuclear-transcribed mRNA catabolic process, non-stop decay / establishment of protein localization to telomere / telomere tethering at nuclear periphery / establishment of protein localization to chromatin / shelterin complex ...positive regulation of ribosomal protein gene transcription by RNA polymerase II / G-quadruplex DNA formation / telomeric G-quadruplex DNA binding / establishment of protein-containing complex localization to telomere / protection from non-homologous end joining at telomere / nuclear-transcribed mRNA catabolic process, non-stop decay / establishment of protein localization to telomere / telomere tethering at nuclear periphery / establishment of protein localization to chromatin / shelterin complex / telomere maintenance via telomere lengthening / double-stranded telomeric DNA binding / G-quadruplex DNA binding / mitotic DNA replication checkpoint signaling / chromatin silencing complex / silent mating-type cassette heterochromatin formation / DNA binding, bending / regulation of glycolytic process / nucleosomal DNA binding / nuclear chromosome / telomeric DNA binding / negative regulation of DNA replication / TFIID-class transcription factor complex binding / DNA replication origin binding / DNA replication initiation / subtelomeric heterochromatin formation / heterochromatin / cis-regulatory region sequence-specific DNA binding / nucleosome binding / telomere maintenance / TBP-class protein binding / protein-DNA complex / double-strand break repair via nonhomologous end joining / heterochromatin formation / single-stranded DNA binding / double-stranded DNA binding / histone binding / transcription regulator complex / sequence-specific DNA binding / nucleic acid 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 / chromatin binding / nucleolus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / identical protein binding / nucleus / cytosol
Similarity search - Function
Arc Repressor Mutant, subunit A - #2170 / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1480 / : / Regulatory protein SIR3, C-terminal 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 ...Arc Repressor Mutant, subunit A - #2170 / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1480 / : / Regulatory protein SIR3, C-terminal 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 / AAA lid domain / AAA lid domain / : / BRCT domain / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / 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 / SANT/Myb domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Regulatory protein SIR3 / DNA-binding protein RAP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChen, Y. / Yang, Y. / Lei, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: A conserved motif within RAP1 has diversified roles in telomere protection and regulation in different organisms.
Authors: Chen, Y. / Rai, R. / Zhou, Z.R. / Kanoh, J. / Ribeyre, C. / Yang, Y. / Zheng, H. / Damay, P. / Wang, F. / Tsujii, H. / Hiraoka, Y. / Shore, D. / Hu, H.Y. / Chang, S. / Lei, M.
History
DepositionSep 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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

Downloads & links

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Assembly

Deposited unit
A: DNA-binding protein RAP1
B: DNA-binding protein RAP1
C: Regulatory protein SIR3


Theoretical massNumber of molelcules
Total (without water)39,5903
Polymers39,5903
Non-polymers00
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.831, 89.831, 211.791
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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


Mass: 18221.559 Da / Num. of mol.: 2 / Fragment: C-terminal domain (UNP residues 672 to 827)
Source method: isolated from a genetically manipulated source
Details: Rap1 C-terminal domain (672-827) was cloned in a PET28b-based vector with an N-terminal Sumo tag.
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GRF1, N1310, RAP1, TUF1, YNL216W / Plasmid: PET28b-sumo-Rap1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11938
#2: Protein/peptide Regulatory protein SIR3 / Silent information regulator 3


Mass: 3146.766 Da / Num. of mol.: 1 / Fragment: Rap1-interaction motif (UNP residues 456 to 481)
Source method: isolated from a genetically manipulated source
Details: Sir3 fragment (456-481) was cloned in a PET28b-based vector with an N-terminal Sumo tag.
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CMT1, L9753.10, MAR2, SIR3, STE8, YLR442C / Plasmid: PET28b-sumo-Sir3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06701
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.08 Å3/Da / Density % sol: 40.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 100 mM sodium citrate pH 4.8, 30% PEG4K, 200 mM ammonium acetate, and 10 mM DTT , VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 19, 2008
RadiationMonochromator: Kohzu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 27940 / % possible obs: 89.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Rmerge(I) obs: 0.064
Reflection shell
Resolution (Å)Rmerge(I) obs% possible all
1.79-1.850.31333.4
1.85-1.930.62769.7
1.93-2.020.44390.4
2.02-2.120.33698.5
2.12-2.260.254100
2.26-2.430.162100
2.43-2.670.104100
2.67-3.060.071100
3.06-3.860.062100
3.86-500.06199.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3CZ6

3cz6


Resolution: 2→38.258 Å / SU ML: 0.31 / σ(F): 0.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2604 2145 9.89 %random
Rwork0.2101 ---
obs0.2151 21686 95.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.86 Å2 / ksol: 0.356 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.7175 Å20 Å2-0 Å2
2--4.7175 Å20 Å2
3----9.435 Å2
Refinement stepCycle: LAST / Resolution: 2→38.258 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2569 0 0 100 2669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082631
X-RAY DIFFRACTIONf_angle_d1.0183549
X-RAY DIFFRACTIONf_dihedral_angle_d17.849991
X-RAY DIFFRACTIONf_chiral_restr0.068381
X-RAY DIFFRACTIONf_plane_restr0.005464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.07160.34291850.28851645X-RAY DIFFRACTION83
2.0716-2.15450.33462060.25421819X-RAY DIFFRACTION91
2.1545-2.25260.30282040.24351924X-RAY DIFFRACTION95
2.2526-2.37130.29192120.24471956X-RAY DIFFRACTION96
2.3713-2.51980.29632260.22971951X-RAY DIFFRACTION98
2.5198-2.71440.29662310.22671988X-RAY DIFFRACTION99
2.7144-2.98740.31272180.24722019X-RAY DIFFRACTION99
2.9874-3.41950.28172030.2252057X-RAY DIFFRACTION100
3.4195-4.30720.22822210.18652065X-RAY DIFFRACTION100
4.3072-38.2650.21562390.1782117X-RAY DIFFRACTION99

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