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- PDB-1ign: DNA-BINDING DOMAIN OF RAP1 IN COMPLEX WITH TELOMERIC DNA SITE -

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Basic information

Entry
Database: PDB / ID: 1ign
TitleDNA-BINDING DOMAIN OF RAP1 IN COMPLEX WITH TELOMERIC DNA SITE
Components
  • DNA (5'-D(*CP*CP*GP*CP*AP*CP*AP*CP*CP*CP*AP*CP*AP*CP*AP*CP*C P*AP*G)-3')
  • DNA (5'-D(*CP*CP*TP*GP*GP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*TP*G P*CP*G)-3')
  • PROTEIN (RAP1)
KeywordsDNA BINDING PROTEIN/DNA / RAP1 / YEAST / TELOMERES / HOMOEODOMAIN / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


positive regulation of ribosomal protein gene transcription by RNA polymerase II / G-quadruplex DNA formation / protection from non-homologous end joining at telomere / establishment of protein localization to chromatin / establishment of protein localization to telomere / telomere maintenance via telomere lengthening / shelterin complex / G-quadruplex DNA binding / double-stranded telomeric DNA binding / silent mating-type cassette heterochromatin formation ...positive regulation of ribosomal protein gene transcription by RNA polymerase II / G-quadruplex DNA formation / protection from non-homologous end joining at telomere / establishment of protein localization to chromatin / establishment of protein localization to telomere / telomere maintenance via telomere lengthening / shelterin complex / G-quadruplex DNA binding / double-stranded telomeric DNA binding / silent mating-type cassette heterochromatin formation / nucleosomal DNA binding / DNA binding, bending / regulation of glycolytic process / nuclear chromosome / telomeric DNA binding / subtelomeric heterochromatin formation / TFIID-class transcription factor complex binding / cis-regulatory region sequence-specific DNA binding / TBP-class protein binding / telomere maintenance / protein-DNA complex / histone binding / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / chromosome, telomeric region / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / regulation of DNA-templated transcription / 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 / TRF2-interacting telomeric protein/Rap1, C-terminal / TRF2-interacting telomeric protein/Rap1, C-terminal domain superfamily / Rap1, DNA-binding / TRF2-interacting telomeric protein/Rap1 - C terminal domain / TE2IP/Rap1 / BRCT domain, a BRCA1 C-terminus domain / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain ...Rap1, DNA-binding domain / TRF2-interacting telomeric protein/Rap1, C-terminal / TRF2-interacting telomeric protein/Rap1, C-terminal domain superfamily / Rap1, DNA-binding / TRF2-interacting telomeric protein/Rap1 - C terminal domain / TE2IP/Rap1 / BRCT domain, a BRCA1 C-terminus domain / 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 / breast cancer carboxy-terminal domain / Homeodomain-like / 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 / Resolution: 2.25 Å
AuthorsKoenig, P. / Giraldo, R. / Chapman, L. / Rhodes, D.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1996
Title: The crystal structure of the DNA-binding domain of yeast RAP1 in complex with telomeric DNA.
Authors: Konig, P. / Giraldo, R. / Chapman, L. / Rhodes, D.
#1: Journal: Embo J. / Year: 1994
Title: The Yeast Telomere-Binding Protein RAP1 Binds to and Promotes the Formation of DNA Quadruplexes in Telomeric DNA
Authors: Giraldo, R. / Rhodes, D.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1987
Title: Purification and Cloning of a DNA Binding Protein from Yeast that Binds to Both Silencer and Activator Elements
Authors: Shore, D. / Nasmyth, K.
History
DepositionFeb 29, 1996Deposition site: BNL / Processing site: NDB
Revision 1.0Jan 27, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Database references / Category: struct_ref / struct_ref_seq
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
C: DNA (5'-D(*CP*CP*GP*CP*AP*CP*AP*CP*CP*CP*AP*CP*AP*CP*AP*CP*C P*AP*G)-3')
D: DNA (5'-D(*CP*CP*TP*GP*GP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*TP*G P*CP*G)-3')
E: DNA (5'-D(*CP*CP*GP*CP*AP*CP*AP*CP*CP*CP*AP*CP*AP*CP*AP*CP*C P*AP*G)-3')
F: DNA (5'-D(*CP*CP*TP*GP*GP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*TP*G P*CP*G)-3')
A: PROTEIN (RAP1)
B: PROTEIN (RAP1)


Theoretical massNumber of molelcules
Total (without water)80,6356
Polymers80,6356
Non-polymers00
Water3,711206
1
C: DNA (5'-D(*CP*CP*GP*CP*AP*CP*AP*CP*CP*CP*AP*CP*AP*CP*AP*CP*C P*AP*G)-3')
D: DNA (5'-D(*CP*CP*TP*GP*GP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*TP*G P*CP*G)-3')
A: PROTEIN (RAP1)


Theoretical massNumber of molelcules
Total (without water)40,3183
Polymers40,3183
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: DNA (5'-D(*CP*CP*GP*CP*AP*CP*AP*CP*CP*CP*AP*CP*AP*CP*AP*CP*C P*AP*G)-3')
F: DNA (5'-D(*CP*CP*TP*GP*GP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*TP*G P*CP*G)-3')
B: PROTEIN (RAP1)


Theoretical massNumber of molelcules
Total (without water)40,3183
Polymers40,3183
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.610, 90.610, 80.360
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.57, 0.8216, -0.0054), (0.8217, -0.57, 0.0067), (0.0024, -0.0082, -1)
Vector: -42.46, 81.58, 80.71)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 360 .. A 594 B 360 .. B 594 0.62

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Components

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


Mass: 5673.695 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*CP*TP*GP*GP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*TP*G P*CP*G)-3')


Mass: 5939.803 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Protein PROTEIN (RAP1)


Mass: 28704.143 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Description: T7 PROMOTER / Gene: RAP1 DNA BINDING DOMAIN / Plasmid: PET3C / Gene (production host): RAP1 DNA BINDING DOMAIN 353 TO 598 / Production host: Escherichia coli (E. coli) / References: UniProt: P11938
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 49.1 %
Crystal
*PLUS
Density % sol: 49.1 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.08-0.1 mMprotein-DNA complex1drop
220 mMMES1droppH6.0
320 mM1dropKCl
42 mMspermine1drop
510-20 %MPD1drop
640 %MPD1reservoir

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Data collection

DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 22, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.25→16 Å / Num. obs: 33281 / % possible obs: 96 % / Observed criterion σ(I): 4 / Redundancy: 2.9 % / Rmerge(I) obs: 0.047
Reflection
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 16 Å / % possible obs: 96 % / Observed criterion σ(I): 4 / Redundancy: 2.9 % / Rmerge(I) obs: 0.047

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4data reduction
RefinementResolution: 2.25→16 Å / σ(F): 2
Details: ESTIMATED COORD. ERROR 0.426 ANGSTROMS FINAL RMS COORD. SHIFT 0.111 ANGSTROMS
RfactorNum. reflection% reflection
Rfree0.294 -5 %
Rwork0.219 --
obs0.219 33264 95.9 %
Displacement parametersBiso mean: 30 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.25→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3178 1524 0 206 4908
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.61
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 16 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.219 / Rfactor Rfree: 0.294 / Rfactor Rwork: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2.9
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.61

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