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- PDB-3k6g: Crystal structure of Rap1 and TRF2 complex -

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Basic information

Entry
Database: PDB / ID: 3k6g
TitleCrystal structure of Rap1 and TRF2 complex
Components
  • Telomeric repeat-binding factor 2-interacting protein 1
  • Telomeric repeat-binding factor 2
KeywordsPROTEIN BINDING / helix / Chromosomal protein / Nucleus / Phosphoprotein / Telomere / Cell cycle / DNA-binding
Function / homology
Function and homology information


negative regulation of DNA recombination at telomere / negative regulation of telomere maintenance / axonal transport of messenger ribonucleoprotein complex / negative regulation of beta-galactosidase activity / negative regulation of telomere single strand break repair / negative regulation of telomere maintenance via recombination / telomeric loop formation / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly ...negative regulation of DNA recombination at telomere / negative regulation of telomere maintenance / axonal transport of messenger ribonucleoprotein complex / negative regulation of beta-galactosidase activity / negative regulation of telomere single strand break repair / negative regulation of telomere maintenance via recombination / telomeric loop formation / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / negative regulation of telomere capping / protection from non-homologous end joining at telomere / negative regulation of t-circle formation / telomerase activity / telomere maintenance via telomere lengthening / telomeric D-loop disassembly / shelterin complex / Telomere C-strand synthesis initiation / double-stranded telomeric DNA binding / regulation of telomere maintenance via telomerase / Telomere C-strand (Lagging Strand) Synthesis / positive regulation of telomere maintenance / nuclear telomere cap complex / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / anterograde axonal transport / G-rich strand telomeric DNA binding / telomere capping / regulation of telomere maintenance / negative regulation of telomere maintenance via telomere lengthening / protein localization to chromosome, telomeric region / regulation of double-strand break repair via homologous recombination / nuclear chromosome / telomeric DNA binding / negative regulation of cellular senescence / negative regulation of telomere maintenance via telomerase / Telomere Extension By Telomerase / telomere maintenance via telomerase / phosphatase binding / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / axon cytoplasm / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere maintenance / negative regulation of protein phosphorylation / male germ cell nucleus / positive regulation of nitric-oxide synthase activity / DNA Damage/Telomere Stress Induced Senescence / positive regulation of non-canonical NF-kappaB signal transduction / cellular senescence / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / in utero embryonic development / chromosome, telomeric region / nuclear body / intracellular signal transduction / cell cycle / negative regulation of gene expression / protein-containing complex binding / regulation of DNA-templated transcription / positive regulation of gene expression / enzyme binding / protein homodimerization activity / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Rap1 Myb domain / Rap1 Myb domain / TRF2-interacting telomeric protein/Rap1, C-terminal / TRF2-interacting telomeric protein/Rap1, C-terminal domain superfamily / TRF2-interacting telomeric protein/Rap1 - C terminal domain / Telomeric repeat-binding factor 2, Rap1-binding domain / Telomeric repeat-binding factor 2 Rap1-binding motif / TE2IP/Rap1 / Telomeric repeat-binding factor 2 / Telomeric repeat-binding factor 1/2 ...Rap1 Myb domain / Rap1 Myb domain / TRF2-interacting telomeric protein/Rap1, C-terminal / TRF2-interacting telomeric protein/Rap1, C-terminal domain superfamily / TRF2-interacting telomeric protein/Rap1 - C terminal domain / Telomeric repeat-binding factor 2, Rap1-binding domain / Telomeric repeat-binding factor 2 Rap1-binding motif / TE2IP/Rap1 / Telomeric repeat-binding factor 2 / Telomeric repeat-binding factor 1/2 / Telomere repeat-binding factor, dimerisation domain superfamily / Telomere repeat-binding factor, dimerisation domain / Telomere repeat binding factor (TRF) / 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 / BRCT domain / BRCT domain superfamily / Homeobox-like domain superfamily
Similarity search - Domain/homology
Telomeric repeat-binding factor 2 / Telomeric repeat-binding factor 2-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.95 Å
AuthorsChen, Y. / Rai, R. / Yang, Y.T. / Zheng, H. / Chang, S. / 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
DepositionOct 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Telomeric repeat-binding factor 2-interacting protein 1
B: Telomeric repeat-binding factor 2-interacting protein 1
C: Telomeric repeat-binding factor 2-interacting protein 1
D: Telomeric repeat-binding factor 2
E: Telomeric repeat-binding factor 2
F: Telomeric repeat-binding factor 2


Theoretical massNumber of molelcules
Total (without water)50,1826
Polymers50,1826
Non-polymers00
Water4,053225
1
A: Telomeric repeat-binding factor 2-interacting protein 1
D: Telomeric repeat-binding factor 2


Theoretical massNumber of molelcules
Total (without water)16,7272
Polymers16,7272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-20 kcal/mol
Surface area7260 Å2
MethodPISA
2
B: Telomeric repeat-binding factor 2-interacting protein 1
E: Telomeric repeat-binding factor 2


Theoretical massNumber of molelcules
Total (without water)16,7272
Polymers16,7272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-23 kcal/mol
Surface area7350 Å2
MethodPISA
3
C: Telomeric repeat-binding factor 2-interacting protein 1
F: Telomeric repeat-binding factor 2


Theoretical massNumber of molelcules
Total (without water)16,7272
Polymers16,7272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-19 kcal/mol
Surface area7380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.568, 72.105, 150.993
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Telomeric repeat-binding factor 2-interacting protein 1 / TRF2-interacting telomeric protein Rap1 / hRap1


Mass: 12110.344 Da / Num. of mol.: 3 / Fragment: Rap1 C-terminal domain (residues 303-399)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TERF2IP, RAP1, PP8000 / Plasmid: PET28sumo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9NYB0
#2: Protein/peptide Telomeric repeat-binding factor 2 / / TTAGGG repeat-binding factor 2 / Telomeric DNA-binding protein


Mass: 4617.044 Da / Num. of mol.: 3 / Fragment: TRF2 (residues 275-316)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TERF2, TRBF2, TRF2 / Plasmid: PET28sumo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q15554
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.31 Å3/Da / Density % sol: 46.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 20% PEG2K, 16% isopropanol, 0.1 M sodium Citrate, 10 mM DTT, pH 5.2, 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 34177 / Num. obs: 33796 / % possible obs: 98.9 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 40.3

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Processing

Software
NameVersionClassification
SHARPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 1.95→50 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2356 6302 -
Rwork0.2242 --
all-65428 -
obs-33796 97.6 %
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2959 0 0 225 3184
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004895
X-RAY DIFFRACTIONc_angle_deg0.99954
X-RAY DIFFRACTIONc_dihedral_angle_d17.90525
X-RAY DIFFRACTIONc_improper_angle_d0.7048

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