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- PDB-4rqi: Structure of TRF2/RAP1 secondary interaction binding site -

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Basic information

Entry
Database: PDB / ID: 4rqi
TitleStructure of TRF2/RAP1 secondary interaction binding site
Components
  • Telomeric repeat-binding factor 2
  • Telomeric repeat-binding factor 2-interacting protein 1
KeywordsCELL CYCLE / telomeres
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 / RNA-templated DNA biosynthetic process / negative regulation of t-circle formation / telomeric D-loop disassembly / telomere maintenance via telomere lengthening / 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 / anterograde axonal transport / Removal of the Flap Intermediate from the C-strand / G-rich strand telomeric DNA binding / telomere capping / regulation of telomere maintenance / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / 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 maintenance via telomerase / Telomere Extension By 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 / positive regulation of nitric-oxide synthase activity / negative regulation of protein phosphorylation / male germ cell nucleus / 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 / negative regulation of gene expression / regulation of DNA-templated transcription / positive regulation of gene expression / protein-containing complex binding / enzyme binding / protein homodimerization activity / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Rap1 Myb domain / Rap1 Myb domain / Telomere repeat-binding factor, dimerisation 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 ...Rap1 Myb domain / Rap1 Myb domain / Telomere repeat-binding factor, dimerisation 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Homeobox-like domain superfamily / Alpha Horseshoe / Mainly Alpha
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 / MOLECULAR REPLACEMENT / Resolution: 2.4405 Å
AuthorsMiron, S. / Guimaraes, B. / Gaullier, G. / Giraud-Panis, M.-J. / Gilson, E. / Le Du, M.-H.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: A higher-order entity formed by the flexible assembly of RAP1 with TRF2.
Authors: Gaullier, G. / Miron, S. / Pisano, S. / Buisson, R. / Le Bihan, Y.V. / Tellier-Lebegue, C. / Messaoud, W. / Roblin, P. / Guimaraes, B.G. / Thai, R. / Giraud-Panis, M.J. / Gilson, E. / Le Du, M.H.
History
DepositionNov 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)103,18811
Polymers102,9808
Non-polymers2083
Water1,69394
1
A: Telomeric repeat-binding factor 2
B: Telomeric repeat-binding factor 2
E: Telomeric repeat-binding factor 2-interacting protein 1
F: Telomeric repeat-binding factor 2-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5825
Polymers51,4904
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-31 kcal/mol
Surface area20010 Å2
MethodPISA
2
C: Telomeric repeat-binding factor 2
D: Telomeric repeat-binding factor 2
G: Telomeric repeat-binding factor 2-interacting protein 1
H: Telomeric repeat-binding factor 2-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6066
Polymers51,4904
Non-polymers1162
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-36 kcal/mol
Surface area20150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.790, 104.850, 85.310
Angle α, β, γ (deg.)90.00, 94.39, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

#1: Protein
Telomeric repeat-binding factor 2 / TTAGGG repeat-binding factor 2 / Telomeric DNA-binding protein


Mass: 23667.596 Da / Num. of mol.: 4 / Fragment: TRFH: residues 43-245
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TERF2, TRBF2, TRF2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15554
#2: Protein/peptide
Telomeric repeat-binding factor 2-interacting protein 1 / TERF2-interacting telomeric protein 1 / TRF2-interacting telomeric protein 1 / Dopamine receptor- ...TERF2-interacting telomeric protein 1 / TRF2-interacting telomeric protein 1 / Dopamine receptor-interacting protein 5 / Repressor/activator protein 1 homolog / RAP1 homolog / hRap1


Mass: 2077.280 Da / Num. of mol.: 4 / Fragment: YXLXP interaction motif: residues 89-106 / Source method: obtained synthetically / Details: RAP1 Peptide sequence / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9NYB0
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.33 Å3/Da / Density % sol: 47.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEGmme 550, Hepes buffer, pH 8.0, VAPOR DIFFUSION, HANGING 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: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 14, 2012
Details: channel cut cryogenically cooled monochromator crystal
RadiationMonochromator: channel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.44→47.02 Å / Num. all: 34700 / Num. obs: 33979 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 60.59 Å2 / Rmerge(I) obs: 0.068
Reflection shellResolution: 2.44→2.63 Å / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 2.26 / % possible all: 79.4

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
MOLREPphasing
BUSTER2.8.0refinement
XDSdata reduction
XDSdata scaling
Pcubedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4405→47.02 Å / Cor.coef. Fo:Fc: 0.9489 / Cor.coef. Fo:Fc free: 0.9286 / SU ML: 0.34 / σ(F): 1.99 / Phase error: 28.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2406 1679 5 %
Rwork0.1974 --
obs0.1996 33575 95.52 %
all-33600 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.1897 Å20 Å27.5197 Å2
2--3.6522 Å20 Å2
3----3.4625 Å2
Refine analyzeLuzzati coordinate error obs: 0.386 Å
Refinement stepCycle: LAST / Resolution: 2.4405→47.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6924 0 13 94 7031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047039
X-RAY DIFFRACTIONf_angle_d0.9769461
X-RAY DIFFRACTIONf_dihedral_angle_d15.252695
X-RAY DIFFRACTIONf_chiral_restr0.0361080
X-RAY DIFFRACTIONf_plane_restr0.0041210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4405-2.51230.3469750.30231425X-RAY DIFFRACTION51
2.5123-2.59340.38651450.28182754X-RAY DIFFRACTION100
2.5934-2.68610.33041460.26542770X-RAY DIFFRACTION99
2.6861-2.79360.30271440.23742737X-RAY DIFFRACTION100
2.7936-2.92070.29331460.23172759X-RAY DIFFRACTION100
2.9207-3.07470.2631460.23622781X-RAY DIFFRACTION100
3.0747-3.26730.28791450.22392763X-RAY DIFFRACTION100
3.2673-3.51950.27451450.20382756X-RAY DIFFRACTION99
3.5195-3.87350.22761470.18692783X-RAY DIFFRACTION99
3.8735-4.43360.20841450.16682753X-RAY DIFFRACTION99
4.4336-5.58450.1971460.17392778X-RAY DIFFRACTION100
5.5845-47.02860.21221490.18122837X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -12.6661 Å / Origin y: 1.4751 Å / Origin z: 22.287 Å
111213212223313233
T0.3609 Å2-0.0112 Å20.0005 Å2-0.2658 Å20.0543 Å2--0.3287 Å2
L0.3998 °2-0.0719 °2-0.0889 °2-0.2531 °20.2114 °2--0.7804 °2
S-0.0052 Å °0.0034 Å °0.0533 Å °-0.0174 Å °-0.0124 Å °-0.0188 Å °-0.0557 Å °0.0138 Å °0.0149 Å °
Refinement TLS groupSelection details: all

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