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- PDB-1h6p: Dimeristion domain from human TRF2 -

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Basic information

Entry
Database: PDB / ID: 1h6p
TitleDimeristion domain from human TRF2
ComponentsTELOMERIC REPEAT BINDING FACTOR 2
KeywordsTELOMERE BINDING / TRF2 / TELOMERE / DIMERISATION / TRFH / DNA-BINDING / NUCLEAR PROTEIN
Function / homology
Function and homology information


axonal transport of messenger ribonucleoprotein complex / 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 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 telomere maintenance ...axonal transport of messenger ribonucleoprotein complex / 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 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 telomere maintenance / negative regulation of t-circle formation / telomeric D-loop disassembly / shelterin complex / Telomere C-strand synthesis initiation / regulation of telomere maintenance via telomerase / double-stranded telomeric DNA binding / Telomere C-strand (Lagging Strand) Synthesis / nuclear telomere cap complex / G-rich strand telomeric DNA binding / telomere capping / 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 / regulation of telomere maintenance / negative regulation of telomere maintenance via telomere lengthening / protein localization to chromosome, telomeric region / telomeric DNA binding / negative regulation of telomere maintenance via telomerase / positive regulation of telomere maintenance / negative regulation of cellular senescence / Telomere Extension By Telomerase / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere maintenance / Inhibition of DNA recombination at telomere / Meiotic synapsis / male germ cell nucleus / DNA Damage/Telomere Stress Induced Senescence / cellular senescence / in utero embryonic development / chromosome, telomeric region / nuclear body / axon / protein-containing complex binding / enzyme binding / protein homodimerization activity / nucleoplasm / nucleus
Similarity search - Function
Telomere repeat-binding factor, dimerisation domain / Telomeric repeat-binding factor 2, Rap1-binding domain / Telomeric repeat-binding factor 2 Rap1-binding motif / 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) / Myb-type HTH DNA-binding domain profile. / Myb domain ...Telomere repeat-binding factor, dimerisation domain / Telomeric repeat-binding factor 2, Rap1-binding domain / Telomeric repeat-binding factor 2 Rap1-binding motif / 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) / 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 / Homeobox-like domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Telomeric repeat-binding factor 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.2 Å
AuthorsChapman, L. / Fairall, L. / Rhodes, D.
Citation
Journal: Mol.Cell / Year: 2001
Title: Structure of the Trfh Dimerization Domain of the Human Telomere Proteins Trf1 and Trf2
Authors: Fairall, L. / Chapman, L. / Moss, H. / de Lange, T. / Rhodes, D.
#1: Journal: Nat.Genet. / Year: 1997
Title: Telomeric Localisation of Trf2, a Novel Human Telobox Protein
Authors: Bilaud, T. / Brun, C. / Ancelin, K. / Koering, C.E. / Laroche, T. / Gilson, E.
#2: Journal: Nat.Genet. / Year: 1997
Title: Human Telomere Contain Two Distinct Myb-Related Proteins, Trf1 and Trf2
Authors: Broccoli, D. / Smogorzewska, A. / Chong, L. / de Lange, T.
History
DepositionJun 20, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 13, 2018Group: Data collection / Database references / Category: citation / citation_author / diffrn_radiation
Item: _citation.page_last / _citation_author.name / _diffrn_radiation.pdbx_diffrn_protocol
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TELOMERIC REPEAT BINDING FACTOR 2
B: TELOMERIC REPEAT BINDING FACTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3593
Polymers47,3352
Non-polymers241
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)117.041, 80.284, 52.816
Angle α, β, γ (deg.)90.00, 101.95, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1246-

MG

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.795, -0.0393, 0.6053), (0.0243, -0.9992, -0.0329), (0.6061, -0.0115, 0.7953)
Vector: 60.9461, 0.5817, 7.346)

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Components

#1: Protein TELOMERIC REPEAT BINDING FACTOR 2 / TRF2 / TTAGGG REPEAT BINDING FACTOR 2


Mass: 23667.596 Da / Num. of mol.: 2 / Fragment: DIMERISATION DOMAIN RESIDUES 43-245
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cellular location: NUCLEUS / Plasmid: PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15554
#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.6 Å3/Da / Density % sol: 51.6 %
Crystal growpH: 7
Details: PH7.0, 15-20% PEG 8000, 100-200 MM MAGNESIUM ACETATE, pH 7.00
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMTris-HCl1drop
2200 mM1dropKCl
34 %glycerol1drop
40.4 mMPMSF1drop
54 mMmercaptoethanol1drop
620 mg/mlprotein1drop
7100 mMTris-HCl1reservoir
815-20 %PEG80001reservoir
9100-200 mM1reservoirMg(OAc)2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 15, 1999 / Details: MIRRORS
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.2→26.63 Å / Num. obs: 24415 / % possible obs: 99.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 43.66 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 9.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.231 / % possible all: 99.1
Reflection
*PLUS
Num. measured all: 89685

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
SOLVEphasing
SHARPphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.2→23.72 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.268 2285 9.6 %RANDOM
Rwork0.235 ---
obs0.235 23767 97.6 %-
Solvent computationSolvent model: FLAT MODEL / ksol: 0.363168 e/Å3
Displacement parametersBiso mean: 42.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.57 Å20 Å20.25 Å2
2--2.21 Å20 Å2
3----3.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.2→23.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2923 0 1 133 3057
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.392
X-RAY DIFFRACTIONc_scbond_it12.132
X-RAY DIFFRACTIONc_scangle_it12.392.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 386 10.2 %
Rwork0.24 3389 -
obs--93.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73
LS refinement shell
*PLUS
Rfactor Rwork: 0.24

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