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- PDB-1h6o: Dimerisation domain from human TRF1 -

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Basic information

Entry
Database: PDB / ID: 1h6o
TitleDimerisation domain from human TRF1
ComponentsTELOMERIC REPEAT BINDING FACTOR 1
KeywordsTELOMERE BINDING / TRF1 / TELOMERE / DIMERISATION / TRFH / DNA-BINDING / NUCLEAR PROTEIN
Function / homology
Function and homology information


positive regulation of shelterin complex assembly / negative regulation of establishment of protein localization to telomere / negative regulation of establishment of RNA localization to telomere / negative regulation of establishment of protein-containing complex localization to telomere / negative regulation of telomere maintenance via semi-conservative replication / : / negative regulation of telomeric D-loop disassembly / meiotic telomere clustering / t-circle formation / telomeric D-loop disassembly ...positive regulation of shelterin complex assembly / negative regulation of establishment of protein localization to telomere / negative regulation of establishment of RNA localization to telomere / negative regulation of establishment of protein-containing complex localization to telomere / negative regulation of telomere maintenance via semi-conservative replication / : / negative regulation of telomeric D-loop disassembly / meiotic telomere clustering / t-circle formation / telomeric D-loop disassembly / shelterin complex / Telomere C-strand synthesis initiation / double-stranded telomeric DNA binding / ankyrin repeat 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 / DNA binding, bending / negative regulation of telomere maintenance via telomere lengthening / telomeric DNA binding / negative regulation of DNA replication / negative regulation of telomere maintenance via telomerase / positive regulation of telomere maintenance / Telomere Extension By Telomerase / telomere maintenance via 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 / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere maintenance / DNA Damage/Telomere Stress Induced Senescence / spindle / fibrillar center / microtubule binding / chromosome, telomeric region / nuclear body / response to xenobiotic stimulus / cell division / nucleolus / protein homodimerization activity / DNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Telomere repeat-binding factor, dimerisation domain / : / 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 ...Telomere repeat-binding factor, dimerisation domain / : / 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 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.9 Å
AuthorsFairall, L. / Chapman, L. / Rhodes, D.
Citation
Journal: Mol.Cell / Year: 2001
Title: Structure of the TRFH dimerization domain of the human telomeric proteins TRF1 and TRF2.
Authors: Fairall, L. / Chapman, L. / Moss, H. / de Lange, T. / Rhodes, D.
#1: Journal: Science / Year: 1995
Title: A Human Telomeric Protein
Authors: Chong, L. / Van Steensel, B. / Broccoli, D. / Erdjument-Bromage, H. / Hannish, J. / Tempst, P. / 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.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _diffrn_radiation.pdbx_diffrn_protocol
Revision 1.4Oct 9, 2019Group: Data collection / Database references / Other / Category: citation / pdbx_database_status
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI / _pdbx_database_status.status_code_sf
Revision 1.5Apr 24, 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

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Assembly

Deposited unit
A: TELOMERIC REPEAT BINDING FACTOR 1


Theoretical massNumber of molelcules
Total (without water)23,3271
Polymers23,3271
Non-polymers00
Water00
1
A: TELOMERIC REPEAT BINDING FACTOR 1

A: TELOMERIC REPEAT BINDING FACTOR 1


Theoretical massNumber of molelcules
Total (without water)46,6542
Polymers46,6542
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)85.390, 85.390, 91.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein TELOMERIC REPEAT BINDING FACTOR 1 / TRF1


Mass: 23326.758 Da / Num. of mol.: 1 / Fragment: DIMERISATION DOMAIN RESIDUES 63-265
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: P54274

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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: 3.2 Å3/Da / Density % sol: 61 %
Crystal growpH: 6
Details: PH6, 5-15% GLYCEROL, 1-5 MM MAGNESIUM ACETATE, 1 % PEG 8000, pH 6.00
Crystal grow
*PLUS
pH: 9 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMTris-HCl1drop
2200 mM1dropKCl
310 %glycerol1drop
40.5 mMPMSF1drop
510 mMmercaptoethanol1drop
634 mg/mlprotein1drop
7100 mMsodium cacodylate1reservoir
85-15 %glycerol1reservoir
91-5 mM1reservoirMg(OAc)2
101 %PEG80001reservoir

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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: Mar 15, 2000 / 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: 2.9→23.69 Å / Num. obs: 8514 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Biso Wilson estimate: 60.65 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 8.4
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 5 / Rsym value: 0.14 / % possible all: 97.1
Reflection
*PLUS
Num. measured all: 45019

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
SOLVEphasing
SHARPphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.9→24.84 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 4200344.17 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.303 801 9.8 %RANDOM
Rwork0.25 ---
obs0.25 8186 92.1 %-
Solvent computationSolvent model: FLAT MODEL / ksol: 0.290203 e/Å3
Displacement parametersBiso mean: 64.6 Å2
Baniso -1Baniso -2Baniso -3
1-16.5 Å219.54 Å20 Å2
2--16.5 Å20 Å2
3----33.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.9→24.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1475 0 0 0 1475
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.472
X-RAY DIFFRACTIONc_scbond_it1.762
X-RAY DIFFRACTIONc_scangle_it2.762.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.4 84 7.1 %
Rwork0.325 1099 -
obs--81.9 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.25 / Rfactor Rwork: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74
LS refinement shell
*PLUS
Rfactor Rfree: 0.4

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