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- PDB-5xup: Crystal structure of TRF1 and TERB1 -

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Basic information

Entry
Database: PDB / ID: 5xup
TitleCrystal structure of TRF1 and TERB1
Components
  • Telomere repeats-binding bouquet formation protein 1
  • Telomeric repeat-binding factor 1
KeywordsDNA BINDING PROTEIN / telomere / meiosis
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 / meiotic attachment of telomere to nuclear envelope / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / meiotic telomere clustering / t-circle formation ...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 / meiotic attachment of telomere to nuclear envelope / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / meiotic telomere clustering / t-circle formation / telomeric D-loop disassembly / shelterin complex / homologous chromosome pairing at meiosis / Telomere C-strand synthesis initiation / double-strand break repair involved in meiotic recombination / double-stranded telomeric DNA binding / Telomere C-strand (Lagging Strand) Synthesis / : / positive regulation of telomere maintenance / nuclear telomere cap complex / ankyrin repeat binding / 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 / G-rich strand telomeric DNA binding / telomere capping / nuclear inner membrane / 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 / telomere maintenance via telomerase / 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 / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere maintenance / DNA Damage/Telomere Stress Induced Senescence / fibrillar center / spindle / microtubule binding / chromosome, telomeric region / nuclear body / cell division / nucleolus / protein homodimerization activity / DNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Telomere repeats-binding bouquet formation protein 1 / 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 ...Telomere repeats-binding bouquet formation protein 1 / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Homeobox-like domain superfamily / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Telomeric repeat-binding factor 1 / Telomere repeats-binding bouquet formation protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLong, J. / Huang, C. / Wu, J. / Lei, M.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Telomeric TERB1-TRF1 interaction is crucial for male meiosis.
Authors: Long, J. / Huang, C. / Chen, Y. / Zhang, Y. / Shi, S. / Wu, L. / Liu, Y. / Liu, C. / Wu, J. / Lei, M.
History
DepositionJun 24, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
A: Telomeric repeat-binding factor 1
B: Telomeric repeat-binding factor 1
C: Telomere repeats-binding bouquet formation protein 1
D: Telomere repeats-binding bouquet formation protein 1


Theoretical massNumber of molelcules
Total (without water)49,3074
Polymers49,3074
Non-polymers00
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-36 kcal/mol
Surface area20560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.579, 161.579, 45.925
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Telomeric repeat-binding factor 1 / NIMA-interacting protein 2 / TTAGGG repeat-binding factor 1 / Telomeric protein Pin2/TRF1


Mass: 23098.561 Da / Num. of mol.: 2 / Fragment: TRFH domain (UNP RESIDUES 65-266)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TERF1, PIN2, TRBF1, TRF, TRF1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P54274
#2: Protein/peptide Telomere repeats-binding bouquet formation protein 1 / Coiled-coil domain-containing protein 79


Mass: 1554.949 Da / Num. of mol.: 2 / Fragment: TRF1 binding motif (UNP RESIDUES 644-655)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TERB1, CCDC79 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8NA31
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 3.57 Å3/Da / Density % sol: 65.55 % / Mosaicity: 0.167 °
Crystal growTemperature: 289 K / Method: evaporation / pH: 8.5 / Details: 10% 2-propanol, 0.1M Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: CCD / Date: May 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 40395 / % possible obs: 100 % / Redundancy: 10 % / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.04 / Rrim(I) all: 0.127 / Χ2: 0.511 / Net I/σ(I): 3.1 / Num. measured all: 402507
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2
2.1-2.189.80.75539690.8310.2540.7970.429
2.18-2.269.50.56540190.8860.1920.5970.432
2.26-2.3710.30.44839910.9370.1460.4710.441
2.37-2.4910.20.32539950.9620.1060.3420.453
2.49-2.659.80.26340170.9740.0880.2780.459
2.65-2.859.90.19740470.9840.0660.2080.479
2.85-3.1410.40.14240250.9910.0460.150.499
3.14-3.599.70.09940690.9950.0330.1050.558
3.59-4.5210.50.07840740.9960.0250.0820.666
4.52-509.60.07341890.9950.0250.0770.684

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.22data extraction
HKL-2000data collection
MLPHAREmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BQO

3bqo


Resolution: 2.1→46.69 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 8.394 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.273 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2207 2022 5 %RANDOM
Rwork0.1768 ---
obs0.179 38307 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 120.45 Å2 / Biso mean: 44.877 Å2 / Biso min: 17.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20.45 Å20 Å2
2--0.45 Å20 Å2
3----1.47 Å2
Refinement stepCycle: final / Resolution: 2.1→46.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3352 0 0 152 3504
Biso mean---46.34 -
Num. residues----416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193418
X-RAY DIFFRACTIONr_angle_refined_deg0.9851.9494587
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7875413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.30723.58162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.81115650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8471525
X-RAY DIFFRACTIONr_chiral_restr0.0740.2511
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022517
X-RAY DIFFRACTIONr_rigid_bond_restr2.12433418
X-RAY DIFFRACTIONr_sphericity_free30.325572
X-RAY DIFFRACTIONr_sphericity_bonded20.22753437
LS refinement shellResolution: 2.101→2.156 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 154 -
Rwork0.206 2769 -
all-2923 -
obs--99.76 %

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