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- PDB-5wir: Structure of the TRF1-TERB1 interface -

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Basic information

Entry
Database: PDB / ID: 5wir
TitleStructure of the TRF1-TERB1 interface
Components
  • TERB1-TBM
  • Telomeric repeat-binding factor 1
KeywordsDNA BINDING PROTEIN / meiosis / telomere / CDK phosphorylation
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 capping / 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 / 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 / telomere maintenance / Meiotic synapsis / 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
AuthorsNandakumar, J. / Pendlebury, D.F. / Smith, E.M. / Tesmer, V.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R00CA167644 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM120094 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)R01AG050509 United States
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Dissecting the telomere-inner nuclear membrane interface formed in meiosis.
Authors: Pendlebury, D.F. / Fujiwara, Y. / Tesmer, V.M. / Smith, E.M. / Shibuya, H. / Watanabe, Y. / Nandakumar, J.
History
DepositionJul 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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
D: TERB1-TBM
B: Telomeric repeat-binding factor 1
C: TERB1-TBM
A: Telomeric repeat-binding factor 1


Theoretical massNumber of molelcules
Total (without water)50,5444
Polymers50,5444
Non-polymers00
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, immunoprecipitation, not from IP, but we have evidence for the TERFH-TERB1 complex from GST pull down
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-34 kcal/mol
Surface area20560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.720, 161.720, 45.170
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein/peptide TERB1-TBM


Mass: 1858.284 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The N-terminal serine remains after cleavage of the purification tag.
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NA31*PLUS
#2: Protein Telomeric repeat-binding factor 1 / NIMA-interacting protein 2 / TTAGGG repeat-binding factor 1 / Telomeric protein Pin2/TRF1


Mass: 23413.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The N-terminal serine remains after cleavage of the purification tag.
Source: (gene. exp.) Homo sapiens (human) / Gene: TERF1, PIN2, TRBF1, TRF, TRF1 / Production host: Escherichia coli (E. coli) / References: UniProt: P54274
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 3.37 Å3/Da / Density % sol: 63.54 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: TRF1-TRFH and TERB1-TBM were mixed in a 1:5 molar ratio and crystal screens set up using 0.3 microliter protein solution and 0.3 microliter reservoir solution in a sitting drop format. ...Details: TRF1-TRFH and TERB1-TBM were mixed in a 1:5 molar ratio and crystal screens set up using 0.3 microliter protein solution and 0.3 microliter reservoir solution in a sitting drop format. Diffracting crystals were obtained in 0.1 M Tris-Cl (pH 8.5) and 30% PEG 300. Crystals were cryoprotected in the crystallization solution plus 10% PEG 400 and harvested in liquid nitrogen.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.1→52.94 Å / Num. obs: 39942 / % possible obs: 100 % / Redundancy: 11.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.036 / Net I/σ(I): 12.4
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 3.8 / Num. unique all: 3274 / CC1/2: 0.939 / Rpim(I) all: 0.166 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BQO

3bqo


Resolution: 2.1→46.685 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.68
RfactorNum. reflection% reflection
Rfree0.2104 1962 4.92 %
Rwork0.179 --
obs0.1806 39913 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→46.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3446 0 0 332 3778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093508
X-RAY DIFFRACTIONf_angle_d0.9934710
X-RAY DIFFRACTIONf_dihedral_angle_d14.4311312
X-RAY DIFFRACTIONf_chiral_restr0.041522
X-RAY DIFFRACTIONf_plane_restr0.004602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.15260.22061370.19322751X-RAY DIFFRACTION100
2.1526-2.21080.22651330.19152624X-RAY DIFFRACTION100
2.2108-2.27580.22221170.19042715X-RAY DIFFRACTION100
2.2758-2.34930.23721420.19162687X-RAY DIFFRACTION100
2.3493-2.43320.23481400.18362690X-RAY DIFFRACTION100
2.4332-2.53070.21661430.18342691X-RAY DIFFRACTION100
2.5307-2.64580.19971390.19112701X-RAY DIFFRACTION100
2.6458-2.78530.23351340.1872681X-RAY DIFFRACTION100
2.7853-2.95980.25021530.20382675X-RAY DIFFRACTION100
2.9598-3.18830.231440.19482731X-RAY DIFFRACTION100
3.1883-3.5090.21081620.19242698X-RAY DIFFRACTION100
3.509-4.01650.19861590.16712694X-RAY DIFFRACTION100
4.0165-5.05940.20551400.15262757X-RAY DIFFRACTION100
5.0594-46.69610.16871190.16852856X-RAY DIFFRACTION100

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