[English] 日本語
Yorodumi
- PDB-5wir: Structure of the TRF1-TERB1 interface -

+
Open data


ID or keywords:

Loading...

-
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 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 telomeric D-loop disassembly / meiotic telomere clustering / t-circle formation / telomeric D-loop disassembly / shelterin complex / Telomere C-strand synthesis initiation / double-strand break repair involved in meiotic recombination / homologous chromosome pairing at meiosis / double-stranded telomeric DNA binding / Telomere C-strand (Lagging Strand) Synthesis / ankyrin repeat binding / 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 / 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 / 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 / telomere maintenance / Inhibition of DNA recombination at telomere / Meiotic synapsis / 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 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 / Homeobox-like domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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.

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more