[English] 日本語
Yorodumi
- PDB-6usp: Telomerase Reverse Transcriptase product complex, TERT:DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6usp
TitleTelomerase Reverse Transcriptase product complex, TERT:DNA
Components
  • DNA (5'-D(P*GP*GP*TP*CP*AP*GP*GP*TP*CP*AP*GP*GP*TP*CP*AP*G)-3')
  • DNA/RNA (5'-R(*CP*UP*GP*AP*CP*CP*UP*GP*AP*C)-D(P*CP*T)-R(P*GP*AP*C)-D(P*C)-3')
  • Telomerase reverse transcriptase
KeywordsNUCLEAR PROTEIN / TRANSFERASE/RNA/DNA / Telomerase / reverse transcriptase / polymerase / TRANSFERASE-RNA-DNA complex
Function / homology
Function and homology information


telomere maintenance / RNA-directed DNA polymerase / telomerase activity / chromosome, telomeric region / DNA binding / nucleus / metal ion binding
Similarity search - Function
Arc Repressor Mutant, subunit A - #2210 / Telomerase reverse transcriptase (TERT), thumb domain / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 - #20 / Alpha-Beta Plaits - #2630 / Telomerase reverse transcriptase, thumb DNA-binding domain / Telomerase reverse transcriptase thumb DNA binding domain / Topoisomerase I; Chain A, domain 4 - #70 / Telomerase reverse transcriptase / Telomerase ribonucleoprotein complex - RNA-binding domain / Telomerase ribonucleoprotein complex - RNA binding domain ...Arc Repressor Mutant, subunit A - #2210 / Telomerase reverse transcriptase (TERT), thumb domain / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 - #20 / Alpha-Beta Plaits - #2630 / Telomerase reverse transcriptase, thumb DNA-binding domain / Telomerase reverse transcriptase thumb DNA binding domain / Topoisomerase I; Chain A, domain 4 - #70 / Telomerase reverse transcriptase / Telomerase ribonucleoprotein complex - RNA-binding domain / Telomerase ribonucleoprotein complex - RNA binding domain / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Topoisomerase I; Chain A, domain 4 / Tetracycline Repressor; domain 2 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Arc Repressor Mutant, subunit A / Alpha-Beta Plaits / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / Telomerase reverse transcriptase
Similarity search - Component
Biological speciesTribolium castaneum (red flour beetle)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.56 Å
AuthorsSchaich, M.A. / Freudenthal, B.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM128562 United States
CitationJournal: Elife / Year: 2020
Title: Mechanisms of nucleotide selection by telomerase.
Authors: Schaich, M.A. / Sanford, S.L. / Welfer, G.A. / Johnson, S.A. / Khoang, T.H. / Opresko, P.L. / Freudenthal, B.D.
History
DepositionOct 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 6, 2021Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2Oct 11, 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
A: Telomerase reverse transcriptase
E: DNA (5'-D(P*GP*GP*TP*CP*AP*GP*GP*TP*CP*AP*GP*GP*TP*CP*AP*G)-3')
F: DNA/RNA (5'-R(*CP*UP*GP*AP*CP*CP*UP*GP*AP*C)-D(P*CP*T)-R(P*GP*AP*C)-D(P*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6484
Polymers80,6243
Non-polymers241
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-39 kcal/mol
Surface area33100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.378, 100.378, 167.999
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

-
Components

#1: Protein Telomerase reverse transcriptase / Telomerase catalytic subunit


Mass: 70645.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tribolium castaneum (red flour beetle) / Gene: TERT, TcasGA2_TC010963 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0QHL8, RNA-directed DNA polymerase
#2: DNA chain DNA (5'-D(P*GP*GP*TP*CP*AP*GP*GP*TP*CP*AP*GP*GP*TP*CP*AP*G)-3')


Mass: 4979.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA/RNA hybrid DNA/RNA (5'-R(*CP*UP*GP*AP*CP*CP*UP*GP*AP*C)-D(P*CP*T)-R(P*GP*AP*C)-D(P*C)-3')


Mass: 4999.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.64 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 11% isopropanol, 0.1 M KCl, 25 mM MgCl2, and 50 mM sodium cacodylate pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Dec 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.56→48.09 Å / Num. obs: 12249 / % possible obs: 99.9 % / Redundancy: 9.8 % / Biso Wilson estimate: 146.55 Å2 / CC1/2: 0.998 / Net I/σ(I): 7.3
Reflection shellResolution: 3.56→3.9 Å / Num. unique obs: 2869 / CC1/2: 0.51

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Cootmodel building
Blu-Icedata collection
XDSdata scaling
PHENIXphasing
XDSdata processing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3kyl

3kyl


Resolution: 3.56→48.09 Å / SU ML: 0.6865 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 39.2171
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.304 527 4.32 %
Rwork0.2608 11670 -
obs0.2625 12197 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 143.76 Å2
Refinement stepCycle: LAST / Resolution: 3.56→48.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4866 656 1 0 5523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01345728
X-RAY DIFFRACTIONf_angle_d1.69517885
X-RAY DIFFRACTIONf_chiral_restr0.0896878
X-RAY DIFFRACTIONf_plane_restr0.0119876
X-RAY DIFFRACTIONf_dihedral_angle_d19.4262171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.56-3.920.42111200.37492855X-RAY DIFFRACTION99.56
3.92-4.480.33661230.33742877X-RAY DIFFRACTION99.8
4.48-5.650.36681290.29922921X-RAY DIFFRACTION99.97
5.65-48.090.25711550.21023017X-RAY DIFFRACTION99.72

+
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