[English] 日本語
Yorodumi
- PDB-3du6: Structure of the catalytic subunit of telomerase, TERT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3du6
TitleStructure of the catalytic subunit of telomerase, TERT
ComponentsTelomerase reverse transcriptase
KeywordsTRANSFERASE / Reverse Transcriptase / RNA-directed DNA polymerase
Function / homology
Function and homology information


telomerase RNA reverse transcriptase activity / RNA-directed DNA polymerase / chromosome, telomeric region / DNA binding / metal ion binding / nucleus
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 / Topoisomerase I; Chain A, domain 4 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Tetracycline Repressor; domain 2 / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / 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
Telomerase reverse transcriptase
Similarity search - Component
Biological speciesTribolium castaneum (red flour beetle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.71 Å
AuthorsSkordalakes, E.
CitationJournal: Nature / Year: 2008
Title: Structure of the Tribolium castaneum telomerase catalytic subunit TERT.
Authors: Gillis, A.J. / Schuller, A.P. / Skordalakes, E.
History
DepositionJul 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: Telomerase reverse transcriptase


Theoretical massNumber of molelcules
Total (without water)141,1772
Polymers141,1772
Non-polymers00
Water6,395355
1
A: Telomerase reverse transcriptase


Theoretical massNumber of molelcules
Total (without water)70,5891
Polymers70,5891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Telomerase reverse transcriptase


Theoretical massNumber of molelcules
Total (without water)70,5891
Polymers70,5891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.042, 122.657, 212.406
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Telomerase reverse transcriptase /


Mass: 70588.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tribolium castaneum (red flour beetle) / Production host: Escherichia coli (E. coli) / References: UniProt: Q0QHL8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 3.92 Å3/Da / Density % sol: 68.65 %

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.71→20 Å / Num. obs: 56173 / % possible obs: 96.97 % / Observed criterion σ(F): 2 / Redundancy: 4.2 % / Rsym value: 0.107 / Net I/σ(I): 9.3

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.71→20 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.9 / SU B: 27.117 / SU ML: 0.249 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.553 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27763 3016 5.1 %RANDOM
Rwork0.2384 ---
obs0.24038 56173 96.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 52.127 Å2
Baniso -1Baniso -2Baniso -3
1-3.25 Å20 Å20 Å2
2---3.56 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.71→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9964 0 0 355 10319
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02210228
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8481.95513786
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.84851190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31222.979470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.929151922
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1681564
X-RAY DIFFRACTIONr_chiral_restr0.0640.21494
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027584
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.24908
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.26991
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2418
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4551.56099
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.81829754
X-RAY DIFFRACTIONr_scbond_it0.86534628
X-RAY DIFFRACTIONr_scangle_it1.3924.54032
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.71→2.778 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 211 -
Rwork0.33 4005 -
obs--95.84 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4471-1.1920.30414.550.71321.99680.07770.0827-0.15770.1353-0.06970.44070.02310.0144-0.008-0.17770.01420.0345-0.0886-0.02650.0052-9.5264-0.4465-50.7696
21.447-1.1163-0.14554.714-0.73411.60120.10160.07970.14090.2413-0.1272-0.4365-0.1193-0.01270.0256-0.18170.0034-0.0372-0.07260.0244-0.0224-32.967371.2159-50.7326
30.68320.30610.0764.7887-0.36161.45480.1066-0.05950.00980.8548-0.05990.17590.3688-0.0539-0.04670.34430.0326-0.0916-0.07790.0164-0.455-4.435420.6881-13.5766
41.08830.2229-0.12895.58060.1881.4930.0666-0.08740.07081.2094-0.0723-0.3866-0.40570.03710.00570.4865-0.00830.0078-0.1032-0.0041-0.4873-37.399550.121-13.6151
50.9250.3710.3863.67560.55140.6454-0.03810.0438-0.07420.06370.0361-0.0652-0.0450.11520.002-0.10160.01120.0084-0.03490.0251-0.0412-7.046433.9301-45.4446
60.76210.5402-0.23884.1215-0.72150.859-0.03250.0590.04180.14730.02650.0155-0.0069-0.13890.006-0.11360.0165-0.0102-0.0342-0.0149-0.059-35.466336.8074-45.4568
70.5017-0.32570.02250.3946-0.05360.1256-0.0711-0.0905-0.00690.13590.0435-0.0570.04040.0140.0276-0.1501-0.0299-0.0049-0.0563-0.0062-0.1171-21.80535.2008-44.3948
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 155
2X-RAY DIFFRACTION2B1 - 155
3X-RAY DIFFRACTION3A156 - 403
4X-RAY DIFFRACTION4B156 - 403
5X-RAY DIFFRACTION5A404 - 596
6X-RAY DIFFRACTION6B404 - 596
7X-RAY DIFFRACTION7A597 - 773
8X-RAY DIFFRACTION7B597 - 764

+
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