[English] 日本語
Yorodumi
- PDB-6zd2: Structure of apo telomerase from Candida Tropicalis truncated fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zd2
TitleStructure of apo telomerase from Candida Tropicalis truncated from C-terminal domain
ComponentsTelomerase reverse transcriptase
KeywordsREPLICATION / Telomerase / catalytic core / RNA binding / telomere
Function / homology
Function and homology information


telomerase catalytic core complex / : / telomerase RNA binding / telomeric DNA binding / telomere maintenance via telomerase / RNA-directed DNA polymerase / chromosome, telomeric region / metal ion binding
Similarity search - Function
Telomerase ribonucleoprotein complex - RNA binding domain / Telomerase reverse transcriptase / Telomerase ribonucleoprotein complex - RNA-binding domain / Telomerase ribonucleoprotein complex - RNA binding domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile.
Similarity search - Domain/homology
Telomerase reverse transcriptase
Similarity search - Component
Biological speciesCandida tropicalis MYA-3404 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.84 Å
AuthorsZhai, L. / Rety, S. / Chen, W.F. / Auguin, D. / Xi, X.G.
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Crystal structures of N-terminally truncated telomerase reverse transcriptase from fungi‡.
Authors: Zhai, L.T. / Rety, S. / Chen, W.F. / Song, Z.Y. / Auguin, D. / Sun, B. / Dou, S.X. / Xi, X.G.
History
DepositionJun 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / Item: _citation.title
Revision 1.2May 12, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 15, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8823
Polymers68,8361
Non-polymers462
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-22 kcal/mol
Surface area27220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.900, 154.850, 107.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

-
Components

#1: Protein Telomerase reverse transcriptase / Telomerase catalytic subunit


Mass: 68836.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida tropicalis MYA-3404 (yeast) / Gene: CTRG_04008
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: C5MCQ7, RNA-directed DNA polymerase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.47 Å3/Da / Density % sol: 64.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7 / Details: Tacsimate 60%

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97891 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 2.84→82.82 Å / Num. obs: 22283 / % possible obs: 96.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 81.42 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.07759 / Rrim(I) all: 0.08429 / Net I/σ(I): 17.32
Reflection shellResolution: 2.842→2.944 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.6251 / Mean I/σ(I) obs: 2.53 / Num. unique obs: 2280 / CC1/2: 0.916 / CC star: 0.978 / Rpim(I) all: 0.2574 / Rrim(I) all: 0.6767 / % possible all: 99.56

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.84→70.01 Å / SU ML: 0.3795 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.6497
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.238 1078 4.85 %
Rwork0.202 21162 -
obs0.2038 22240 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.93 Å2
Refinement stepCycle: LAST / Resolution: 2.84→70.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4338 0 2 0 4340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00194418
X-RAY DIFFRACTIONf_angle_d0.47165940
X-RAY DIFFRACTIONf_chiral_restr0.0384661
X-RAY DIFFRACTIONf_plane_restr0.0023741
X-RAY DIFFRACTIONf_dihedral_angle_d17.30581680
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.84-2.970.35531230.28732687X-RAY DIFFRACTION99.54
2.97-3.130.33771440.27082681X-RAY DIFFRACTION99.65
3.13-3.320.28781230.24882694X-RAY DIFFRACTION99.61
3.32-3.580.3091340.23892478X-RAY DIFFRACTION91.42
3.58-3.940.23191190.21372305X-RAY DIFFRACTION85.71
3.94-4.510.24721250.18862754X-RAY DIFFRACTION99.86
4.51-5.680.20281600.18192724X-RAY DIFFRACTION99.97
5.68-700.20771500.17942839X-RAY DIFFRACTION99.3
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)
12.168918932670.2616171451190.09500332600515.14162656372-2.732943026234.460196492710.172939492524-0.0996898853160.04449946489290.0603532409836-0.02494233182490.140478998877-0.206987743352-0.180439992803-0.1023449800730.4143860654090.0755758092959-0.004236580945560.499997373911-0.0500642240450.510991539127-24.95199637694.35063189244-33.7227037284
20.418002776946-0.9545083416031.633619946593.64699392135-3.210638161916.31266713720.0907718447762-0.08379941845390.08211205081850.3756579303280.09215756018570.0210474176169-0.2500804706570.0802668657644-0.2105925811810.528613680671-0.00941387572650.1006192095310.56814588583-0.04247900578320.587440228212-17.6376017723-5.40353023855-19.5873135692
33.008551262412.73504771930.1704700549815.856463241740.1295509940020.899103748686-0.1114861193980.114399434583-0.168599135489-0.02000501480650.0975941960448-0.1763218915180.01758772542620.05709309582360.02747094083140.707181978176-0.06566496977430.006641591042460.6832112685010.003837744658410.569088102709-9.52324434583-33.3005689958-8.5307716731
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 158 through 327 )
2X-RAY DIFFRACTION2chain 'A' and (resid 328 through 438 )
3X-RAY DIFFRACTION3chain 'A' and (resid 439 through 744 )

+
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://pdbjlvh1.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