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- PDB-6zd6: Structure of apo telomerase from Candida Tropicalis -

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Basic information

Entry
Database: PDB / ID: 6zd6
TitleStructure of apo telomerase from Candida Tropicalis
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 / telomerase activity / chromosome, telomeric region / metal ion binding
Similarity search - Function
Topoisomerase I; Chain A, domain 4 - #70 / Telomerase ribonucleoprotein complex - RNA binding domain / Telomerase reverse transcriptase / Telomerase ribonucleoprotein complex - RNA-binding domain / Telomerase ribonucleoprotein complex - RNA binding domain / Topoisomerase I; Chain A, domain 4 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Telomerase reverse transcriptase
Similarity search - Component
Biological speciesCandida tropicalis MYA-3404 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 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 1.3Jan 24, 2024Group: 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Telomerase reverse transcriptase


Theoretical massNumber of molelcules
Total (without water)81,7791
Polymers81,7791
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area33160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.695, 65.695, 387.615
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Telomerase reverse transcriptase / Telomerase catalytic subunit


Mass: 81779.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: mutation R366C and S774C / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.56 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.1
Details: 0.2 M sodium citrate tribasic dihydrate 0.1 M Bis-Tris propane (pH 6.1) 15% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980109 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980109 Å / Relative weight: 1
ReflectionResolution: 2.64→64.77 Å / Num. obs: 47515 / % possible obs: 83.19 % / Redundancy: 14.5 % / Biso Wilson estimate: 87.42 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1768 / Rpim(I) all: 0.04795 / Rrim(I) all: 0.1832 / Net I/σ(I): 10.99
Reflection shellResolution: 2.642→2.736 Å / Redundancy: 14.8 % / Rmerge(I) obs: 2.347 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 225 / CC1/2: 0.575 / Rpim(I) all: 0.635 / Rrim(I) all: 2.432 / % possible all: 48.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZD1

6zd1


Resolution: 2.64→64.77 Å / SU ML: 0.388 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 34.2104
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2725 1091 4.99 %
Rwork0.2195 20758 -
obs0.2222 21849 83.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 105.05 Å2
Refinement stepCycle: LAST / Resolution: 2.64→64.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5355 0 0 8 5363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00285448
X-RAY DIFFRACTIONf_angle_d0.62377321
X-RAY DIFFRACTIONf_chiral_restr0.0417833
X-RAY DIFFRACTIONf_plane_restr0.0033907
X-RAY DIFFRACTIONf_dihedral_angle_d18.2392057
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.760.2881180.2865354X-RAY DIFFRACTION11.68
2.76-2.910.3171900.32271858X-RAY DIFFRACTION61.01
2.91-3.090.36491290.30782698X-RAY DIFFRACTION87.96
3.09-3.330.36651620.2843071X-RAY DIFFRACTION99.57
3.33-3.660.30391730.23613089X-RAY DIFFRACTION99.97
3.66-4.190.26391670.22063106X-RAY DIFFRACTION100
4.19-5.280.23661710.19573167X-RAY DIFFRACTION100
5.28-64.770.26281810.20093415X-RAY DIFFRACTION99.92
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)
12.129145123891.81319458184-1.801609096394.16211757795-2.820535425994.06413969570.3103316342920.0272845520838-0.1528272328580.372345453488-0.213782195999-0.377585213764-0.8418319616760.350939454831-0.114670970160.9224172093350.07835346707720.1160178010730.59196704019-0.09859777176590.63377607677415.6152700547.4757902203159.252384318
21.74197446827-0.1867462106090.6842810128252.002730759340.4239241448314.31538627469-0.0995617736146-0.3281899641690.03491989396470.05096185727640.05552209311370.1675978152730.294070499479-0.2198794158980.01756258322070.5124743894690.04976690481030.03591016830620.382110738394-0.1453108526450.657628508419-6.068761690330.9134014013182.703342112
32.90995714967-0.3164984345210.08615189330861.02028862182-1.474786738743.55915228162-0.203102244286-0.122232879964-0.2910183366140.3568088775330.201971798151-0.0617386408462-0.200726242367-0.174355868492-0.01988064322390.6972527289980.1446014059790.1371386434480.28348581608-0.05763784394840.571820936441-2.5481191567557.4140723581177.882645098
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 177 through 438 )177 - 4381 - 238
22chain 'A' and (resid 439 through 735 )439 - 735239 - 507
33chain 'A' and (resid 736 through 881 )736 - 881508 - 653

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