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- PDB-6zdp: Structure of telomerase from Candida Tropicalis in complexe with ... -

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Basic information

Entry
Database: PDB / ID: 6zdp
TitleStructure of telomerase from Candida Tropicalis in complexe with TWJ fragment of telomeric RNA
Components
  • Chains: B
  • Telomerase 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
: / RNA / RNA (> 10) / Telomerase reverse transcriptase
Similarity search - Component
Biological speciesCandida tropicalis (yeast)
Candida tropicalis MYA-3404 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.85 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 15, 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 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Telomerase reverse transcriptase
B: Chains: B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,0016
Polymers107,8452
Non-polymers1564
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-26 kcal/mol
Surface area46160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.095, 201.729, 138.840
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

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Components

#1: Protein Telomerase reverse transcriptase / Telomerase catalytic subunit


Mass: 84867.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida tropicalis (strain ATCC MYA-3404 / T1) (yeast)
Strain: ATCC MYA-3404 / T1 / Gene: CTRG_04008
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: C5MCQ7, RNA-directed DNA polymerase
#2: RNA chain Chains: B


Mass: 22977.496 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Candida tropicalis MYA-3404 (yeast)
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.09 Å3/Da / Density % sol: 60.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.1
Details: 0.2M sodium citrate tribasic dihydrate 0.1M Bis-Tris propane 13% PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.85→100.865 Å / Num. obs: 41766 / % possible obs: 93.6 % / Redundancy: 13.2 % / Biso Wilson estimate: 87.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.059 / Rrim(I) all: 0.157 / Net I/σ(I): 13.4
Reflection shellResolution: 2.85→2.952 Å / Rmerge(I) obs: 1.831 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 805 / CC1/2: 0.616 / Rpim(I) all: 0.75 / Rrim(I) all: 1.98

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.85→20.7 Å / SU ML: 0.3845 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.0545
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2782 816 5.1 %
Rwork0.2197 15170 -
obs0.2227 15986 50.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 107.33 Å2
Refinement stepCycle: LAST / Resolution: 2.85→20.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5623 1419 4 2 7048
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00167309
X-RAY DIFFRACTIONf_angle_d0.433810160
X-RAY DIFFRACTIONf_chiral_restr0.03211199
X-RAY DIFFRACTIONf_plane_restr0.00251025
X-RAY DIFFRACTIONf_dihedral_angle_d13.95072963
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-3.030.46220.4196174X-RAY DIFFRACTION3.39
3.03-3.260.3228300.3581503X-RAY DIFFRACTION10.28
3.26-3.580.3103660.30541308X-RAY DIFFRACTION26.34
3.59-4.10.2951550.2663077X-RAY DIFFRACTION61.75
4.1-5.150.25842690.21064966X-RAY DIFFRACTION99.3
5.15-20.70.2842940.20025142X-RAY DIFFRACTION99.94
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)
17.13745020949-0.241465794092-1.320668059651.786053618891.139397857492.57065069863-0.321784430806-0.8354220081790.5651656027280.1634699962510.00323756434094-0.0416927070385-0.1486480989580.3725173939930.02934323859740.1721838908840.166902471746-0.09496815595910.213796398106-0.1692256503190.2097665181720.3312213870371.406034213583.6135966898
24.01432716228-1.187237146110.005366885710422.656041587790.54976333113.102597342860.3517069193460.7565766712050.804232690877-0.495955103616-0.1598272348160.0731382226245-0.3537754128220.111448167391-0.1546957592820.488098356703-0.109492597460.06984372532440.5037555924690.1809649023310.71840494997824.846241746775.518601607154.0473740954
33.69822226463-2.36366426942-1.300144046922.39645552305-1.075008114064.559375384780.0689884135086-1.105867335150.7499204264010.416157519993-0.3241971917670.615327634291-0.111560118214-0.6018728677390.2567153270520.454521658731-0.0511986899144-0.01413844134870.964768610788-0.3592705718970.983399318946-45.282191077366.982623054777.9860647591
42.264682982052.00436475474-0.6359585159792.62253927993-2.912614877166.68902931013-0.0799431892177-1.328594827391.262221995912.284820423861.17762775436-0.108713436947-1.42516930855-0.92782082643-0.8547752256091.917516551880.332500825685-0.09421216629491.61142468333-0.7277953167681.91682134794-29.12369067894.50712673996.9241743509
58.44868476723.5217853915.982259706438.868762925810.7775388250856.97374082088-1.62104274833-0.623394741121-2.426326467360.784171192261.5144855172-0.825777070353-1.35985579728-0.36335787002-0.3244820568881.272002526930.02832449329390.5471571969341.69684168681-0.7956238341531.76495592976-21.649679958486.753674584101.130950801
65.336628094221.04610115801-2.869076544999.596299581265.253595106475.550936874061.89229104016-0.328181769540.539483365142-2.11199838064-0.01345666406381.08456981004-1.87975837222-0.851725968461-1.995491172352.228118357140.5137428158160.01450681368342.20925128918-0.3717500921213.21085757683-41.175643325994.508977451592.0007435785
74.758869498-4.66316904872-5.231125611595.987157118664.144067770346.625671369220.9047812996692.80111335841.30287515916-0.068691300108-2.0516429392-1.09208174418-1.19053344704-1.635292996591.151282908970.9090269101970.240286788613-0.3298511995041.460143260530.1721635493761.85192127777-37.365684682482.910155822177.1724783655
82.01004225001-3.171120255170.668030136258.583313210812.581149135981.060645809580.1550225908262.31764938066-0.0485986943985-1.600597977980.098193010872-0.708776013521-0.216067937939-1.05532563987-0.3240425400640.5290561744580.00640348576448-0.09920513750921.62978071146-0.3910001810020.98959642691-27.343808592371.092265484569.6228482764
90.392843835625-1.40217033501-0.511709898224.898778795431.802444996810.6693124357360.455803223761-0.717755006504-0.619033566648-0.311806394831-0.8854578068421.02700335872-0.178623350638-1.170087440060.4755146663120.517151661313-0.0731508408752-0.1277197961861.08018598902-0.2613735497270.796041181565-48.336936305260.109338212270.7208416903
108.464446515060.117498514014-1.256493881622.82215031204-2.230666074276.79755503635-0.3807766502611.59345812163-1.52982459011-0.2535605104640.502772581450.4583213143780.549138596982-0.837509371077-0.16082668140.8824350006070.121624264835-0.1117512827541.222296532350.03184124136320.945875503677-3.0234669952168.211204595848.0419263987
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 158 through 425 )AA158 - 4251 - 263
22chain 'A' and (resid 426 through 754 )AA426 - 754264 - 558
33chain 'B' and (resid 1282 through 1297 )BB1282 - 1297
44chain 'B' and (resid 1298 through 1307 )BB1298 - 1307
55chain 'B' and (resid 1308 through 1312 )BB1308 - 1312
66chain 'B' and (resid 1313 through 1317 )BB1313 - 1317
77chain 'B' and (resid 1318 through 1324 )BB1318 - 1324
88chain 'B' and (resid 1325 through 1344 )BB1325 - 1344
99chain 'B' and (resid 1345 through 1357 )BB1345 - 1357
1010chain 'A' and (resid 755 through 879 )AA755 - 879559 - 683

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