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- PDB-6zdu: Structure of telomerase from Candida albicans in complexe with TW... -

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Basic information

Entry
Database: PDB / ID: 6zdu
TitleStructure of telomerase from Candida albicans in complexe with TWJ fragment of telomeric RNA
Components
  • Chains: C,D
  • Telomerase reverse transcriptase
KeywordsREPLICATION / Telomerase / catalytic core / RNA binding / telomere
Function / homology
Function and homology information


telomerase catalytic core complex / telomere capping / telomerase holoenzyme 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
Telomerase ribonucleoprotein complex - RNA binding domain / Telomerase reverse transcriptase / Telomerase ribonucleoprotein complex - RNA-binding domain / Telomerase ribonucleoprotein complex - RNA binding domain / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / Telomerase reverse transcriptase
Similarity search - Component
Biological speciesCandida albicans (yeast)
Candida albicans SC5314 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 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 1.3Jan 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Telomerase reverse transcriptase
B: Telomerase reverse transcriptase
C: Chains: C,D
D: Chains: C,D


Theoretical massNumber of molelcules
Total (without water)222,2364
Polymers222,2364
Non-polymers00
Water00
1
A: Telomerase reverse transcriptase
B: Telomerase reverse transcriptase


Theoretical massNumber of molelcules
Total (without water)180,1852
Polymers180,1852
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Chains: C,D
D: Chains: C,D


Theoretical massNumber of molelcules
Total (without water)42,0512
Polymers42,0512
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.884, 245.836, 72.471
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_1ens_2chain "C"
d_2ens_2chain "D"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1VALILEA1 - 693
d_21ens_1VALILEB1 - 693
d_11ens_2GCC
d_21ens_2GCD

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.15930908192, 0.93087034645, -0.328787187278), (0.911593073871, -0.266551268728, -0.312967232804), (-0.378970558338, -0.249861600171, -0.891038998402)-6.10346580538, 31.0038088744, 61.1230053164
2given(0.159679207912, 0.97307020529, -0.166243574723), (0.94172764454, -0.200659164073, -0.269972115935), (-0.296060119012, -0.113447236414, -0.94840820878)-12.6357104084, 25.7622518703, 54.4290271389

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Components

#1: Protein Telomerase reverse transcriptase / Telomerase catalytic subunit


Mass: 90092.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast)
Strain: SC5314 / ATCC MYA-2876 / Gene: TERT, orf19.5089, CAALFM_C108130CA
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A1D8PEA0, RNA-directed DNA polymerase
#2: RNA chain Chains: C,D


Mass: 21025.496 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Candida albicans SC5314 (yeast)

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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 Å3/Da / Density % sol: 59.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: 0.1 M imidazole 0.1 M MES monohydrate, pH 6.5 0.02 M sodium formate 0.02 M ammonium acetate 0.02 M sodium citrate tribasic dihydrate 0.02 M sodium potassium tartrate tetrahydrate 0.02 M ...Details: 0.1 M imidazole 0.1 M MES monohydrate, pH 6.5 0.02 M sodium formate 0.02 M ammonium acetate 0.02 M sodium citrate tribasic dihydrate 0.02 M sodium potassium tartrate tetrahydrate 0.02 M sodium oxamate 12% glycerol and 7 % PEG4000

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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 EIGER2 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: 3.45→71.9 Å / Num. obs: 23166 / % possible obs: 92.1 % / Redundancy: 13.4 % / Biso Wilson estimate: 141.98 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.043 / Rrim(I) all: 0.123 / Net I/σ(I): 14.1
Reflection shellResolution: 3.45→3.788 Å / Redundancy: 13.1 % / Rmerge(I) obs: 1.824 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1158 / CC1/2: 0.617 / Rpim(I) all: 0.735 / Rrim(I) all: 1.94 / % possible all: 53.9

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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: 6ZDP

6zdp


Resolution: 3.45→71.9 Å / SU ML: 0.6035 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 40.9535
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3008 1097 4.74 %
Rwork0.2477 22055 -
obs0.2503 23152 63.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 166.47 Å2
Refinement stepCycle: LAST / Resolution: 3.45→71.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11450 2788 0 0 14238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214806
X-RAY DIFFRACTIONf_angle_d0.513720592
X-RAY DIFFRACTIONf_chiral_restr0.03712414
X-RAY DIFFRACTIONf_plane_restr0.00272070
X-RAY DIFFRACTIONf_dihedral_angle_d14.89635928
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.64252284518
ens_2d_2CX-RAY DIFFRACTIONTorsion NCS2.22021669453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.45-3.610.695180.3692248X-RAY DIFFRACTION5.77
3.61-3.80.4035620.3362920X-RAY DIFFRACTION22.03
3.8-4.030.3382940.31912030X-RAY DIFFRACTION47.74
4.04-4.350.31441450.28382681X-RAY DIFFRACTION63.43
4.35-4.780.3431530.26093303X-RAY DIFFRACTION76.9
4.78-5.480.32361780.26423991X-RAY DIFFRACTION92.3
5.48-6.90.37832270.29884343X-RAY DIFFRACTION100
6.9-71.90.24712300.20784539X-RAY DIFFRACTION99.62
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)
19.35441722434.29302535186-2.260046948426.39423440456-1.49262099872.16699059312-0.252305879052-0.06529482932850.561484827166-0.1954980485820.3516063402990.09783934979070.517857848851-0.111264715247-0.07161276272660.7588473399910.130429595174-0.02706452598520.618758646305-0.04018571726250.27026219811963.222735112614.794457740840.6242742268
22.62135461855-1.20397495032.921242430081.902635435510.1432371592311.964143823350.2863555634-0.611168667109-0.513383238957-0.0456247907975-0.1659180365550.1209729749130.390048177162-0.120235541911-0.0809572714090.815394463794-0.1470637962560.1271362545460.8318774604060.2909657879010.99605535458730.01339135064.6361221660531.7070792128
32.60995506433-1.78100447806-0.2938743971875.3370166465-3.160891257074.699901808820.6944468322780.662156701117-0.426621721872-0.540539669001-0.711288466789-0.7508420803880.7210398713970.980500025141-0.002029115291021.105647200050.05804353487420.02878056930510.793037328334-0.116435036520.78343014876127.03633181235.3686743951918.9158153678
42.717705688761.10271523293-0.3739237288534.22247864928-0.4291023180660.8050929237480.254375498848-1.164507950640.4615980088310.68911281166-0.3683754170540.649777586960.0577357411299-0.4167778850.1060364632550.7363212237410.038306707254-0.0775526307431.18504431314-0.02735154630240.69314076623923.266109376924.702259539542.4473786743
51.975820456920.379739922034-2.555343535522.21327534645-1.263970678542.06480843586-0.3601359171890.06024257820350.434880627911-0.3955757035720.1813909590260.787604461359-0.281453224516-0.6318969746560.1852053339131.358540921450.114941971897-0.6449981393771.230945094710.131748649791.6621031630.011012623598468.99257897380.897282950036
61.85887475888-1.186340798991.630729823760.5363362452420.269156511240.06966509155-0.464586242605-0.2836832506670.880850817853-0.6632566174910.2459247557680.85085523225-0.416701439372-0.1763577828690.2402771097321.183960767920.023737985224-0.3205927439541.154240680670.1051889828971.83019374711-2.1216353293445.16715462726.7921545129
74.56140492985-0.54963619185-0.2218615213914.52864244079-0.2281942878552.188066243960.1061989327510.515708484266-0.0890639230061-1.16796459709-0.1647142331110.3588472415880.562855355177-0.426165971235-0.01909460499661.27514280314-0.0162733109524-0.5164701128830.7899342225530.1609414340450.5699957226956.3649522790232.63484133818.45835980615
81.60547093797-0.900578913473-1.130447742413.83208490485-3.134935969985.312402914561.424319717510.4272108073510.7505893800971.28495278747-3.3961912374-1.48568962011-0.535667829082.057101133161.712671913941.610657114910.2301095271880.3157972910612.215594867690.5422464725981.2208382511187.254326231250.376429470628.8456984724
93.48010510571.97319164971-0.9463640846941.63841785349-2.559654329278.87595046149-1.45239542572-0.9766959842071.93770313821.565627680760.134906335241-4.568989410631.486301585392.610313150231.216855116921.344694255440.357744322379-0.3953206971131.431057659980.04269168435031.5689921128188.440354044924.96474204925.1683076066
104.72503173012-3.12747637025-3.19935163331.99131613255-0.6003356836133.46868990763-0.8638357369662.14753672251-3.35122392106-3.363368004040.301795480771.082001753923.015034167451.786670259010.818277440511.790379156570.669369768905-0.009968637021252.05254692174-0.2503979609991.2589622817785.28084620257.1753800593132.5197362366
113.81218346142-2.36602172745-0.6458550542892.976437356522.251087662413.927782512370.790787119403-0.1190313415281.01806496263-1.3354062338-0.528443106449-0.86497758727-0.315312579693.23174728394-0.3205227672231.66322567619-0.03865602743130.08069902807191.778690369040.4077206156461.614146665291.06154277829.532355588624.9828682369
124.36942920803-1.33683987363-1.103838302930.5880483942190.565926542650.51010787947-0.5122259112310.247877007130.0529546794172-0.8809037863160.660347819883-1.38159674727-0.8651904022720.1459737640610.02821818909160.923478314074-0.1851662904160.2322761669170.982197498146-0.01462647000681.804902970558.783724753843.082004354928.7203659278
134.07347591631-0.584660134844-2.063037901037.62784991428-2.02586915472.28608006607-2.56338030195-1.464180972240.577793479241.284528670723.89746594538-1.518124928593.07934785109-0.503112927223-1.24624299442.93815984628-0.0804231665241-0.1720130432462.61142460450.4190329184681.533060229141.339879753346.15141751120.6093129228
142.43278327902-2.16846732580.0604768483134.12415099509-2.683830818032.97211259269-0.1356282877590.487812285201-0.0783266801486-1.275336068380.562363526119-0.6350313838220.4820302645711.53826057339-0.6809211654041.32233521424-0.131847914814-0.05087844239050.896129746433-0.1602979515471.4652090933460.181836337344.027602370632.2181177747
157.16119703488-3.86397530554-7.18737467946.459833031226.184840591568.333963725953.88605375476-0.4353522419221.10118297985-0.9171949103321.34517678637-2.16061441666-5.057776281044.45771877836-2.723502137143.34433649503-1.87215722481-0.2723357094633.65095231063-1.273403288832.1667250762984.29782380548.094114569637.5712386141
169.620957908751.41774574569-0.4363201352834.111854712491.653913965384.387125458240.112505974420.9035565432051.38105721498-2.17612169022-1.02679274152-0.812423802332-1.265943016470.7468021927161.093585290632.264079619560.103578137017-0.1844697724651.451873339060.5044223627562.3586640727836.310109742290.4669987218-0.924530924184
176.1736405716-6.594941334464.210334585347.94888923217-3.293443302484.17059214159-3.806881122940.001883307541813.315711851661.630615219880.7095035861052.31988704597-1.67909902688-1.115217965653.060394169472.557779472350.00461383157504-0.2365531203461.687810273340.185969478932.31576001798.37184025503100.158384334-0.344978415273
180.33777395812-0.0900778020083-0.7070739453040.9227915319140.7588836159040.871789463635-0.06427445061760.1565686532060.2310577290731.46228665787-0.825485174255-2.05102168485-0.4956388279820.3521966657010.7403863077352.19801933175-0.132697313631-0.8022121847481.518194575040.3544071628432.10958148327.294671307490.50528612050.578832915383
194.003106546612.200927349611.437306829521.694224865520.5788383665010.585260857187-2.903218697452.200850384123.925506221491.634477258710.326363024913-1.268380458620.8062904128533.91399791612.05646318091.590400807520.480993161851-0.4964947800682.75129404377-0.05205647797122.1751749089236.736337163456.34708241967.33630141893
207.03050198257-1.49932374924-2.953329183862.46077700969-1.611886721114.51774174806-0.599854698273-1.975167466540.179262222176-0.105418178813-0.250832982868-0.3291942507185.312666699221.40999479780.6787478433154.12418906757-0.7509651525330.4249226213322.25456826952-0.185342367462.1684238607445.555333214346.006369879416.1737248189
219.119878080320.242677125437-4.503723389220.576852961732-1.444432523055.27973850636-0.4992825447080.581733013468-0.212021876149-0.975167503858-2.849493833321.11864033048-3.48795443158-2.055034141372.261331147423.83695708126-0.964674266344-1.52407092375.15772435920.2711024872693.255069508329.551485401354.59957010216.7302354248
228.46793114419-1.782579414643.613957849652.15274776256-0.4665054646466.82869253202-0.100080908666-1.718769559592.96001320323-0.836805202313-1.47391128018-0.813283285035-0.2155316881892.912680464910.7837857309571.688608211710.0146195656703-0.150786118932.041513122820.5556113016161.8506157081933.616824477564.76566581180.965569311435
236.8820548517-5.317543895813.421377728414.3291055222-2.183775491682.61108795588-0.8130319366942.870605478772.4350998617-2.90181227982-2.34152355206-1.543092349292.504028445551.938965923333.097752548012.34721710121-0.0902962490281-0.132184640362.069328922280.3770656819262.6943100557742.457662056183.3680057409-9.33133790314
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 155 through 362 )AA155 - 3621 - 208
22chain 'A' and (resid 363 through 509 )AA363 - 509209 - 355
33chain 'A' and (resid 510 through 619 )AA510 - 619356 - 445
44chain 'A' and (resid 620 through 867 )AA620 - 867446 - 693
55chain 'B' and (resid 155 through 408 )BB155 - 4081 - 254
66chain 'B' and (resid 409 through 619 )BB409 - 619255 - 445
77chain 'B' and (resid 620 through 867 )BB620 - 867446 - 693
88chain 'C' and (resid 1259 through 1264 )CC1259 - 1264
99chain 'C' and (resid 1265 through 1274 )CC1265 - 1274
1010chain 'C' and (resid 1275 through 1279 )CC1275 - 1279
1111chain 'C' and (resid 1280 through 1290 )CC1280 - 1290
1212chain 'C' and (resid 1291 through 1300 )CC1291 - 1300
1313chain 'C' and (resid 1301 through 1310 )CC1301 - 1310
1414chain 'C' and (resid 1311 through 1320 )CC1311 - 1320
1515chain 'C' and (resid 1321 through 1326 )CC1321 - 1326
1616chain 'D' and (resid 1259 through 1269 )DD1259 - 1269
1717chain 'D' and (resid 1270 through 1279 )DD1270 - 1279
1818chain 'D' and (resid 1280 through 1295 )DD1280 - 1295
1919chain 'D' and (resid 1296 through 1300 )DD1296 - 1300
2020chain 'D' and (resid 1301 through 1305 )DD1301 - 1305
2121chain 'D' and (resid 1306 through 1310 )DD1306 - 1310
2222chain 'D' and (resid 1311 through 1320 )DD1311 - 1320
2323chain 'D' and (resid 1321 through 1326 )DD1321 - 1326

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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

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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

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