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- PDB-7kqm: Binary complex of TERT (telomerase reverse transcriptase) with RN... -

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Basic information

Entry
Database: PDB / ID: 7kqm
TitleBinary complex of TERT (telomerase reverse transcriptase) with RNA/telomeric DNA hybrid
Components
  • DNA (5'-D(*TP*TP*CP*TP*TP*TP*GP*TP*GP*CP*AP*CP*CP*TP*G)-3')
  • RNA (5'-R(*AP*UP*CP*CP*AP*GP*GP*UP*GP*CP*AP*C)-D(P*AP*AP*AP*GP*AP*A)-3')
  • Telomerase reverse transcriptase
KeywordsTRANSFERASE/RNA/DNA / RAP / Repeat Addition Processivity / DNA hairpin / RNA template / telomere / TRANSFERASE / TRANSFERASE-RNA-DNA complex
Function / homology
Function and homology information


telomerase activity / telomere maintenance / RNA-directed DNA polymerase / chromosome, telomeric region / DNA binding / metal ion binding / nucleus
Similarity search - Function
Telomerase reverse transcriptase, thumb DNA-binding domain / Telomerase reverse transcriptase thumb DNA 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
DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10) / RNA / RNA (> 10) / Telomerase reverse transcriptase
Similarity search - Component
Biological speciesTribolium castaneum (red flour beetle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsChoi, W.S. / Weng, P.J. / Yang, W.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Flexibility of telomerase in binding the RNA template and DNA telomeric repeat.
Authors: Choi, W.S. / Weng, P.J. / Yang, W.
#1: Journal: Nat Struct Mol Biol / Year: 2015
Title: A DNA-hairpin model for repeat-addition processivity in telomere synthesis.
Authors: Yang, W. / Lee, Y.S.
History
DepositionNov 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Telomerase reverse transcriptase
B: RNA (5'-R(*AP*UP*CP*CP*AP*GP*GP*UP*GP*CP*AP*C)-D(P*AP*AP*AP*GP*AP*A)-3')
C: DNA (5'-D(*TP*TP*CP*TP*TP*TP*GP*TP*GP*CP*AP*CP*CP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,37811
Polymers80,8373
Non-polymers5418
Water7,476415
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-12 kcal/mol
Surface area33290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.350, 96.350, 368.990
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-874-

HOH

21A-940-

HOH

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Components

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Protein / RNA chain / DNA chain , 3 types, 3 molecules ABC

#1: Protein Telomerase reverse transcriptase


Mass: 70588.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tribolium castaneum (red flour beetle) / Gene: TERT, TcasGA2_TC010963 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: Q0QHL8, RNA-directed DNA polymerase
#2: RNA chain RNA (5'-R(*AP*UP*CP*CP*AP*GP*GP*UP*GP*CP*AP*C)-D(P*AP*AP*AP*GP*AP*A)-3')


Mass: 5706.577 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Tribolium castaneum (red flour beetle)
#3: DNA chain DNA (5'-D(*TP*TP*CP*TP*TP*TP*GP*TP*GP*CP*AP*CP*CP*TP*G)-3')


Mass: 4541.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Tribolium castaneum (red flour beetle)

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Non-polymers , 3 types, 423 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.06 Å3/Da / Density % sol: 59.78 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.18 M tri-ammonium citrate, 20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.73→30 Å / Num. obs: 28107 / % possible obs: 100 % / Redundancy: 20.9 % / Biso Wilson estimate: 70.45 Å2 / CC1/2: 0.999 / Net I/σ(I): 19.1
Reflection shellResolution: 2.73→2.87 Å / Mean I/σ(I) obs: 2.02 / Num. unique obs: 2020 / CC1/2: 0.703

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KYL

3kyl


Resolution: 2.73→29.84 Å / SU ML: 0.3517 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.6101
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2316 998 3.56 %
Rwork0.193 27068 -
obs0.1943 28066 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.75 Å2
Refinement stepCycle: LAST / Resolution: 2.73→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4961 659 35 415 6070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00615922
X-RAY DIFFRACTIONf_angle_d0.86578122
X-RAY DIFFRACTIONf_chiral_restr0.0544893
X-RAY DIFFRACTIONf_plane_restr0.0055904
X-RAY DIFFRACTIONf_dihedral_angle_d22.66912296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.73-2.870.3661390.28363759X-RAY DIFFRACTION100
2.87-3.050.28431390.25413762X-RAY DIFFRACTION100
3.05-3.290.26761390.22413793X-RAY DIFFRACTION99.97
3.29-3.620.22251410.19933816X-RAY DIFFRACTION99.95
3.62-4.140.23721420.18183844X-RAY DIFFRACTION100
4.14-5.210.17841450.16263916X-RAY DIFFRACTION100
5.21-29.840.23761530.18814178X-RAY DIFFRACTION99.95
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)
14.035070045860.7985909737841.223327117495.42968160773-1.520589074752.758040552940.278577325744-0.544624350363-0.3992301715740.2298267985980.4519857817831.164326339970.343393704392-0.712038542250.02395283543480.659873918227-0.124288143542-0.1054920371820.8281518640630.2598173966880.845022212316-28.7854988582-41.989463651820.8056548065
23.05546969548-0.804029694332-0.4454266849013.6600150198-0.7669346958420.5331192573820.261363587579-0.2271791102530.07818199399680.350759130905-0.03457200679150.312318529513-0.157860376466-0.577004127844-7.902466868E-80.682522402718-0.00764359560146-0.0009590383492160.6381982972120.01533363626040.551560721706-22.0475297846-15.90801157333.86561093319
32.246845375760.1549411962470.233431706612.27725463197-2.177092315052.13855513926-0.19053183731-0.237658930029-0.80031982326-0.313771053976-0.0436659411258-0.1116757306870.2973100129770.305659976228-4.20008088888E-80.616800256563-0.0206551425559-0.01868846544280.6119516237360.04095271725630.582257695647-2.8545295203-23.6070899513-2.98084932202
40.336675263254-0.05801337335860.6973280493541.47378029408-0.006634199758483.237980612260.07408257173420.2050318378810.101808028612-0.176472816507-0.447571106813-0.7124380666480.1142259815760.287476529619-1.33699981758E-70.64954925227-0.112974680805-0.08490227582990.6891695797960.1726595750870.80428655086111.1749797477-10.65488453811.2313315235
51.75787319713-0.2010888012620.6572296276831.889988073710.1652234309570.5988813365270.2995124242270.3459499352310.0953875609943-0.718766049366-0.215266017821-0.1610067543180.1860126931840.06149822723955.84675539221E-90.6444098016890.119860471871-0.02652418409880.5916302932750.07538285879180.470733493506-7.17212908577-17.1462071858-9.73241059377
61.09950965417-0.9442883539860.9078033358790.906006707868-0.5200453952971.1181331270.06077182759610.131899331897-0.00832373573618-0.0984347474331-0.281503705434-0.970099303987-0.5343092426850.7273042451823.02203366518E-80.737716310236-0.1629465234220.03836621759450.7116856789720.1523603531390.7603637395179.49466714445-8.761155505275.04913622789
71.37034250013-0.2551775800760.5323664390482.84106144594-1.851235208681.43113882573-0.04491285746650.1269324308070.1481881350540.557033660844-0.268285866271-0.348290860438-0.3251897260130.100187244296-0.0021647261620.693613392172-0.000661819259004-0.06696006627080.515913380131-0.009433100551230.4900469851211.49370932799-16.681813671919.7048802644
83.838093060860.05664259903580.2746120233093.98070702143-0.1844591279182.97807145672-0.1213217801850.24216766357-0.03378351621970.253940023124-0.101365752829-0.555870477320.2548032530790.112289545309-4.64708733015E-80.5551751268240.0532075818151-0.09010485875780.4872937239110.06076958794210.4070884794568.32609568237-35.694719419228.9636954041
91.7412487767-0.3451187098230.2753741772943.67643657502-0.661463571133.5054880876-0.214485873989-0.5179318621590.3627549609240.994352291911-0.226152178756-0.505382958891-0.5818115796970.230239660879-7.19503003162E-60.85541646066-0.0210987202575-0.1396114477090.6492982007480.02290820065610.6422493526553.55316635452-31.420077656938.5094460289
100.312290595402-0.1227842412280.4905620889520.3121231397220.1449261639630.93502826116-1.6253668913-0.48146511935-0.3982180161790.8234162584140.40947069996-0.5144580286280.664467967990.436969929905-0.002993700372310.9014832357380.2180986681260.04689313891190.9491373981440.04908884353150.814054969608-5.8097715505-26.37530752444.59310295436
110.7281383418690.72971231446-0.06712958559770.663299691145-0.04853186134961.41771696591-0.06699268842780.427427403033-0.05917092060770.1295458229290.0758980230989-0.5238111213630.6641558234940.6264917331112.46064573809E-70.8261908918890.289190752140.08650607472881.025904968010.009583301720930.88561591897912.768153196-45.02410296115.37630831573
12-0.196353002519-0.4015301355670.07209842164021.504249161480.631099823460.02599919137480.207654625590.6802489721660.260831365785-0.377952221552-0.649992297678-0.973054779510.1688385304920.116855661813-8.91627595822E-70.8534856545070.2184264847330.1298409290370.9053231093270.0274103699430.8665666532098.52469022849-39.75847263187.37471712434
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 145 )AA1 - 1451 - 145
22chain 'A' and (resid 146 through 189 )AA146 - 189146 - 190
33chain 'A' and (resid 190 through 223 )AA190 - 223191 - 225
44chain 'A' and (resid 224 through 260 )AA224 - 260226 - 262
55chain 'A' and (resid 261 through 312 )AA261 - 312263 - 314
66chain 'A' and (resid 313 through 351 )AA313 - 351315 - 353
77chain 'A' and (resid 352 through 430 )AA352 - 430354 - 435
88chain 'A' and (resid 431 through 547 )AA431 - 547436 - 553
99chain 'A' and (resid 548 through 596 )AA548 - 596554 - 603
1010chain 'B' and (resid 2 through 6 )BB2 - 6
1111chain 'B' and (resid 7 through 18 )BB7 - 18
1212chain 'C' and (resid 1 through 15 )CC1 - 15

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