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- PDB-6usq: Telomerase Reverse Transcriptase binary complex with Y256A mutati... -

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Basic information

Entry
Database: PDB / ID: 6usq
TitleTelomerase Reverse Transcriptase binary complex with Y256A mutation, TERT:DNA
Components
  • DNA (5'-D(*GP*GP*TP*CP*AP*GP*GP*TP*CP*AP*GP*GP*TP*CP*A)-3')
  • DNA/RNA (5'-R(*CP*UP*GP*AP*CP*CP*UP*GP*AP*C)-D(P*CP*T)-R(P*GP*AP*C)-D(P*C)-3')
  • Telomerase reverse transcriptase
KeywordsNUCLEAR PROTEIN / TRANSFERASE/RNA/DNA / Telomerase / reverse transcriptase / polymerase / 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
Arc Repressor Mutant, subunit A - #2210 / Telomerase reverse transcriptase (TERT), thumb domain / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 - #20 / Alpha-Beta Plaits - #2630 / Telomerase reverse transcriptase, thumb DNA-binding domain / Telomerase reverse transcriptase thumb DNA binding domain / Topoisomerase I; Chain A, domain 4 - #70 / Telomerase reverse transcriptase / Telomerase ribonucleoprotein complex - RNA-binding domain / Telomerase ribonucleoprotein complex - RNA binding domain ...Arc Repressor Mutant, subunit A - #2210 / Telomerase reverse transcriptase (TERT), thumb domain / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 - #20 / Alpha-Beta Plaits - #2630 / Telomerase reverse transcriptase, thumb DNA-binding domain / Telomerase reverse transcriptase thumb DNA binding domain / Topoisomerase I; Chain A, domain 4 - #70 / Telomerase reverse transcriptase / Telomerase ribonucleoprotein complex - RNA-binding domain / Telomerase ribonucleoprotein complex - RNA binding domain / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Topoisomerase I; Chain A, domain 4 / Tetracycline Repressor; domain 2 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Arc Repressor Mutant, subunit A / Alpha-Beta Plaits / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / Telomerase reverse transcriptase
Similarity search - Component
Biological speciesTribolium castaneum (red flour beetle)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.62 Å
AuthorsSchaich, M.A. / Freudenthal, B.D. / Khoang, T.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM128562 United States
CitationJournal: Elife / Year: 2020
Title: Mechanisms of nucleotide selection by telomerase.
Authors: Schaich, M.A. / Sanford, S.L. / Welfer, G.A. / Johnson, S.A. / Khoang, T.H. / Opresko, P.L. / Freudenthal, B.D.
History
DepositionOct 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 6, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 11, 2023Group: 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
E: DNA (5'-D(*GP*GP*TP*CP*AP*GP*GP*TP*CP*AP*GP*GP*TP*CP*A)-3')
F: DNA/RNA (5'-R(*CP*UP*GP*AP*CP*CP*UP*GP*AP*C)-D(P*CP*T)-R(P*GP*AP*C)-D(P*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,2515
Polymers80,2033
Non-polymers492
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-38 kcal/mol
Surface area34030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.009, 101.009, 379.086
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

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Components

#1: Protein Telomerase reverse transcriptase / Telomerase catalytic subunit


Mass: 70553.680 Da / Num. of mol.: 1 / Mutation: Y256A
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) / References: UniProt: Q0QHL8, RNA-directed DNA polymerase
#2: DNA chain DNA (5'-D(*GP*GP*TP*CP*AP*GP*GP*TP*CP*AP*GP*GP*TP*CP*A)-3')


Mass: 4650.021 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA/RNA hybrid DNA/RNA (5'-R(*CP*UP*GP*AP*CP*CP*UP*GP*AP*C)-D(P*CP*T)-R(P*GP*AP*C)-D(P*C)-3')


Mass: 4999.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
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: 3.49 Å3/Da / Density % sol: 64.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 11% isopropanol, 0.1 M KCl, 25 mM MgCl2, and 50 mM sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Apr 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→48.8 Å / Num. obs: 16740 / % possible obs: 99.7 % / Redundancy: 18.3 % / Biso Wilson estimate: 126.63 Å2 / CC1/2: 0.999 / Net I/σ(I): 9
Reflection shellResolution: 3.4→3.67 Å / Num. unique obs: 3311 / CC1/2: 0.624

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Cootmodel building
Blu-Icedata collection
XDSdata scaling
PHENIXphasing
XDSdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3kyl

3kyl


Resolution: 3.62→46.9 Å / SU ML: 1.0971 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 45.624
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2967 696 5.05 %
Rwork0.2812 13088 -
obs0.282 13784 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 159.19 Å2
Refinement stepCycle: LAST / Resolution: 3.62→46.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4885 634 2 1 5522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00585731
X-RAY DIFFRACTIONf_angle_d1.14857884
X-RAY DIFFRACTIONf_chiral_restr0.0636874
X-RAY DIFFRACTIONf_plane_restr0.012882
X-RAY DIFFRACTIONf_dihedral_angle_d20.73752173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.62-3.90.56071270.54142473X-RAY DIFFRACTION96.4
3.9-4.290.49351250.38612536X-RAY DIFFRACTION98.78
4.29-4.910.34291330.29432605X-RAY DIFFRACTION99.93
4.91-6.190.31781440.29942647X-RAY DIFFRACTION99.96
6.19-46.90.21471670.20962827X-RAY DIFFRACTION99.53

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