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- PDB-6usp: Telomerase Reverse Transcriptase product complex, TERT:DNA -

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Basic information

Entry
Database: PDB / ID: 6usp
TitleTelomerase Reverse Transcriptase product complex, TERT:DNA
Components
  • DNA (5'-D(P*GP*GP*TP*CP*AP*GP*GP*TP*CP*AP*GP*GP*TP*CP*AP*G)-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


: / RNA-directed DNA polymerase / chromosome, telomeric region / DNA binding / nucleus / metal ion binding
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 / Topoisomerase I; Chain A, domain 4 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / 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: 3.56 Å
AuthorsSchaich, M.A. / Freudenthal, B.D.
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 / Derived calculations / Category: citation / citation_author / struct_conn
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 / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
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(P*GP*GP*TP*CP*AP*GP*GP*TP*CP*AP*GP*GP*TP*CP*AP*G)-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)80,6484
Polymers80,6243
Non-polymers241
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-39 kcal/mol
Surface area33100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.378, 100.378, 167.999
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Telomerase reverse transcriptase / Telomerase catalytic subunit


Mass: 70645.773 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) / References: UniProt: Q0QHL8, RNA-directed DNA polymerase
#2: DNA chain DNA (5'-D(P*GP*GP*TP*CP*AP*GP*GP*TP*CP*AP*GP*GP*TP*CP*AP*G)-3')


Mass: 4979.227 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.: 1 / Source method: obtained synthetically / Formula: Mg
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: 3.05 Å3/Da / Density % sol: 59.64 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 11% isopropanol, 0.1 M KCl, 25 mM MgCl2, and 50 mM sodium cacodylate pH 6.5

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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: Dec 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.56→48.09 Å / Num. obs: 12249 / % possible obs: 99.9 % / Redundancy: 9.8 % / Biso Wilson estimate: 146.55 Å2 / CC1/2: 0.998 / Net I/σ(I): 7.3
Reflection shellResolution: 3.56→3.9 Å / Num. unique obs: 2869 / CC1/2: 0.51

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Processing

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

3kyl


Resolution: 3.56→48.09 Å / SU ML: 0.6865 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 39.2171
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.304 527 4.32 %
Rwork0.2608 11670 -
obs0.2625 12197 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 143.76 Å2
Refinement stepCycle: LAST / Resolution: 3.56→48.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4866 656 1 0 5523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01345728
X-RAY DIFFRACTIONf_angle_d1.69517885
X-RAY DIFFRACTIONf_chiral_restr0.0896878
X-RAY DIFFRACTIONf_plane_restr0.0119876
X-RAY DIFFRACTIONf_dihedral_angle_d19.4262171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.56-3.920.42111200.37492855X-RAY DIFFRACTION99.56
3.92-4.480.33661230.33742877X-RAY DIFFRACTION99.8
4.48-5.650.36681290.29922921X-RAY DIFFRACTION99.97
5.65-48.090.25711550.21023017X-RAY DIFFRACTION99.72

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