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- PDB-6e53: Structure of TERT in complex with a novel telomerase inhibitor -

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Basic information

Entry
Database: PDB / ID: 6.0E+53
TitleStructure of TERT in complex with a novel telomerase inhibitor
Components
  • RNA/DNA hairpin
  • Telomerase reverse transcriptase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / telomerase / catalytic subunit / telomerase inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


telomerase RNA reverse transcriptase activity / 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 / Topoisomerase I; Chain A, domain 4 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Tetracycline Repressor; domain 2 / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / 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
Chem-HUV / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / Telomerase reverse transcriptase
Similarity search - Component
Biological speciesTribolium castaneum (red flour beetle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHernandez-Sanchez, W. / Huang, W. / Plucinsky, B. / Garcia-Vazquez, N. / Berdis, A.J. / Skordalakes, E. / Taylor, D.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)CA201312-02 United States
CitationJournal: Plos Biol. / Year: 2019
Title: A non-natural nucleotide uses a specific pocket to selectively inhibit telomerase activity.
Authors: Hernandez-Sanchez, W. / Huang, W. / Plucinsky, B. / Garcia-Vazquez, N. / Robinson, N.J. / Schiemann, W.P. / Berdis, A.J. / Skordalakes, E. / Taylor, D.J.
History
DepositionJul 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Telomerase reverse transcriptase
E: RNA/DNA hairpin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3335
Polymers77,7532
Non-polymers5803
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-27 kcal/mol
Surface area31950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.020, 52.100, 100.480
Angle α, β, γ (deg.)90.00, 98.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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: Tribolium castaneum (red flour beetle) / References: UniProt: Q0QHL8, RNA-directed DNA polymerase
#2: DNA/RNA hybrid RNA/DNA hairpin


Mass: 7164.479 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tribolium castaneum (red flour beetle) / Production host: Tribolium castaneum (red flour beetle)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-HUV / methyl 1-{2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-alpha-D-erythro-pentofuranosyl}-1H-indole-5-carboxylate


Mass: 531.239 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H20NO14P3

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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: 2.66 Å3/Da / Density % sol: 53.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES, pH 7.5, 8% PEG8000, 0.1 M potassium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 20467 / % possible obs: 99.5 % / Redundancy: 20 % / CC1/2: 0.997 / Net I/σ(I): 13.26
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 18 % / Num. unique obs: 1608 / CC1/2: 0.521 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3KYL

3kyl


Resolution: 2.8→19.986 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.288 1022 5 %
Rwork0.2302 --
obs0.2331 20452 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→19.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4983 474 35 0 5492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055679
X-RAY DIFFRACTIONf_angle_d0.8857767
X-RAY DIFFRACTIONf_dihedral_angle_d7.9263341
X-RAY DIFFRACTIONf_chiral_restr0.049851
X-RAY DIFFRACTIONf_plane_restr0.006882
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.94720.38941440.3452720X-RAY DIFFRACTION100
2.9472-3.13120.431440.2982763X-RAY DIFFRACTION100
3.1312-3.37190.3041450.26372753X-RAY DIFFRACTION100
3.3719-3.70930.28561470.23492788X-RAY DIFFRACTION100
3.7093-4.24160.28721450.21872752X-RAY DIFFRACTION100
4.2416-5.32710.23561470.2052798X-RAY DIFFRACTION100
5.3271-19.98610.27251500.20092856X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 1.6028 Å / Origin y: -6.9832 Å / Origin z: 125.0397 Å
111213212223313233
T0.2824 Å2-0.0399 Å2-0.049 Å2-0.2874 Å20.104 Å2--0.2783 Å2
L2.9232 °2-0.0918 °2-1.6687 °2-1.8732 °20.5319 °2--2.9752 °2
S0.1372 Å °-0.5535 Å °-0.1795 Å °0.1194 Å °-0.1342 Å °0.1043 Å °0.1254 Å °-0.3934 Å °-0.0799 Å °
Refinement TLS groupSelection details: ALL

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