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- PDB-5c9h: Structural Basis of Template Boundary Definition in Tetrahymena T... -

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Basic information

Entry
Database: PDB / ID: 5c9h
TitleStructural Basis of Template Boundary Definition in Tetrahymena Telomerase
Components
  • RNA (5'-R(P*AP*GP*AP*AP*CP*UP*GP*UP*CP*A)-3')
  • RNA (5'-R(P*UP*CP*AP*UP*UP*CP*AP*GP*UP*UP*CP*U)-3')
  • Telomerase reverse transcriptase
KeywordsRNA binding protein/RNA / Telomerase / RNA-Protein complex / RNA binding protein-RNA complex
Function / homology
Function and homology information


telomerase RNA reverse transcriptase activity / telomerase RNA binding / telomerase holoenzyme complex / telomeric DNA binding / telomere maintenance via telomerase / RNA-directed DNA polymerase / chromosome, telomeric region / metal ion binding
Similarity search - Function
Topoisomerase I; Chain A, domain 4 - #70 / Telomerase reverse transcriptase TEN domain / Telomerase ribonucleoprotein complex - RNA binding domain / Telomerase reverse transcriptase / Telomerase ribonucleoprotein complex - RNA-binding domain / Telomerase ribonucleoprotein complex - RNA binding domain / Topoisomerase I; Chain A, domain 4 / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. ...Topoisomerase I; Chain A, domain 4 - #70 / Telomerase reverse transcriptase TEN domain / Telomerase ribonucleoprotein complex - RNA binding domain / Telomerase reverse transcriptase / Telomerase ribonucleoprotein complex - RNA-binding domain / Telomerase ribonucleoprotein complex - RNA binding domain / Topoisomerase I; Chain A, domain 4 / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA / RNA (> 10) / Telomerase reverse transcriptase
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsJansson, L.I. / Akiyama, B.M. / Ooms, A. / Lu, C. / Rubin, S.M. / Stone, M.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM095850 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008646-16 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Structural basis of template-boundary definition in Tetrahymena telomerase.
Authors: Jansson, L.I. / Akiyama, B.M. / Ooms, A. / Lu, C. / Rubin, S.M. / Stone, M.D.
History
DepositionJun 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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
B: Telomerase reverse transcriptase
D: RNA (5'-R(P*AP*GP*AP*AP*CP*UP*GP*UP*CP*A)-3')
C: RNA (5'-R(P*UP*CP*AP*UP*UP*CP*AP*GP*UP*UP*CP*U)-3')
E: RNA (5'-R(P*AP*GP*AP*AP*CP*UP*GP*UP*CP*A)-3')
G: RNA (5'-R(P*UP*CP*AP*UP*UP*CP*AP*GP*UP*UP*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,8218
Polymers89,7736
Non-polymers492
Water43224
1
A: Telomerase reverse transcriptase
D: RNA (5'-R(P*AP*GP*AP*AP*CP*UP*GP*UP*CP*A)-3')
C: RNA (5'-R(P*UP*CP*AP*UP*UP*CP*AP*GP*UP*UP*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9114
Polymers44,8863
Non-polymers241
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-30 kcal/mol
Surface area15790 Å2
MethodPISA
2
B: Telomerase reverse transcriptase
E: RNA (5'-R(P*AP*GP*AP*AP*CP*UP*GP*UP*CP*A)-3')
G: RNA (5'-R(P*UP*CP*AP*UP*UP*CP*AP*GP*UP*UP*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9114
Polymers44,8863
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-27 kcal/mol
Surface area14480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.530, 117.770, 131.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Telomerase reverse transcriptase / / Telomerase catalytic subunit / Telomerase subunit P133


Mass: 36765.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila (eukaryote) / Gene: TERT / Production host: Escherichia coli (E. coli) / References: UniProt: O77448, RNA-directed DNA polymerase
#2: RNA chain RNA (5'-R(P*AP*GP*AP*AP*CP*UP*GP*UP*CP*A)-3')


Mass: 4103.469 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Tetrahymena thermophila (eukaryote)
#3: RNA chain RNA (5'-R(P*UP*CP*AP*UP*UP*CP*AP*GP*UP*UP*CP*U)-3')


Mass: 4017.366 Da / Num. of mol.: 2 / Mutation: A10U / Source method: obtained synthetically / Source: (synth.) Tetrahymena thermophila (eukaryote)
#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 / Water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 200mM KCl, 10mM MgCl2, 50mM MES monohydrate pH 5.6, 4% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→41.512 Å / Num. obs: 18728 / % possible obs: 99.5 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.231 / Net I/σ(I): 7.8
Reflection shellResolution: 3→3.16 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.969 / Mean I/σ(I) obs: 2.1 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2R4G

2r4g


Resolution: 3→41.512 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.29 1865 10.01 %
Rwork0.2387 --
obs0.2439 18640 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→41.512 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3885 882 2 24 4793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034951
X-RAY DIFFRACTIONf_angle_d0.826866
X-RAY DIFFRACTIONf_dihedral_angle_d14.7481942
X-RAY DIFFRACTIONf_chiral_restr0.032793
X-RAY DIFFRACTIONf_plane_restr0.004717
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.08110.40451390.32231252X-RAY DIFFRACTION98
3.0811-3.17170.31781370.29221240X-RAY DIFFRACTION100
3.1717-3.27410.31621440.26451290X-RAY DIFFRACTION98
3.2741-3.39110.35191400.26261260X-RAY DIFFRACTION100
3.3911-3.52680.29741420.26091272X-RAY DIFFRACTION98
3.5268-3.68720.31431420.27311274X-RAY DIFFRACTION99
3.6872-3.88140.32051420.24541287X-RAY DIFFRACTION99
3.8814-4.12440.29661420.21851275X-RAY DIFFRACTION100
4.1244-4.44250.24681430.19661283X-RAY DIFFRACTION99
4.4425-4.8890.25261460.18751318X-RAY DIFFRACTION99
4.889-5.59490.26461430.20951279X-RAY DIFFRACTION100
5.5949-7.04350.25661480.25571341X-RAY DIFFRACTION100
7.0435-41.51580.27621570.23581404X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 62.1211 Å / Origin y: 32.7153 Å / Origin z: 145.0066 Å
111213212223313233
T0.145 Å20.009 Å20.0491 Å2-0.2255 Å20.0631 Å2--0.1944 Å2
L1.5367 °2-0.03 °20.1301 °2-1.891 °20.3402 °2--1.1481 °2
S0.0164 Å °-0.2708 Å °0.0164 Å °0.3162 Å °-0.0312 Å °-0.0583 Å °0.0192 Å °-0.0111 Å °0.0273 Å °
Refinement TLS groupSelection details: all

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