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- PDB-4lmo: Structure of a vertebrate RNA binding domain of telomerase (TRBD) -

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Basic information

Entry
Database: PDB / ID: 4lmo
TitleStructure of a vertebrate RNA binding domain of telomerase (TRBD)
ComponentsTelomerase reverse transcriptase
KeywordsRNA BINDING PROTEIN / RNA binding domain of the reverse transcriptase telomerase
Function / homology
Function and homology information


DNA strand elongation / telomerase catalytic core complex / telomerase activity / telomerase RNA binding / telomeric repeat 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, C-terminal extension / 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 ...Topoisomerase I; Chain A, domain 4 - #70 / : / Telomerase reverse transcriptase, C-terminal extension / 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. / DNA/RNA polymerase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Telomerase reverse transcriptase
Similarity search - Component
Biological speciesTakifugu rubripes (torafugu)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.37 Å
AuthorsHarkisheimer, M. / Mason, M. / Shuvaeva, E. / Skordalakes, E.
CitationJournal: Structure / Year: 2013
Title: A Motif in the Vertebrate Telomerase N-Terminal Linker of TERT Contributes to RNA Binding and Telomerase Activity and Processivity.
Authors: Harkisheimer, M. / Mason, M. / Shuvaeva, E. / Skordalakes, E.
History
DepositionJul 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
C: Telomerase reverse transcriptase
D: Telomerase reverse transcriptase


Theoretical massNumber of molelcules
Total (without water)119,0244
Polymers119,0244
Non-polymers00
Water2,594144
1
A: Telomerase reverse transcriptase


Theoretical massNumber of molelcules
Total (without water)29,7561
Polymers29,7561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Telomerase reverse transcriptase


Theoretical massNumber of molelcules
Total (without water)29,7561
Polymers29,7561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Telomerase reverse transcriptase


Theoretical massNumber of molelcules
Total (without water)29,7561
Polymers29,7561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Telomerase reverse transcriptase


Theoretical massNumber of molelcules
Total (without water)29,7561
Polymers29,7561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.629, 84.508, 137.174
Angle α, β, γ (deg.)90.00, 94.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Telomerase reverse transcriptase


Mass: 29756.006 Da / Num. of mol.: 4 / Fragment: RNA Binding Domain (UNP residues 295-544)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Takifugu rubripes (torafugu) / Gene: TERT / Production host: Escherichia coli (E. coli) / References: UniProt: Q4KTA7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.38 Å3/Da / Density % sol: 48.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 50 mM Hepes 7.0, 40% v/v Tacsimate, pH 7.0, 0.002 M Spermine, 0.002 M Hexammine cobalt(III) chloride, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2511.1, 1.008
2
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELJul 27, 2012
2
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
21.0081
ReflectionResolution: 2.37→40 Å / Num. all: 42409 / Num. obs: 42409 / % possible obs: 98.64 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.37→2.43 Å / % possible all: 87.08

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Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.37→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.915 / SU B: 21.37 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.528 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25901 2163 4.9 %RANDOM
Rwork0.21999 ---
obs0.22191 42409 98.64 %-
all-44682 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.913 Å2
Baniso -1Baniso -2Baniso -3
1-4.29 Å20 Å21.57 Å2
2---3.44 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 2.37→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8312 0 0 144 8456
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0198520
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9431.95811440
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.76251000
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.05620.98408
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.287151576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.76415108
X-RAY DIFFRACTIONr_chiral_restr0.0650.21196
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216412
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.37→2.431 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 153 -
Rwork0.304 2651 -
obs--87.08 %
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)
10.3180.19-0.27340.73370.2221.5282-0.0133-0.02270.06190.05510.0528-0.06840.040.1153-0.03950.0264-0.0052-0.00710.0961-0.00860.08814.47538.753753.2334
20.173-0.063-0.09760.6644-0.27521.8137-0.0139-0.0102-0.0003-0.0634-0.00370.0192-0.0055-0.03930.01760.03030.0113-0.01480.09520.0080.090118.0922-32.571416.9759
30.0789-0.1760.08011.0070.06691.87920.0081-0.0265-0.0433-0.05030.0708-0.1238-0.020.0513-0.07880.0210.0115-0.01410.1061-0.01020.11931.2268-51.934516.7659
40.33880.2932-0.33440.7494-0.31581.762-0.01560.0159-0.0119-0.02890.06420.07870.0699-0.0113-0.04850.0470.0022-0.02520.07380.01120.08-7.8696-10.64750.3534
50.0194-0.046-0.03690.21910.10990.2027-0.0086-0.0283-0.01450.0110.01750.0015-0.0170.0272-0.00890.0229-0.0035-0.04150.13110.02150.152510.682-22.534533.6053
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A294 - 544
2X-RAY DIFFRACTION2B294 - 544
3X-RAY DIFFRACTION3C294 - 544
4X-RAY DIFFRACTION4D294 - 544
5X-RAY DIFFRACTION5A601 - 630
6X-RAY DIFFRACTION5B601 - 637
7X-RAY DIFFRACTION5C601 - 638
8X-RAY DIFFRACTION5D601 - 639

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