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- PDB-4erd: Crystal structure of the C-terminal domain of Tetrahymena telomer... -

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Basic information

Entry
Database: PDB / ID: 4erd
TitleCrystal structure of the C-terminal domain of Tetrahymena telomerase protein p65 in complex with stem IV of telomerase RNA
Components
  • 5'-R(P*GP*GP*UP*CP*GP*AP*CP*AP*UP*CP*UP*UP*CP*GP*GP*AP*UP*GP*GP*AP*CP*C)-3'
  • Telomerase associated protein p65
KeywordsRNA BINDING PROTEIN/RNA / La protein / LARP7 / RRM / xRRM / TER / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


telomerase catalytic core complex assembly / telomerase RNA stabilization / telomerase RNA binding / telomerase holoenzyme complex / telomere maintenance via telomerase / chromosome, telomeric region
Similarity search - Function
xRRM domain profile. / La protein, xRRM domain / La domain containing protein / La domain / Domain in the RNA-binding Lupus La protein; unknown function / La-type HTH domain / La-type HTH domain profile. / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif ...xRRM domain profile. / La protein, xRRM domain / La domain containing protein / La domain / Domain in the RNA-binding Lupus La protein; unknown function / La-type HTH domain / La-type HTH domain profile. / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / RNA / RNA (> 10) / La-related protein 7 homolog / La-related protein 7 homolog
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.589 Å
AuthorsSingh, M. / Wang, Z. / Koo, B.-K. / Patel, A. / Cascio, D. / Collins, K. / Feigon, J.
CitationJournal: Mol.Cell / Year: 2012
Title: Structural Basis for Telomerase RNA Recognition and RNP Assembly by the Holoenzyme La Family Protein p65.
Authors: Singh, M. / Wang, Z. / Koo, B.K. / Patel, A. / Cascio, D. / Collins, K. / Feigon, J.
History
DepositionApr 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2012Group: Database references
Revision 1.2Aug 1, 2012Group: Database references
Revision 1.3Apr 23, 2014Group: Derived calculations
Revision 1.4Jul 26, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.5Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Telomerase associated protein p65
B: Telomerase associated protein p65
C: 5'-R(P*GP*GP*UP*CP*GP*AP*CP*AP*UP*CP*UP*UP*CP*GP*GP*AP*UP*GP*GP*AP*CP*C)-3'
D: 5'-R(P*GP*GP*UP*CP*GP*AP*CP*AP*UP*CP*UP*UP*CP*GP*GP*AP*UP*GP*GP*AP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7115
Polymers45,6724
Non-polymers391
Water39622
1
A: Telomerase associated protein p65
C: 5'-R(P*GP*GP*UP*CP*GP*AP*CP*AP*UP*CP*UP*UP*CP*GP*GP*AP*UP*GP*GP*AP*CP*C)-3'
D: 5'-R(P*GP*GP*UP*CP*GP*AP*CP*AP*UP*CP*UP*UP*CP*GP*GP*AP*UP*GP*GP*AP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9254
Polymers29,8863
Non-polymers391
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-30 kcal/mol
Surface area20450 Å2
2
B: Telomerase associated protein p65
C: 5'-R(P*GP*GP*UP*CP*GP*AP*CP*AP*UP*CP*UP*UP*CP*GP*GP*AP*UP*GP*GP*AP*CP*C)-3'
D: 5'-R(P*GP*GP*UP*CP*GP*AP*CP*AP*UP*CP*UP*UP*CP*GP*GP*AP*UP*GP*GP*AP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)29,8863
Polymers29,8863
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.830, 88.830, 119.210
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-701-

HOH

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Components

#1: Protein Telomerase associated protein p65


Mass: 15785.705 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila (eukaryote) / Gene: TAP65 / Plasmid: pET30 LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6JXI6, UniProt: W7X6T2*PLUS
#2: RNA chain 5'-R(P*GP*GP*UP*CP*GP*AP*CP*AP*UP*CP*UP*UP*CP*GP*GP*AP*UP*GP*GP*AP*CP*C)-3'


Mass: 7050.227 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: RNA was prepared by in vitro transcription with T7 RNA polymerase
Source: (synth.) Tetrahymena thermophila (eukaryote)
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPROTEIN CONSTRUCT COMPRISES THE C-TERMINAL DOMAIN OF P65 XRRM2 (UNP RESIDUES 375-542) WITH THE LOOP ...PROTEIN CONSTRUCT COMPRISES THE C-TERMINAL DOMAIN OF P65 XRRM2 (UNP RESIDUES 375-542) WITH THE LOOP (UNP RESIDUES 413-459) DELETED.

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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: 2.97 Å3/Da / Density % sol: 58.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.05 M sodium cacodylate, 0.04 M magnesium chloride, 5% v/v MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792,0.9794,0.9718
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97941
30.97181
ReflectionResolution: 2.588→76.929 Å / Num. obs: 16940 / % possible obs: 99.9 % / Redundancy: 7.48 % / Rsym value: 0.078 / Net I/σ(I): 16.18
Reflection shellResolution: 2.588→2.67 Å / Mean I/σ(I) obs: 2.57 / Rsym value: 0.844 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: MAD / Resolution: 2.589→64.638 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.46 / Phase error: 28.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2717 844 4.98 %
Rwork0.2197 --
obs0.2221 16940 97.02 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.561 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.055 Å20 Å2-0 Å2
2--7.055 Å2-0 Å2
3----14.1101 Å2
Refinement stepCycle: LAST / Resolution: 2.589→64.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1826 938 1 22 2787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022906
X-RAY DIFFRACTIONf_angle_d0.4964118
X-RAY DIFFRACTIONf_dihedral_angle_d13.251244
X-RAY DIFFRACTIONf_chiral_restr0.045482
X-RAY DIFFRACTIONf_plane_restr0.002366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.589-2.75150.43841340.36552414X-RAY DIFFRACTION89
2.7515-2.96390.34231270.30132633X-RAY DIFFRACTION97
2.9639-3.26220.28171670.24162666X-RAY DIFFRACTION99
3.2622-3.73420.24711410.20342707X-RAY DIFFRACTION98
3.7342-4.70450.23371350.18362776X-RAY DIFFRACTION100
4.7045-64.65850.26611400.20952900X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 59.4449 Å / Origin y: 51.4566 Å / Origin z: 60.2417 Å
111213212223313233
T0.1825 Å20.0282 Å2-0.0362 Å2-0.1779 Å2-0.0405 Å2--0.1934 Å2
L2.2386 °20.5222 °2-0.5194 °2-0.317 °20.1567 °2--0.831 °2
S-0.0156 Å °0.2384 Å °0.0358 Å °-0.0414 Å °0.087 Å °-0.044 Å °-0.1314 Å °0.023 Å °-0.0417 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA378 - 711
2X-RAY DIFFRACTION1allC117 - 203
3X-RAY DIFFRACTION1allB378 - 605
4X-RAY DIFFRACTION1allD117 - 203

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