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- PDB-8bh8: Structure of Est1 from Candida Tropicalis in complex with TLC1 te... -

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Basic information

Entry
Database: PDB / ID: 8bh8
TitleStructure of Est1 from Candida Tropicalis in complex with TLC1 telomerase RNA fragment 444-456
Components
  • PCIF1_WW domain-containing protein
  • RNA (5'-R(P*AP*CP*AP*CP*AP*AP*GP*G)-3')
KeywordsRNA BINDING PROTEIN / Telomerase TLC1 RNA
Function / homology
Function and homology information


telomerase holoenzyme complex / telomerase RNA binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / telomeric DNA binding
Similarity search - Function
Telomerase activating protein Est1-like, N-terminal / Telomerase activating protein Est1 / DNA/RNA-binding domain, Est1-type / Est1/Ebs1-like / Est1 DNA/RNA binding domain / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / Uncharacterized protein
Similarity search - Component
Biological speciesCandida tropicalis MYA-3404 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.88 Å
AuthorsRety, S. / Chen, W.F. / Xi, X.G.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: To Be Published
Title: Structure of Est1 from Candida Tropicalis in complex with TLC1 telomerase RNA fragment 444-456
Authors: Rety, S. / Chen, W.F. / Xi, X.G.
History
DepositionOct 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PCIF1_WW domain-containing protein
B: RNA (5'-R(P*AP*CP*AP*CP*AP*AP*GP*G)-3')
C: RNA (5'-R(P*AP*CP*AP*CP*AP*AP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)70,9843
Polymers70,9843
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-12 kcal/mol
Surface area27470 Å2
Unit cell
Length a, b, c (Å)36.300, 79.069, 108.431
Angle α, β, γ (deg.)90.000, 96.246, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein PCIF1_WW domain-containing protein


Mass: 62701.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida tropicalis MYA-3404 (yeast) / Strain: ATCC MYA-3404 / T1 / Gene: CTRG_06152 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: C5MJA9
#2: RNA chain RNA (5'-R(P*AP*CP*AP*CP*AP*AP*GP*G)-3')


Mass: 4141.525 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Candida tropicalis MYA-3404 (yeast)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 43.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 4K 20% PEG 200 5% Tris-HCl 0.1 M PH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97888 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97888 Å / Relative weight: 1
ReflectionResolution: 2.876→44.533 Å / Num. obs: 13852 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Biso Wilson estimate: 65.48 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.049 / Rrim(I) all: 0.084 / Net I/σ(I): 10.9
Reflection shellResolution: 2.876→2.926 Å / Redundancy: 3 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2 / Num. unique obs: 705 / CC1/2: 0.795 / Rpim(I) all: 0.364 / Rrim(I) all: 0.637 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
autoPROCdata reduction
autoPROCdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.88→36.08 Å / SU ML: 0.3545 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 30.4901
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2794 673 4.86 %
Rwork0.221 13173 -
obs0.2239 13846 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 89.18 Å2
Refinement stepCycle: LAST / Resolution: 2.88→36.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4343 341 0 5 4689
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00464829
X-RAY DIFFRACTIONf_angle_d0.74326587
X-RAY DIFFRACTIONf_chiral_restr0.0446724
X-RAY DIFFRACTIONf_plane_restr0.0082781
X-RAY DIFFRACTIONf_dihedral_angle_d8.4685763
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.88-3.10.34251460.27352639X-RAY DIFFRACTION99.54
3.1-3.410.36171190.26392630X-RAY DIFFRACTION99.49
3.41-3.90.26631430.22352617X-RAY DIFFRACTION99.07
3.9-4.910.26141290.19622640X-RAY DIFFRACTION98.68
4.92-36.080.26331360.21292647X-RAY DIFFRACTION97.48
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)
12.130027175681.376045650342.450870919574.54643829462.308444818925.90755612687-0.05065633052290.165516100273-0.571229493841-0.3213755563840.101067466959-0.2726841897160.7398462253880.0387119124801-0.1132899013820.502978861505-0.07075533981060.1942712397710.4650651761740.009347887414130.5785393498336.82499726646-30.757520413736.84499665
26.205902625981.332165874091.683514672145.228138015171.468608803127.23466292579-0.4834306132450.07070939406970.171477920728-0.5883209611940.03706987483461.14874721659-0.0344822048186-0.4798092211380.4798475878080.294524378011-0.0579802192167-0.07520632539910.3385074153540.08080077858740.6118946152342.06943252302-16.442035828539.4500755076
32.63883365982-0.6380629900450.5507731996844.22724652095-0.1518985587553.122932888440.1671463756880.2420695040550.11146782358-0.488181492461-0.194632703050.0956548516647-0.120862327445-0.1161067916520.03649369357760.2541879541020.0497115925870.0493295532550.392332132487-0.01499676569940.3496464207640.7065851783973.23369295921.9280075801
45.13024012806-2.063207316811.156850183342.39670360631-0.8245529244538.64184745333-0.262105812704-0.87026862355-0.419601287641.080571300580.0581771957946-0.136252906852-0.54356308916-0.622394548320.08780199033130.628457625792-0.04757173223290.05817549205140.503698657861-0.05170024943020.6829672721492.9382854425613.171315224642.4461224714
53.97167473767-0.01249725186171.457466663020.00195987782011-0.1583032052066.31081019637-0.932557332836-1.24978995055-0.04304904865970.4826041192340.5691496808850.301565040958-2.0713622643-0.456650522340.09626701849823.50830542515-0.416315012959-0.4964173422131.688557283370.6006838703231.18242504771-2.6490526251216.7679375894-1.70834844156
66.735063064091.588193872110.6202466561591.73235937173-1.055786160441.253806423710.4569979086671.83641709161.20035969446-0.631022710079-0.439812953811-0.417722716651-1.068094683050.0890128144396-0.08637271867792.646557122950.7219009148810.003391742010111.498817736080.395469515221.02037443411-4.8278927299814.78799181-4.21641703454
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 138 )AA3 - 1381 - 136
22chain 'A' and (resid 139 through 219 )AA139 - 219137 - 217
33chain 'A' and (resid 220 through 469 )AA220 - 469218 - 467
44chain 'A' and (resid 470 through 525 )AA470 - 525468 - 523
55chain 'B' and (resid 449 through 456 )BB449 - 456
66chain 'C' and (resid 444 through 451 )CC444 - 451

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