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- PDB-8bh9: Structure of Est1 from Candida Tropicalis in complex with TLC1 te... -

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Basic information

Entry
Database: PDB / ID: 8bh9
TitleStructure of Est1 from Candida Tropicalis in complex with TLC1 telomerase RNA fragment 427-435 / 496-504
Components
  • PCIF1_WW domain-containing protein
  • RNA (5'-R(P*AP*AP*GP*AP*AP*UP*GP*CP*AP*UP*UP*C)-3')
KeywordsRNA BINDING PROTEIN / Telomerase TLC1 RNA
Function / homology
Function and homology information


telomerase RNA binding / telomerase holoenzyme complex / 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: 2.09 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 427-435 / 496-504
Authors: Rety, S. / Chen, W.F. / Xi, X.G.
History
DepositionOct 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 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*AP*GP*AP*AP*UP*GP*CP*AP*UP*UP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7568
Polymers66,5222
Non-polymers2356
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-9 kcal/mol
Surface area26710 Å2
Unit cell
Length a, b, c (Å)36.448, 79.462, 218.252
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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*AP*GP*AP*AP*UP*GP*CP*AP*UP*UP*C)-3')


Mass: 3820.344 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: TLC1 RNA fragment 427-435/ 496-504 with 436-495 deletion
Source: (synth.) Candida tropicalis MYA-3404 (yeast)
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 48.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 4K 20% PEG 200 5% Tris-HCl 0.1M

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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: 2.086→109.126 Å / Num. obs: 37916 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 42.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.032 / Rrim(I) all: 0.083 / Net I/σ(I): 13.8
Reflection shellResolution: 2.086→2.122 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.927 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1910 / CC1/2: 0.834 / Rpim(I) all: 0.366 / Rrim(I) all: 0.998 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
autoPROC1.0.5data reduction
autoPROC1.0.5data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.09→34.87 Å / SU ML: 0.2252 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.7187
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.238 1826 4.82 %
Rwork0.2057 36079 -
obs0.2072 37905 97.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.51 Å2
Refinement stepCycle: LAST / Resolution: 2.09→34.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4343 256 6 128 4733
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00624734
X-RAY DIFFRACTIONf_angle_d0.75166439
X-RAY DIFFRACTIONf_chiral_restr0.0439704
X-RAY DIFFRACTIONf_plane_restr0.0063777
X-RAY DIFFRACTIONf_dihedral_angle_d10.7752715
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.140.31771590.28072829X-RAY DIFFRACTION99.87
2.14-2.210.3121460.24322724X-RAY DIFFRACTION99.93
2.21-2.280.26581330.22822855X-RAY DIFFRACTION99.97
2.28-2.360.26791230.21732772X-RAY DIFFRACTION99.97
2.36-2.450.26971610.22792839X-RAY DIFFRACTION99.93
2.45-2.560.27641360.21932825X-RAY DIFFRACTION99.97
2.56-2.70.24361340.2142794X-RAY DIFFRACTION100
2.7-2.870.25081390.22442850X-RAY DIFFRACTION100
2.87-3.090.27171470.23272845X-RAY DIFFRACTION99.97
3.09-3.40.26181350.22042847X-RAY DIFFRACTION99.57
3.46-3.880.23031220.19112165X-RAY DIFFRACTION91.01
3.9-4.90.17241420.16282876X-RAY DIFFRACTION99.87
4.9-34.870.24071490.20792858X-RAY DIFFRACTION92.64
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)
10.0133111365761-0.0146687430444-0.01171943438770.01223429900170.01400982673680.006001368714160.1339469093520.2159776625010.081795182903-0.002444271553970.0520518939231-0.0943849406722-0.0701338763180.119297612867.20095673244E-51.570244494540.0818792430472-0.390881667751.91263795668-0.21506966021.70033989204-12.025685254316.8443260579-5.52585331653
20.00521080223807-0.003468365659080.003992412576550.00152973270266-0.0118290563810.0153557588670.3243348554320.0282352887305-0.129577409523-0.02223418650050.03227872343060.195782068003-0.02015658158370.0415123942685-2.63907520871E-51.268919195290.080106493923-0.08578855079531.37442888587-0.1194874988330.962181299206-10.563472083512.64360035461.20865218919
32.961395316050.5431106743260.6668961914913.217983055781.831274773054.87327559347-0.1027128060590.413649261455-0.422245471878-0.267079985775-0.0812302836059-0.1131364134910.604895563745-0.28204333683-0.01611228585710.382215025769-0.0617942027820.06077128064290.321695384791-0.01237036882720.340688118259-5.25277792131-30.788397237.2215498571
42.956445015180.231683329787-1.581146486853.510721921240.2424469544121.33342622431-0.1728883604680.1947053113710.178294409609-0.253063816155-0.1480315190910.438508781083-0.0993694320693-0.378387795020.2914697051870.223080942871-0.00104119421246-0.08475280481350.338294451332-0.002659473856750.367695230208-10.0024478449-15.349564005239.4482803255
51.80823055618-0.3371553090730.4772934477323.874308377350.9129314198333.300723351080.08971271769610.08748585728190.146842677834-0.336669984162-0.2108411338880.0928168147102-0.177004245649-0.1690463582960.1093803619990.1930787347210.027903774497-0.03300514342550.2898933842360.0005246182665050.26747398047-10.75059141786.2563368636425.4236783011
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 427 through 433 )BB427 - 433
22chain 'B' and (resid 500 through 504 )BB500 - 504
33chain 'A' and (resid 3 through 138 )AA3 - 1381 - 136
44chain 'A' and (resid 139 through 241 )AA139 - 241137 - 239
55chain 'A' and (resid 242 through 525 )AA242 - 525240 - 523

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