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- PDB-5c0y: Crystal structure of the Rrp6 catalytic domain bound to poly(U) RNA -

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Basic information

Entry
Database: PDB / ID: 5c0y
TitleCrystal structure of the Rrp6 catalytic domain bound to poly(U) RNA
Components
  • Exosome complex exonuclease RRP6
  • poly U RNA
KeywordsHYDROLASE / Exoribonuclease / RNA processing and degradation / nuclear RNA Exosome
Function / homology
Function and homology information


nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process ...nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / exosome (RNase complex) / nuclear exosome (RNase complex) / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / histone mRNA catabolic process / nuclear mRNA surveillance / rRNA primary transcript binding / RNA catabolic process / Major pathway of rRNA processing in the nucleolus and cytosol / RNA processing / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / single-stranded RNA binding / nucleotide binding / nucleolus / nucleus
Similarity search - Function
: / Exosome-associated factor Rrp6, N-terminal / Exosome complex exonuclease Rrp6-like / PMC2NT (NUC016) domain / HRDC domain / Helicase and RNase D C-terminal / HRDC domain / HRDC domain / HRDC domain profile. / HRDC domain superfamily ...: / Exosome-associated factor Rrp6, N-terminal / Exosome complex exonuclease Rrp6-like / PMC2NT (NUC016) domain / HRDC domain / Helicase and RNase D C-terminal / HRDC domain / HRDC domain / HRDC domain profile. / HRDC domain superfamily / 3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / HRDC-like superfamily / Ribonuclease H-like superfamily/Ribonuclease H / DNA polymerase; domain 1 / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Exosome complex exonuclease RRP6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSchuch, B. / Conti, E.
Funding support Germany, Switzerland, 4items
OrganizationGrant numberCountry
European Research CouncilAdvanced Investigator Grant 294371 Germany
Marie CurieITN RNPnet Germany
German Research FoundationSFB646, SFB1035, GRK1721, FOR1680 and CIPSM Germany
Louis Jeantet Foundation Switzerland
CitationJournal: Nature / Year: 2015
Title: RNA degradation paths in a 12-subunit nuclear exosome complex.
Authors: Makino, D.L. / Schuch, B. / Stegmann, E. / Baumgartner, M. / Basquin, C. / Conti, E.
History
DepositionJun 12, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exosome complex exonuclease RRP6
B: Exosome complex exonuclease RRP6
D: poly U RNA
C: poly U RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,2645
Polymers103,2404
Non-polymers241
Water10,593588
1
A: Exosome complex exonuclease RRP6
C: poly U RNA


Theoretical massNumber of molelcules
Total (without water)51,6202
Polymers51,6202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Exosome complex exonuclease RRP6
D: poly U RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6443
Polymers51,6202
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.186, 110.186, 78.883
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA127 - 515
211chain BB127 - 515

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Components

#1: Protein Exosome complex exonuclease RRP6 / Ribosomal RNA-processing protein 6


Mass: 47072.430 Da / Num. of mol.: 2 / Fragment: residues 122-518 / Mutation: D296N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: RRP6, UNC733, YOR001W / Production host: Escherichia coli (E. coli)
References: UniProt: Q12149, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: RNA chain poly U RNA


Mass: 4547.529 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 588 / 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: 2.68 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 25% PEG3350, 100 mM Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.5
ReflectionResolution: 2.1→47.71 Å / Num. obs: 62575 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 1 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.022 / Net I/σ(I): 22.5 / Num. measured all: 402597 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible allRmerge(I) obs
2.1-2.155.91.52753547050.520.553100
9.39-47.716.7103.2471370310.00699.20.015

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.1 Å47.71 Å
Translation2.1 Å47.71 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.1.27data scaling
PHASER2.5.6phasing
PHENIXrefinement
Cootmodel building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→47.71 Å / Cross valid method: FREE R-VALUE / Phase error: 20.31 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1801 3003 4.8 %
Rwork0.1481 59518 -
obs0.1507 62547 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 160.5 Å2 / Biso mean: 54.8674 Å2 / Biso min: 24.18 Å2
Refinement stepCycle: final / Resolution: 2.1→47.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6341 166 54 588 7149
Biso mean--63.55 48.92 -
Num. residues----781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0176693
X-RAY DIFFRACTIONf_angle_d1.269124
X-RAY DIFFRACTIONf_chiral_restr0.0581021
X-RAY DIFFRACTIONf_plane_restr0.0071142
X-RAY DIFFRACTIONf_dihedral_angle_d15.1612540
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3581X-RAY DIFFRACTION7.488TORSIONAL
12B3581X-RAY DIFFRACTION7.488TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1002-2.13640.33171600.27972972313295
2.1364-2.17520.29791380.25942965310396
2.1752-2.21710.25851190.25073025314496
2.2171-2.26230.27671220.23793051317396
2.2623-2.31150.26961280.24092944307296
2.3115-2.36520.28051410.23032966310795
2.3652-2.42440.28021190.21663032315196
2.4244-2.48990.22851420.2092997313995
2.4899-2.56310.24521740.2052966314094
2.5631-2.64580.22691650.19222946311195
2.6458-2.74040.2181690.18242959312895
2.7404-2.850.18691650.17582943310895
2.85-2.97970.17891550.16482988314395
2.9797-3.13660.20431410.15432988312995
3.1366-3.3330.19611510.14372959311095
3.333-3.590.15871850.13942950313594
3.59-3.95080.15861620.12242957311995
3.9508-4.52120.15571550.10782968312395
4.5212-5.69130.1421430.10452985312895
5.6913-32.80490.14591690.12272957312695
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)
12.10160.5286-0.32480.4272-0.02471.99170.0854-0.4704-0.41490.37960.1917-0.79940.30730.735-0.15140.48950.1224-0.17180.6929-0.08740.78622.678228.56481.0748
22.010.0163-0.29022.15540.55062.7038-0.0466-0.2024-0.10690.16070.0659-0.3280.256-0.1148-0.03820.27740.0017-0.0270.3964-0.03910.36034.097130.2338-5.7686
32.9763-0.59530.20622.42761.0563.62150.0972-0.11580.2804-0.10490.004-0.2078-0.3225-0.4230.01880.27980.00840.04850.39370.00430.3485-1.653238.8575-9.0913
43.0818-0.1347-0.08061.96370.42372.2358-0.03560.25470.2945-0.01480.2355-0.8053-0.00780.7454-0.08490.4025-0.00190.02970.5327-0.10530.718819.66829.161-15.0222
51.34770.41380.54432.14710.03072.35210.11660.5798-0.1179-0.2687-0.1125-0.0124-0.16790.08210.03070.34410.0723-0.02890.5864-0.09590.313232.289259.9407-7.2417
62.16210.93550.19162.8934-0.18921.94290.08480.13720.6969-0.23180.10780.7166-0.3037-0.4143-0.14890.49440.1531-0.02840.54490.17480.722213.222534.8914-48.6009
71.3924-0.09460.22.2459-0.33372.29690.11650.19630.1559-0.3104-0.11860.25030.2512-0.1172-0.04580.35220.05170.01560.28690.02620.34423.984618.7439-42.5651
82.2393-0.4691-0.40892.8711-0.95233.02250.11770.04010.2992-0.1399-0.2028-0.25970.13580.4810.06580.3420.08460.03960.27860.02810.309234.610417.8966-39.2893
92.37070.001-0.25810.06380.00392.4880.11530.11080.75620.2722-0.11420.281-0.591-0.1532-0.19910.35350.05910.13320.35270.03080.656215.88931.5077-33.1812
101.70390.51020.59312.9898-0.05632.6538-0.107-0.5772-0.16210.56870.19620.2162-0.15230.0889-0.05130.45280.14130.07140.45060.07350.249936.041157.8311-41.7807
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 127 through 183 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 184 through 336 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 337 through 382 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 383 through 420 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 423 through 515 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 127 through 183 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 184 through 335 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 336 through 382 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 383 through 419 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 428 through 515 )B0

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