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- PDB-6r9p: Structure of Saccharomyces cerevisiae apo Pan2 pseudoubiquitin hy... -

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Basic information

Entry
Database: PDB / ID: 6r9p
TitleStructure of Saccharomyces cerevisiae apo Pan2 pseudoubiquitin hydrolase-RNA exonuclease (UCH-Exo) module in complex with AAUUAA RNA
Components
  • AAUUAA RNA
  • PAN2-PAN3 deadenylation complex catalytic subunit PAN2
KeywordsHYDROLASE / DEDD RNase / deadenylase / pseudoubiquitin hydrolase
Function / homology
Function and homology information


PAN complex / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / nuclear-transcribed mRNA poly(A) tail shortening / postreplication repair / P-body / mRNA processing / nucleic acid binding / metal ion binding / cytoplasm
Similarity search - Function
PAN2, UCH domain / PAN2-PAN3 deadenylation complex catalytic subunit PAN2 / Ubiquitin carboxyl-terminal hydrolase / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Quinoprotein alcohol dehydrogenase-like superfamily / Cysteine proteinases ...PAN2, UCH domain / PAN2-PAN3 deadenylation complex catalytic subunit PAN2 / Ubiquitin carboxyl-terminal hydrolase / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Quinoprotein alcohol dehydrogenase-like superfamily / Cysteine proteinases / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / WD40/YVTN repeat-like-containing domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
RNA / PAN2-PAN3 deadenylation complex catalytic subunit PAN2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.98 Å
AuthorsTang, T.T.L. / Stowell, J.A.W. / Hill, C.H. / Passmore, L.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
European Research Council725685
Medical Research Council (United Kingdom)MC_U105192715 United Kingdom
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2019
Title: The intrinsic structure of poly(A) RNA determines the specificity of Pan2 and Caf1 deadenylases.
Authors: Tang, T.T.L. / Stowell, J.A.W. / Hill, C.H. / Passmore, L.A.
History
DepositionApr 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jun 19, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Aug 21, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PAN2-PAN3 deadenylation complex catalytic subunit PAN2
B: AAUUAA RNA


Theoretical massNumber of molelcules
Total (without water)79,6602
Polymers79,6602
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-12 kcal/mol
Surface area28360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.885, 117.091, 255.888
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein PAN2-PAN3 deadenylation complex catalytic subunit PAN2 / PAB1P-dependent poly(A)-specific ribonuclease / Poly(A)-nuclease deadenylation complex subunit 2 / ...PAB1P-dependent poly(A)-specific ribonuclease / Poly(A)-nuclease deadenylation complex subunit 2 / PAN deadenylation complex subunit 2


Mass: 77776.102 Da / Num. of mol.: 1 / Mutation: E912A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: PAN2, YGL094C / Plasmid: pACEBac1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P53010, poly(A)-specific ribonuclease
#2: RNA chain AAUUAA RNA


Mass: 1884.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in all eukaryotes. / Source: (synth.) Saccharomyces cerevisiae (baker's yeast)

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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: 4.32 Å3/Da / Density % sol: 71.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.4 M ammonium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 9, 2019
RadiationMonochromator: Single bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.98→106.45 Å / Num. obs: 28662 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.5
Reflection shellResolution: 2.98→3.06 Å / Redundancy: 6.21 % / Rmerge(I) obs: 1.512 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4551 / CC1/2: 0.726 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
xia21.12data scaling
PHASER2.8phasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CZW

4czw


Resolution: 2.98→86.478 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.66
RfactorNum. reflection% reflection
Rfree0.3086 1461 5.11 %
Rwork0.261 --
obs0.2635 28616 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 287.24 Å2 / Biso mean: 133.2483 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.98→86.478 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4550 81 0 0 4631
Num. residues----611
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9804-3.08690.43721660.39626562822100
3.0869-3.21050.4351360.35052661279799
3.2105-3.35670.37951320.310126962828100
3.3567-3.53360.33921380.29526912829100
3.5336-3.7550.32771400.297226802820100
3.755-4.0450.29681620.247926972859100
4.045-4.4520.3051310.238527182849100
4.452-5.09620.30381510.219327352886100
5.0962-6.42030.33721350.286127612896100
6.4203-86.51470.27521700.247828603030100
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)
16.2351-1.0848-2.20259.35221.92969.576-0.2433-0.68710.09110.59880.2009-0.35720.3383-0.22530.08990.62290.0326-0.04350.78480.03230.3933-157.3419168.682297.2344
24.080.1001-0.11134.2260.43938.0993-0.02090.73030.529-0.62750.03390.498-1.2257-1.5085-0.02660.89640.3147-0.07721.40970.06310.5848-163.9065178.5653281.3233
32.7973-0.7486-0.13975.087-1.75788.01570.142-0.2712-0.51610.3717-0.2924-0.36631.7019-0.18650.07331.1313-0.25230.03310.77610.02820.8246-150.6234147.236309.4601
48.4694-1.4153-1.96485.6897-5.48016.6413-1.01716.03691.25293.7001-0.07450.71914.6375-2.32581.09022.9018-0.83040.12433.69140.17581.6703-145.22154.8869319.0862
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 461 through 617 )A461 - 617
2X-RAY DIFFRACTION2chain 'A' and (resid 618 through 858 )A618 - 858
3X-RAY DIFFRACTION3chain 'A' and (resid 859 through 1111 )A859 - 1111
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 6 )B3 - 6

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