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- PDB-6r9j: Structure of Saccharomyces cerevisiae apo Pan2 pseudoubiquitin hy... -

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Basic information

Entry
Database: PDB / ID: 6r9j
TitleStructure of Saccharomyces cerevisiae apo Pan2 pseudoubiquitin hydrolase-RNA exonuclease (UCH-Exo) module in complex with A7 RNA
Components
  • A7 RNA
  • PAN2-PAN3 deadenylation complex catalytic subunit PAN2
KeywordsHYDROLASE / DEDD RNase / deadenylase / pseudoubiquitin hydrolase
Function / homology
Function and homology information


PAN complex / Deadenylation of mRNA / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / nuclear-transcribed mRNA poly(A) tail shortening / DNA damage tolerance / 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 / PAN2 N-terminal / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ubiquitin specific protease domain ...PAN2, UCH domain / PAN2-PAN3 deadenylation complex catalytic subunit PAN2 / : / : / Ubiquitin carboxyl-terminal hydrolase / PAN2 N-terminal / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Cysteine proteinases / Cathepsin B; Chain A / Quinoprotein alcohol dehydrogenase-like superfamily / 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 (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.326 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
Revision 1.4Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: A7 RNA


Theoretical massNumber of molelcules
Total (without water)80,0362
Polymers80,0362
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-8 kcal/mol
Surface area27950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.480, 116.409, 257.833
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)
Gene: PAN2, YGL094C / Plasmid: pACEBac1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P53010, poly(A)-specific ribonuclease
#2: RNA chain A7 RNA


Mass: 2259.483 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in all eukaryotic organisms.
Source: (synth.) Saccharomyces cerevisiae (brewer'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: 71.55 %
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: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 21, 2018
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.326→71.928 Å / Num. obs: 20507 / % possible obs: 99.5 % / Redundancy: 4.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.095 / Net I/σ(I): 8.3
Reflection shellResolution: 3.326→3.42 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.821 / Mean I/σ(I) obs: 1 / Num. unique obs: 1481 / CC1/2: 0.59 / % possible all: 98.6

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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_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CZW

4czw


Resolution: 3.326→71.928 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 35.19
RfactorNum. reflection% reflection
Rfree0.2982 1079 5.27 %
Rwork0.2472 --
obs0.25 20482 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 343.56 Å2 / Biso mean: 151.0181 Å2 / Biso min: 71.32 Å2
Refinement stepCycle: final / Resolution: 3.326→71.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4455 107 0 0 4562
Num. residues----600
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3257-3.4770.45691210.38442308242996
3.477-3.66030.34211600.31152370253099
3.6603-3.88960.31511300.27372414254499
3.8896-4.18990.29111250.24862416254199
4.1899-4.61150.26631170.22632435255299
4.6115-5.27860.26931330.217524462579100
5.2786-6.64980.29851470.286524422589100
6.6498-71.94470.29551460.22292572271899
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)
12.1839-1.4974-0.90578.74894.12197.0094-0.4283-0.3973-0.27320.97840.35390.55611.15150.31290.06070.91160.14860.00291.15160.00280.9299-160.9367169.7811302.4845
22.64960.2441-0.48153.098-1.59585.1958-0.17070.32320.2352-0.5923-0.1023-0.1230.06660.10790.30750.7259-0.06370.03651.2425-0.03880.7538-156.3617174.1367282.6806
31.9227-0.55160.58133.7413-1.80663.9430.2323-0.1528-0.21140.2124-0.3391-0.10140.3564-0.15710.10390.95910.015-0.0221.099-0.0780.8813-156.4109155.87305.4181
45.8129-6.199-5.19986.61835.60345.05280.48360.78642.37686.5803-0.4376-3.36020.9227-0.2264-0.1583.1756-1.3147-0.44862.82140.15752.0483-145.3783156.133322.8324
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 462 through 544 )A462 - 544
2X-RAY DIFFRACTION2chain 'A' and (resid 545 through 758 )A545 - 758
3X-RAY DIFFRACTION3chain 'A' and (resid 759 through 1110 )A759 - 1110
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 7 )B3 - 7

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