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- PDB-6r9m: Structure of Saccharomyces cerevisiae apo Pan2 pseudoubiquitin hy... -

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Basic information

Entry
Database: PDB / ID: 6r9m
TitleStructure of Saccharomyces cerevisiae apo Pan2 pseudoubiquitin hydrolase-RNA exonuclease (UCH-Exo) module in complex with AAGGAA RNA
Components
  • AAGGAA 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 S288C (yeast)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.329 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 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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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: AAGGAA RNA


Theoretical massNumber of molelcules
Total (without water)79,7382
Polymers79,7382
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-7 kcal/mol
Surface area27960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.414, 118.105, 257.281
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 S288C (yeast) / Gene: PAN2, YGL094C / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P53010, poly(A)-specific ribonuclease
#2: RNA chain AAGGAA RNA


Mass: 1962.277 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in all eukaryotes. / 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: 4.35 Å3/Da / Density % sol: 71.75 %
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 23, 2018
RadiationMonochromator: Single bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 3.329→86.17 Å / Num. obs: 20875 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.983 / Rmerge(I) obs: 0.097 / Net I/σ(I): 7.3
Reflection shellResolution: 3.329→3.42 Å / Redundancy: 6 % / Rmerge(I) obs: 1.527 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1509 / CC1/2: 0.649 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4czw


Resolution: 3.329→63.021 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2953 1092 5.24 %
Rwork0.2369 19765 -
obs0.2399 20857 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 299.6 Å2 / Biso mean: 152.5386 Å2 / Biso min: 68.98 Å2
Refinement stepCycle: final / Resolution: 3.329→63.021 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4586 87 0 0 4673
Num. residues----604
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.3289-3.48040.41381220.358224512573
3.4804-3.66390.39111570.308423942551
3.6639-3.89340.33481370.27924232560
3.8934-4.1940.30251240.244524652589
4.194-4.61590.28481180.213724752593
4.6159-5.28350.26431370.208824682605
5.2835-6.65550.31721460.279524832629
6.6555-63.0320.2691510.20626062757
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)
13.1307-0.0628-0.33427.42042.64188.4503-0.233-0.05250.03050.16090.1326-0.19050.40220.68360.06910.69460.0847-0.04761.23140.06240.7041-156.5757169.6085295.7448
28.5738-0.6429-5.67132.25961.94254.85910.41831.01150.89740.42520.16710.18050.30750.0671-0.52191.32720.0036-0.1571.78190.19050.7837-157.2929183.8945269.6403
34.3999-0.24150.45487.18121.07667.63870.04140.39450.1873-0.157-0.0202-0.0419-1.1477-0.4204-0.03791.05660.1637-0.15541.21530.02780.6154-166.8549182.1003286.9647
43.4296-0.2281-0.45483.1375-0.54793.65470.3011-0.2787-0.23110.6036-0.4021-0.52920.73230.23850.08731.3383-0.0117-0.12241.07240.11551.161-149.6627147.9999311.6599
54.47044.22950.16484.36191.08532.4813.08671.64290.71692.62841.2528-0.0912-2.7583-1.4267-42.90180.32680.31272.76160.17212.7031-143.9694157.0701321.4219
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 461 through 649 )A461 - 649
2X-RAY DIFFRACTION2chain 'A' and (resid 650 through 694 )A650 - 694
3X-RAY DIFFRACTION3chain 'A' and (resid 695 through 864 )A695 - 864
4X-RAY DIFFRACTION4chain 'A' and (resid 865 through 1110 )A865 - 1110
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 6 )B3 - 6

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