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- PDB-6r9o: Structure of Saccharomyces cerevisiae apo Pan2 pseudoubiquitin hy... -

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Basic information

Entry
Database: PDB / ID: 6r9o
TitleStructure of Saccharomyces cerevisiae apo Pan2 pseudoubiquitin hydrolase-RNA exonuclease (UCH-Exo) module in complex with AAGGA RNA
Components
  • AAGGA 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 / Quinoprotein alcohol dehydrogenase-like superfamily / 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 S288C (yeast)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.319 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: AAGGA RNA


Theoretical massNumber of molelcules
Total (without water)79,4092
Polymers79,4092
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-8 kcal/mol
Surface area27370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.761, 117.593, 256.568
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 / Plasmid: pACEBac1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P53010, poly(A)-specific ribonuclease
#2: RNA chain AAGGA RNA


Mass: 1633.072 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: 4.31 Å3/Da / Density % sol: 71.46 %
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: 3.319→85.565 Å / Num. obs: 20744 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Net I/σ(I): 12
Reflection shellResolution: 3.319→3.41 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.98 / Mean I/σ(I) obs: 1 / Num. unique obs: 1496 / CC1/2: 0.624 / % possible all: 99.8

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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: 3.319→85.565 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.76
RfactorNum. reflection% reflection
Rfree0.3092 1091 5.27 %
Rwork0.2545 --
obs0.2574 20721 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 366.9 Å2 / Biso mean: 159.1017 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.319→85.565 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4457 87 0 0 4544
Num. residues----598
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 (%)
3.3189-3.470.45031250.38362407253299
3.47-3.65290.39161560.342223742530100
3.6529-3.88180.35251400.303324212561100
3.8818-4.18150.27811200.246424592579100
4.1815-4.60230.28081160.221524532569100
4.6023-5.26820.24231380.214724582596100
5.2682-6.63690.3411450.306424672612100
6.6369-85.59370.30521510.231725912742100
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)
13.0688-0.92470.38667.36991.73096.4322-0.1363-0.03310.03190.03320.1568-0.5294-0.03930.30290.1831.10240.04740.0251.65540.01290.761-155.4992169.3756298.105
22.9432-0.49480.13713.87530.60957.6992-0.17240.55230.3742-0.1707-0.06280.1644-0.7838-0.16360.1481.22030.1671-0.08492.01210.03480.6847-162.0431179.4101282.6447
33.1317-0.8127-0.42153.6704-0.75023.6765-0.03530.42960.0446-0.4371-0.0895-0.28630.5576-0.0791-0.01440.98520.0791-0.00140.90630.0120.4497-147.5751148.5363301.3359
42.851-0.8823-0.49763.5919-1.73386.65280.1526-0.61630.05631.1964-0.30390.0435-0.3772-1.0039-0.01161.4868-0.2042-0.14431.24960.02950.7139-151.3322147.1334321.8691
54.87232.5757-6.42227.0966-1.72258.99520.80864.5175-1.82790.16381.0215-0.52942.5085-3.0423-1.36072.8775-0.1210.12743.4906-0.37453.1147-143.8103156.3418320.4993
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 462 through 617 )A462 - 617
2X-RAY DIFFRACTION2chain 'A' and (resid 618 through 858 )A618 - 858
3X-RAY DIFFRACTION3chain 'A' and (resid 859 through 1008 )A859 - 1008
4X-RAY DIFFRACTION4chain 'A' and (resid 1009 through 1109 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 5 )B2 - 5

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