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- PDB-6r9i: Structure of Saccharomyces cerevisiae apo Pan2 pseudoubiquitin hy... -

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Basic information

Entry
Database: PDB / ID: 6r9i
TitleStructure of Saccharomyces cerevisiae apo Pan2 pseudoubiquitin hydrolase-RNA exonuclease (UCH-Exo) module
ComponentsPAN2-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 / PAN2 N-terminal / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. ...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. / 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
PAN2-PAN3 deadenylation complex catalytic subunit PAN2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 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 29, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.d_res_high / _reflns_shell.d_res_low
Revision 1.5Jan 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


Theoretical massNumber of molelcules
Total (without water)77,7761
Polymers77,7761
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area27490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.373, 117.075, 255.319
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

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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: 4.39 Å3/Da / Density % sol: 71.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging 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: Oct 14, 2017
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→106.41 Å / Num. obs: 27902 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Net I/σ(I): 12.4
Reflection shellResolution: 3→3.08 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.761 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1350 / CC1/2: 0.774 / % possible all: 99.9

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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→86.03 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.1
RfactorNum. reflection% reflection
Rfree0.2895 1331 4.78 %
Rwork0.2434 --
obs0.2456 27861 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 231.84 Å2 / Biso mean: 113.6934 Å2 / Biso min: 52.65 Å2
Refinement stepCycle: final / Resolution: 3→86.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4542 0 0 0 4542
Num. residues----605
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 (%)
2.9992-3.10640.42711340.38482580271499
3.1064-3.23070.32891220.324526332755100
3.2307-3.37780.3491290.296426262755100
3.3778-3.55590.32291240.292626042728100
3.5559-3.77870.36111320.276826562788100
3.7787-4.07040.29691360.228426202756100
4.0704-4.480.24221270.213626642791100
4.48-5.12820.20491340.199826642798100
5.1282-6.46070.33951600.259426722832100
6.4607-86.06520.27411330.227728112944100
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)
11.7021-0.73020.43013.9266-0.85754.80270.1172-0.0191-0.4377-0.0694-0.1601-0.0841.09240.07470.06370.7581-0.03730.1490.8332-0.010.5026-150.6929152.1833298.507
21.3883-0.01560.22462.9744-2.99176.12760.3066-0.42780.30270.9399-0.34770.1660.5653-0.2879-0.11431.4134-0.25580.04860.67690.02930.5969-151.3764146.0235320.13
32.783-0.1884-1.67787.04430.31226.304-0.3081-0.5465-0.00460.36370.1776-0.24380.39440.03060.11330.59540.0197-0.02531.0719-0.00350.4305-156.1286168.7061296.0828
42.82360.447-0.27533.01180.22546.2914-0.11080.4390.286-0.35390.11120.2359-0.2817-0.6822-0.05840.63450.167-0.01511.2143-0.01350.484-163.0091178.0781279.4552
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 839 through 1008 )A839 - 1008
2X-RAY DIFFRACTION2chain 'A' and (resid 1009 through 1110 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 462 through 617 )A462 - 617
4X-RAY DIFFRACTION4chain 'A' and (resid 618 through 838 )A618 - 838

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