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- PDB-4q8g: Structure of the Saccharomyces cerevisiae PAN2 pseudoubiquitin-hy... -

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Basic information

Entry
Database: PDB / ID: 4q8g
TitleStructure of the Saccharomyces cerevisiae PAN2 pseudoubiquitin-hydrolase
ComponentsPAB-dependent poly(A)-specific ribonuclease subunit PAN2
KeywordsHYDROLASE / Ubiquitin carboxyl-terminal hydrolase-like domain / UCH / PAN3 / inactive
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 (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsSchaefer, I.B. / Conti, E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: The structure of the Pan2-Pan3 core complex reveals cross-talk between deadenylase and pseudokinase.
Authors: Schafer, I.B. / Rode, M. / Bonneau, F. / Schussler, S. / Conti, E.
History
DepositionApr 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Jul 16, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PAB-dependent poly(A)-specific ribonuclease subunit PAN2
B: PAB-dependent poly(A)-specific ribonuclease subunit PAN2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,7294
Polymers106,5982
Non-polymers1312
Water3,837213
1
A: PAB-dependent poly(A)-specific ribonuclease subunit PAN2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3642
Polymers53,2991
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PAB-dependent poly(A)-specific ribonuclease subunit PAN2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3642
Polymers53,2991
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.508, 74.032, 175.081
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 53299.062 Da / Num. of mol.: 2 / Fragment: UNP residues 416-870
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PAN2, YGL094C / Plasmid: pEC-A-3C-ZTA / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P53010, poly(A)-specific ribonuclease
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O

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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: 2.08 Å3/Da / Density % sol: 40.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 230 mM tri-ammonium citrate, pH 7.0, 16% w/v PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99997 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2013 / Details: mirrors
RadiationMonochromator: double-channel cut fixed-exit Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 52837 / Num. obs: 52731 / % possible obs: 99.8 % / Observed criterion σ(F): -3.7 / Observed criterion σ(I): -3.7 / Redundancy: 5.2 % / Biso Wilson estimate: 36.1 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 10.2
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.21 / Mean I/σ(I) obs: 0.8 / Num. unique all: 4258 / % possible all: 99.7

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Processing

Software
NameVersionClassification
AutoSolphasing
PHENIX(phenix.refine: dev_1631)refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→48.328 Å / SU ML: 0.24 / σ(F): 1.36 / Phase error: 21.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2209 2687 5.1 %RANDOM
Rwork0.1838 ---
obs0.1857 52654 99.66 %-
all-52834 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→48.328 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5505 0 2 213 5720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145654
X-RAY DIFFRACTIONf_angle_d1.4117685
X-RAY DIFFRACTIONf_dihedral_angle_d14.422057
X-RAY DIFFRACTIONf_chiral_restr0.056889
X-RAY DIFFRACTIONf_plane_restr0.007977
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13820.29621330.29512601X-RAY DIFFRACTION99
2.1382-2.17930.31121330.26872583X-RAY DIFFRACTION100
2.1793-2.22380.27681390.2622575X-RAY DIFFRACTION99
2.2238-2.27220.29721500.24352585X-RAY DIFFRACTION100
2.2722-2.3250.27861450.24292595X-RAY DIFFRACTION99
2.325-2.38320.25311310.22062597X-RAY DIFFRACTION99
2.3832-2.44760.2581540.21062602X-RAY DIFFRACTION100
2.4476-2.51960.25731400.20332600X-RAY DIFFRACTION100
2.5196-2.60090.23611380.19992608X-RAY DIFFRACTION100
2.6009-2.69390.23351440.1982615X-RAY DIFFRACTION100
2.6939-2.80170.23251340.19232634X-RAY DIFFRACTION100
2.8017-2.92920.23631700.19572569X-RAY DIFFRACTION99
2.9292-3.08360.2511390.1932648X-RAY DIFFRACTION100
3.0836-3.27680.21521510.18872629X-RAY DIFFRACTION100
3.2768-3.52970.19211470.17942640X-RAY DIFFRACTION100
3.5297-3.88480.22831260.16992688X-RAY DIFFRACTION100
3.8848-4.44660.19481430.14172648X-RAY DIFFRACTION100
4.4466-5.60090.15941440.14152719X-RAY DIFFRACTION100
5.6009-48.34130.22811260.19052831X-RAY DIFFRACTION99
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)
11.61110.1325-0.12785.45991.96813.33860.0477-0.1367-0.18250.40150.3056-0.82330.40130.7639-0.23070.32350.0951-0.11340.4642-0.07460.37733.278322.7817-12.8411
21.25110.32940.24531.35360.66532.39570.0376-0.0147-0.1201-0.02390.0143-0.02970.20810.0303-0.03420.31980.0477-0.06950.27830.01040.3127-9.95618.0815-26.375
34.34650.2204-0.28648.26142.89046.3885-0.0096-0.2103-0.4049-0.13860.08940.49270.6166-0.347-0.03480.3395-0.0309-0.10740.37650.03770.3369-55.6818-21.4065-35.5442
47.0720.86845.03122.41522.1327.03280.24450.0114-0.75620.14490.2128-0.12560.6712-0.0226-0.4920.42560.0382-0.05790.3106-0.04420.3807-41.2704-23.2007-32.6391
55.5709-0.81881.24626.1535-1.63624.89720.30081.065-0.8560.2015-0.2615-0.23370.61390.9567-0.11690.41170.0994-0.03280.5666-0.13830.3757-25.315-25.026-31.7127
64.3917-2.37412.73053.24010.27445.38010.31170.152-0.46150.1319-0.08690.17271.24570.6871-0.27910.6282-0.0248-0.06670.4527-0.0220.6331-37.034-29.8085-27.4097
72.8707-2.8108-1.60083.57490.033.83890.0093-0.3815-0.65810.1180.11340.00710.49350.1091-0.14630.5150.0462-0.10960.38540.01310.482-29.917-23.966-17.5193
83.3806-0.3647-4.33652.22940.26869.568-0.0267-0.4048-0.2814-0.03240.0853-0.7573-0.63931.0117-0.21770.37840.0923-0.15020.4671-0.07740.5317-22.0933-13.7561-12.6901
92.18470.1743-0.57412.78820.23365.6776-0.0242-0.3889-0.63020.47640.1117-0.03480.7080.5062-0.0510.43840.1006-0.03310.3987-0.03340.3876-31.9391-10.676-3.4689
102.61722.9212-1.27664.91430.69045.4020.1599-0.59730.66720.0799-0.2930.95250.1022-0.720.15760.40620.02090.03160.4647-0.08450.4964-44.1071-2.6899-17.5582
114.53283.85980.9544.85010.99862.29590.2017-0.18460.33890.4713-0.0655-0.0079-0.10650.1589-0.13150.29780.0583-0.01490.301-0.05130.274-32.8092-0.0891-18.4537
123.74153.218-0.88865.1831-1.16696.512-0.03080.62910.4324-0.18850.23970.39420.1398-0.3924-0.17420.36230.1119-0.04720.38060.04510.3902-43.8531-12.8506-31.9319
134.83882.04510.92193.68120.8462.9026-0.0257-0.10940.3328-0.21070.01420.1311-0.297-0.0964-0.00180.31440.0317-0.0180.2832-0.00820.2309-41.3936-9.6978-28.994
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 461 through 636 )
2X-RAY DIFFRACTION2chain 'A' and (resid 637 through 863 )
3X-RAY DIFFRACTION3chain 'B' and (resid 461 through 496 )
4X-RAY DIFFRACTION4chain 'B' and (resid 497 through 525 )
5X-RAY DIFFRACTION5chain 'B' and (resid 526 through 560 )
6X-RAY DIFFRACTION6chain 'B' and (resid 561 through 617 )
7X-RAY DIFFRACTION7chain 'B' and (resid 618 through 637 )
8X-RAY DIFFRACTION8chain 'B' and (resid 638 through 657 )
9X-RAY DIFFRACTION9chain 'B' and (resid 658 through 742 )
10X-RAY DIFFRACTION10chain 'B' and (resid 743 through 764 )
11X-RAY DIFFRACTION11chain 'B' and (resid 765 through 797 )
12X-RAY DIFFRACTION12chain 'B' and (resid 798 through 825 )
13X-RAY DIFFRACTION13chain 'B' and (resid 826 through 863 )

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