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- PDB-4czw: Structure of the Neurospora crassa Pan2 catalytic unit (protease ... -

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Basic information

Entry
Database: PDB / ID: 4czw
TitleStructure of the Neurospora crassa Pan2 catalytic unit (protease and nuclease domain)
ComponentsPAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN2
KeywordsGENE REGULATION / DEED EXORIBONUCLEASE / UBIQUITIN SPECIFIC PROTEASE / DEADENYLATION / MRNA DECAY / PAN2-PAN3 COMPLEX
Function / homology
Function and homology information


PAN complex / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / nuclear-transcribed mRNA poly(A) tail shortening / P-body / mRNA processing / nucleic acid binding / metal ion binding
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 speciesNEUROSPORA CRASSA (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsChristie, M. / Izaurralde, E. / Weichenrieder, O.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: An Asymmetric Pan3 Dimer Recruits a Single Pan2 Exonuclease to Mediate Mrna Deadenylation and Decay.
Authors: Jonas, S. / Christie, M. / Peter, D. / Bhandari, D. / Loh, B. / Huntzinger, E. / Weichenrieder, O. / Izaurralde, E.
History
DepositionApr 22, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Jul 16, 2014Group: Database references
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0693
Polymers74,9381
Non-polymers1312
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.565, 85.565, 471.793
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-2100-

HOH

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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 / A-SPECIFIC ...PAB1P-DEPENDENT POLY(A)-NUCLEASE / PAN DEADENYLATION COMPLEX CATALYTIC SUBUNIT 2 / A-SPECIFIC RIBONUCLEASE SUBUNIT PAN2


Mass: 74937.742 Da / Num. of mol.: 1
Fragment: UBIQUITIN SPECIFIC PROTEASE DOMAIN AND EXORIBONUCLEASE DOMAIN, RESIDUES 456-1100
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEUROSPORA CRASSA (fungus) / Plasmid: PETMCN (PNYC) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: P0C581, 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.: 108 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsORIGINALLY THE CONSTRUCT COMPRISED RESIDUES 342-1100 BUT THE N-TERMINUS HYDROLYZED DURING ...ORIGINALLY THE CONSTRUCT COMPRISED RESIDUES 342-1100 BUT THE N-TERMINUS HYDROLYZED DURING PURIFICATION AND IS NOT PART OF THE CRYSTAL. THE 8 C-TERMINAL RESIUDES OF CHAIN A STEM FROM THE MULTIPLE CLONING SITE OF THE EXPRESSION VECTOR.

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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: 3.7 Å3/Da / Density % sol: 66 % / Description: NONE
Crystal growpH: 5.5
Details: 1.4M SODIUM FORMATE, 100MM SODIUM ACETATE, 100MM SODIUM CITRATE (PH5.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99999, 0.97978, 1.28082, 1.28639
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 5, 2013 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.999991
20.979781
31.280821
41.286391
ReflectionResolution: 2.6→47.18 Å / Num. obs: 32906 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 58.2 Å2 / Rsym value: 0.09 / Net I/σ(I): 13.4
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.85 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE 1.8.4_1496)refinement
XDSdata reduction
Aimlessdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.6→46.14 Å / SU ML: 0.38 / σ(F): 1.04 / Phase error: 24.49 / Stereochemistry target values: ML
Details: RESIDUES 668-677, 771-772, 908- -924 AND 1094-1100 ARE DISORDERED. SIDE-CHAINS OF RESIDUES 476-478 WERE TRUNCATED AT CB ATOMS.
RfactorNum. reflection% reflection
Rfree0.2535 1660 5.1 %
Rwork0.2086 --
obs0.2108 32764 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.7 Å2
Refinement stepCycle: LAST / Resolution: 2.6→46.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4876 0 2 108 4986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024996
X-RAY DIFFRACTIONf_angle_d0.546785
X-RAY DIFFRACTIONf_dihedral_angle_d10.2081844
X-RAY DIFFRACTIONf_chiral_restr0.022762
X-RAY DIFFRACTIONf_plane_restr0.002871
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6042-2.68080.34571690.30612480X-RAY DIFFRACTION100
2.6808-2.76730.3041360.27882500X-RAY DIFFRACTION100
2.7673-2.86620.35851330.27432548X-RAY DIFFRACTION100
2.8662-2.9810.31131170.26952525X-RAY DIFFRACTION100
2.981-3.11660.33421290.25172546X-RAY DIFFRACTION100
3.1166-3.28090.32811410.24872560X-RAY DIFFRACTION100
3.2809-3.48640.26961230.23282550X-RAY DIFFRACTION100
3.4864-3.75540.27911460.22212572X-RAY DIFFRACTION100
3.7554-4.13310.21441370.18812598X-RAY DIFFRACTION100
4.1331-4.73070.22441460.16492636X-RAY DIFFRACTION100
4.7307-5.95820.19871380.18182680X-RAY DIFFRACTION100
5.9582-46.15140.22471450.18782909X-RAY DIFFRACTION100

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