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- PDB-4czv: Structure of the Neurospora crassa Pan2 WD40 domain -

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Basic information

Entry
Database: PDB / ID: 4czv
TitleStructure of the Neurospora crassa Pan2 WD40 domain
ComponentsPAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN2
KeywordsGENE REGULATION / SCAFFOLD DOMAIN / 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 ...: / 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 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Papain-like cysteine peptidase superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
PAN2-PAN3 deadenylation complex catalytic subunit pan2
Similarity search - Component
Biological speciesNEUROSPORA CRASSA (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPeter, D. / Jonas, S. / 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
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
B: PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6345
Polymers72,4712
Non-polymers1633
Water6,413356
1
A: PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3633
Polymers36,2351
Non-polymers1282
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)36,2712
Polymers36,2351
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.990, 71.510, 77.120
Angle α, β, γ (deg.)90.00, 94.65, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.0623, -0.0008, -0.9981), (-0.0112, -0.9999, 0.0001), (-0.998, 0.0112, -0.0623)
Vector: 95.6858, 14.0452, 101.4541)

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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: 36235.258 Da / Num. of mol.: 2 / Fragment: WD40 DOMAIN, RESIDUES 1-321
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE 3 N-TERMINAL RESIDUES OF CHAIN A REMAIN FROM THE PURIFICATION TAG THE 3 N-TERMINAL RESIDUES OF ...THE 3 N-TERMINAL RESIDUES OF CHAIN A REMAIN FROM THE PURIFICATION TAG THE 3 N-TERMINAL RESIDUES OF CHAIN B STEM FROM THE PURIFICATION TAG

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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: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growDetails: 0.1M AMMONIUM CHLORIDE, 18% PEG3350, 2% TERT-BUTANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00002
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2013 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.1→49.7 Å / Num. obs: 38536 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 26.4 Å2 / Rsym value: 0.08 / Net I/σ(I): 12.2
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.18 / Rsym value: 0.6 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CZX CHAIN A

4czx


Resolution: 2.1→46.32 Å / SU ML: 0.25 / σ(F): 1.36 / Phase error: 22.31 / Stereochemistry target values: ML
Details: RESIDUE 11 CHAIN B WAS REFINED WITH A DOUBLE CONFORMATION.
RfactorNum. reflection% reflection
Rfree0.2162 1921 5 %
Rwork0.1817 --
obs0.1835 38335 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5098 0 8 356 5462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045243
X-RAY DIFFRACTIONf_angle_d0.8277126
X-RAY DIFFRACTIONf_dihedral_angle_d12.4381901
X-RAY DIFFRACTIONf_chiral_restr0.032783
X-RAY DIFFRACTIONf_plane_restr0.004923
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1033-2.15590.25121300.24572482X-RAY DIFFRACTION97
2.1559-2.21420.28961410.23652582X-RAY DIFFRACTION100
2.2142-2.27930.27331370.23732598X-RAY DIFFRACTION99
2.2793-2.35290.2671360.23052632X-RAY DIFFRACTION100
2.3529-2.4370.25861260.22542586X-RAY DIFFRACTION100
2.437-2.53450.3081250.20922601X-RAY DIFFRACTION100
2.5345-2.64990.24761220.21492618X-RAY DIFFRACTION100
2.6499-2.78960.27161430.20842591X-RAY DIFFRACTION100
2.7896-2.96430.28491360.20912619X-RAY DIFFRACTION100
2.9643-3.19310.22211290.19442616X-RAY DIFFRACTION100
3.1931-3.51440.1891280.16752607X-RAY DIFFRACTION100
3.5144-4.02270.18631480.15962598X-RAY DIFFRACTION99
4.0227-5.06710.15851490.12922624X-RAY DIFFRACTION100
5.0671-46.32720.18361710.14852660X-RAY DIFFRACTION100
Refinement TLS params.

S33: -0 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.82850.3372-0.02110.86410.37061.13130.0353-0.00520.01690.0463-0.02510.0128-0.02190.01870.17020.0033-0.00560.14680.0120.132947.403-9.677566.0983
21.04480.25750.03110.75130.0590.5846-0.02710.0024-0.01890.02910.03-0.00060.0758-0.00540.14140.0092-0.00660.1380.0050.158132.563423.407850.4748
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID -2 THROUGH 321 )
2X-RAY DIFFRACTION2CHAIN 'B' AND (RESID -2 THROUGH 321 )

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