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- PDB-4bwk: Structure of Neurospora crassa PAN3 pseudokinase -

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Basic information

Entry
Database: PDB / ID: 4bwk
TitleStructure of Neurospora crassa PAN3 pseudokinase
ComponentsPAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN-3
KeywordsGENE REGULATION / DEADENYLASE / PAN2 / MIRNA / MRNA DECAY
Function / homology
Function and homology information


PAN complex / nuclear-transcribed mRNA poly(A) tail shortening / poly(A) binding / P-body / mRNA processing / ATP binding / metal ion binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #5160 / Helix Hairpins - #3700 / PAN2-PAN3 deadenylation complex subunit PAN3 / Pan3 pseudokinase domain / Pan3 Pseudokinase domain / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / Transferase(Phosphotransferase) domain 1 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #5160 / Helix Hairpins - #3700 / PAN2-PAN3 deadenylation complex subunit PAN3 / Pan3 pseudokinase domain / Pan3 Pseudokinase domain / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase-like domain superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / PAN2-PAN3 deadenylation complex subunit pan3
Similarity search - Component
Biological speciesNEUROSPORA CRASSA (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsChristie, M. / Boland, A. / Huntzinger, E. / Weichenrieder, O. / Izaurralde, E.
CitationJournal: Mol.Cell / Year: 2013
Title: Structure of the Pan3 Pseudokinase Reveals the Basis for Interactions with the Pan2 Deadenylase and the Gw182 Proteins
Authors: Christie, M. / Boland, A. / Huntzinger, E. / Weichenrieder, O. / Izaurralde, E.
History
DepositionJul 4, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 PAN-3
B: PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,5854
Polymers98,5382
Non-polymers1,0462
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8400 Å2
ΔGint-51.2 kcal/mol
Surface area37990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.521, 89.521, 228.789
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.998, 0.014, 0.057), (0.037, 0.904, 0.426), (-0.046, 0.428, -0.903)
Vector: -61.72517, 16.72507, -60.32031)

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Components

#1: Protein PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN-3 / PAB1P-DEPENDENT POLY(A)-NUCLEASE / PAB-DEPENDENT POLYA-SPECIFIC RIBONUCLEASE SUBUNIT PAN-3


Mass: 49269.078 Da / Num. of mol.: 2
Fragment: PSEUDOKINASE DOMAIN, COILED COIL, CTERMINAL KNOB, RESIDUES 234-656
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEUROSPORA CRASSA (fungus) / Plasmid: PNEA-NPM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7SDP4
#2: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM

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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: 2.65 Å3/Da / Density % sol: 53.5 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1 M HEPES PH 7.5, 7% PEG 6000, 6% ISOPROPANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00001
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 26, 2012 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 3.3→46.03 Å / Num. obs: 15611 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Biso Wilson estimate: 117.45 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.9
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→46.027 Å / SU ML: 0.4 / σ(F): 1.36 / Phase error: 37.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2937 779 5 %
Rwork0.2521 --
obs0.2541 15516 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→46.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6345 0 62 0 6407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086545
X-RAY DIFFRACTIONf_angle_d1.5248866
X-RAY DIFFRACTIONf_dihedral_angle_d14.0022426
X-RAY DIFFRACTIONf_chiral_restr0.057993
X-RAY DIFFRACTIONf_plane_restr0.0071124
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3002-3.50690.39341170.3622445X-RAY DIFFRACTION99
3.5069-3.77750.31371240.30642454X-RAY DIFFRACTION100
3.7775-4.15740.37811310.28032441X-RAY DIFFRACTION100
4.1574-4.75850.31371440.26642458X-RAY DIFFRACTION100
4.7585-5.99310.30441370.26412462X-RAY DIFFRACTION100
5.9931-46.03110.24181260.21112477X-RAY DIFFRACTION100
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)
10.71940.0108-0.07660.58830.27260.57650.89690.6930.0354-0.0327-0.7471-0.23650.52980.23220.07170.54070.06590.36670.26250.13730.5009-23.673527.7266-34.2508
20.3692-0.0794-0.01680.52790.25820.24860.4872-0.13380.04420.0145-0.63-0.14110.0535-0.768-0.15251.2172-0.85990.38840.3648-0.30730.5627-39.742626.6032-16.769
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESSEQ 235:646)
2X-RAY DIFFRACTION2(CHAIN B AND RESSEQ 235:646)

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