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- PDB-4bwp: Structure of Drosophila Melanogaster PAN3 pseudokinase -

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Basic information

Entry
Database: PDB / ID: 4bwp
TitleStructure of Drosophila Melanogaster 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 / positive regulation of cytoplasmic mRNA processing body assembly / nuclear-transcribed mRNA poly(A) tail shortening / poly(A) binding / P-body / mRNA processing / ATP binding / cytoplasm
Similarity search - Function
Domain of unknown function DUF4797 / Domain of unknown function (DUF4797) / 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 C-terminal knob domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / Transferase(Phosphotransferase) domain 1 ...Domain of unknown function DUF4797 / Domain of unknown function (DUF4797) / 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 C-terminal knob domain / 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
AMP PHOSPHORAMIDATE / PAN2-PAN3 deadenylation complex subunit PAN3
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 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 3, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Dec 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

Downloads & links

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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)102,8314
Polymers101,9782
Non-polymers8522
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-37 kcal/mol
Surface area38270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.171, 102.171, 264.715
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.881, -0.457, 0.122), (-0.465, 0.787, -0.405), (0.089, -0.414, -0.906)
Vector: 101.07076, 12.51073, -53.2675)

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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: 50989.195 Da / Num. of mol.: 2
Fragment: PSEUDOKINSE DOMAIN, COILED COIL, CTERMINAL KNOB, RESIDUES 349-790
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PNYC-NPM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q95RR8
#2: Chemical ChemComp-AN2 / AMP PHOSPHORAMIDATE


Mass: 426.216 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N6O9P2

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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: 3.45 Å3/Da / Density % sol: 64 % / Description: NONE
Crystal growpH: 6.8
Details: 220 MM NA-CITRATE PH 7.0, HEPES PH 6.8, 2% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99999
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2012 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 3.6→48.8 Å / Num. obs: 17015 / % possible obs: 99.8 % / Observed criterion σ(I): 2.1 / Redundancy: 6.4 % / Biso Wilson estimate: 113 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.5
Reflection shellResolution: 3.6→3.79 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BWK

4bwk


Resolution: 3.6→48.8 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.9 / SU B: 75.901 / SU ML: 0.513 / Cross valid method: THROUGHOUT / ESU R Free: 0.602 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26878 862 5.1 %RANDOM
Rwork0.21954 ---
obs0.22225 16138 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 135.648 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.6→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6071 0 54 0 6125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.026252
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.9728487
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1335753
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.95123.659287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.952151096
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8071547
X-RAY DIFFRACTIONr_chiral_restr0.0880.2973
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214644
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.6→3.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 65 -
Rwork0.318 1003 -
obs--99.91 %
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)
11.79250.3508-0.21634.1501-1.55792.37090.00720.1639-0.4136-0.5589-0.1754-0.13640.88150.31760.16820.47840.11260.12990.433-0.07930.621754.233910.1268-38.7966
21.4724-1.6151-0.68755.37260.71311.3938-0.0263-0.2229-0.31110.65930.01330.43040.3635-0.22920.0130.40390.00120.04950.32230.11590.548444.267312.2578-18.0602
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B379 - 778
2X-RAY DIFFRACTION2A379 - 787

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