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- PDB-4bwx: Structure of Neurospora crassa PAN3 pseudokinase mutant -

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Basic information

Entry
Database: PDB / ID: 4bwx
TitleStructure of Neurospora crassa PAN3 pseudokinase mutant
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 / zinc ion binding / ATP 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 C-terminal knob 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 C-terminal knob 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: 2.85 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 1.1Dec 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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.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_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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)99,8566
Polymers98,7612
Non-polymers1,0954
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8870 Å2
ΔGint-74.7 kcal/mol
Surface area37460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.312, 90.312, 230.609
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: (-0.993, 0.085, 0.081), (0.113, 0.866, 0.487), (-0.029, 0.493, -0.87)
Vector: -67.59572, 2.26756, 14.07221)

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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: 49380.316 Da / Num. of mol.: 2
Fragment: PSEUDOKINASE DOMAIN, COILED COIL, CTERMINAL KNOB DOMAIN, RESIDUES 234-656
Mutation: YES
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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 2.7 Å3/Da / Density % sol: 54.7 % / Description: NONE
Crystal growpH: 7
Details: 0.1 M HEPES PH 7.0, 15% PEG MONOMETHYL ETHER 5000 MME, 0.1 M POTASSIUM CHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99998
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2013 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 2.85→46.41 Å / Num. obs: 24793 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 65.23 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.9
Reflection shellResolution: 2.85→3 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BWK

4bwk


Resolution: 2.85→45.156 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 29.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2424 1257 5.1 %
Rwork0.211 --
obs0.2126 24707 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 89 Å2
Refinement stepCycle: LAST / Resolution: 2.85→45.156 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6460 0 64 0 6524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016674
X-RAY DIFFRACTIONf_angle_d1.4019041
X-RAY DIFFRACTIONf_dihedral_angle_d11.2092464
X-RAY DIFFRACTIONf_chiral_restr0.1451002
X-RAY DIFFRACTIONf_plane_restr0.0031152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.96410.31041470.29332584X-RAY DIFFRACTION99
2.9641-3.0990.35931530.28572589X-RAY DIFFRACTION99
3.099-3.26230.30971340.26262590X-RAY DIFFRACTION100
3.2623-3.46670.33881190.23492632X-RAY DIFFRACTION100
3.4667-3.73420.23311380.2092607X-RAY DIFFRACTION100
3.7342-4.10980.23661330.19682615X-RAY DIFFRACTION100
4.1098-4.70390.21541540.18842580X-RAY DIFFRACTION100
4.7039-5.92440.231450.19722614X-RAY DIFFRACTION100
5.9244-45.16160.20061340.19612639X-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)
10.68370.4565-0.41091.08020.44641.0465-0.0655-0.118-0.04740.0006-0.13360.09850.22220.3715-0.02950.2836-0.01790.05270.38070.05980.387-24.844130.83026.4487
20.2130.11-0.28041.4744-0.11010.1850.0335-0.1048-0.07780.1824-0.0902-0.00450.0180.1257-00.5838-0.02250.05770.34180.02820.4118-40.188328.927924.2848
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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