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- PDB-4czy: Complex of Neurospora crassa PAN2 (WD40-CS1) with PAN3 (pseudokin... -

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Basic information

Entry
Database: PDB / ID: 4czy
TitleComplex of Neurospora crassa PAN2 (WD40-CS1) with PAN3 (pseudokinase and C-term)
Components
  • PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN2
  • PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN3
KeywordsGENE REGULATION / WD40 DOMAIN / PSEUDOKINASE / C-TERMINAL KNOB 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 / poly(A) binding / P-body / mRNA processing / nucleic acid binding / 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 / PAN2, UCH domain / PAN2-PAN3 deadenylation complex catalytic subunit PAN2 / : / Ubiquitin carboxyl-terminal hydrolase / PAN2 N-terminal ...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 / 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 / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Papain-like cysteine peptidase superfamily / Helix Hairpins / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase-like domain superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / PAN2-PAN3 deadenylation complex catalytic subunit pan2 / PAN2-PAN3 deadenylation complex subunit pan3
Similarity search - Component
Biological speciesNEUROSPORA CRASSA (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsJonas, 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 / 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

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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 PAN3
C: PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN2
D: PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,03010
Polymers177,5784
Non-polymers1,4516
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11950 Å2
ΔGint-87.4 kcal/mol
Surface area63990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.266, 139.976, 157.444
Angle α, β, γ (deg.)90.00, 97.81, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.6854, 0.0724, -0.7245), (-0.0756, -0.9967, -0.0281), (-0.7242, 0.0355, 0.6887)41.4223, 27.8043, 14.5425
2given(-0.9996, 0.0207, -0.0212), (-0.0199, -0.9991, -0.0369), (-0.0219, -0.0365, 0.9991)27.1335, 22.4216, 0.6714
3given(-0.6803, -0.0507, -0.7312), (-0.0614, -0.9901, 0.1258), (-0.7304, 0.1305, 0.6704)41.2042, 19.9139, 16.0672

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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: 39520.059 Da / Num. of mol.: 2 / Fragment: WD40 DOMAIN AND CS1 REGION, RESIDUES 1-351
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: Protein PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN3 / PAB1P-DEPENDENT POLY(A)-NUCLEASE / PAN DEADENYLATION COMPLEX SUBUNIT 3 / A-SPECIFIC RIBONUCLEASE SUBUNIT PAN3


Mass: 49269.078 Da / Num. of mol.: 2 / Fragment: PSEUDOKINASE DOMAIN AND C-TERM, RESIDUES 234-656
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEUROSPORA CRASSA (fungus) / Plasmid: PETMCN (PNEA) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: Q7SDP4
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
Sequence detailsTHE 3 N-TERMINAL RESIDUES OF CHAIN A AND C REMAIN FROM THE PURIFICATION TAG THE 6 N-TERMINAL ...THE 3 N-TERMINAL RESIDUES OF CHAIN A AND C REMAIN FROM THE PURIFICATION TAG THE 6 N-TERMINAL RESIDUES OF CHAIN B AND D REMAIN 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: 3.7 Å3/Da / Density % sol: 67 % / Description: NONE
Crystal growpH: 6.5
Details: 7% PEG 4000, 13% GLYCEROL, 0.1M MES/IMIDAZOLE (PH 6.5), 30MM SODIUM NITRATE, 30MM DI-SODIUM HYDROGEN PHOSPHATE, 30MM AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97859
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2014 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97859 Å / Relative weight: 1
ReflectionResolution: 3.39→48.74 Å / Num. obs: 33318 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 106.8 Å2 / Rsym value: 0.11 / Net I/σ(I): 9.9
Reflection shellResolution: 3.39→3.59 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.4 / Rsym value: 0.89 / % possible all: 94.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE 1.8.4_1496)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 4BWX AND 4CZX

4bwx

4czx


Resolution: 3.4→48.74 Å / SU ML: 0.53 / σ(F): 1.35 / Phase error: 33.77 / Stereochemistry target values: ML
Details: NCS TORSION RESTRAINTS WERE USED THAT RESTRAIN CHAIN A TO C AND CHAIN B TO D. PDB 4CZX CHAIN A WAS USED AS A REFERENCE MODEL FOR CHAINS A AND C. DENSITY FOR THE PAN2 CS1 RESIDUES 322-351 ...Details: NCS TORSION RESTRAINTS WERE USED THAT RESTRAIN CHAIN A TO C AND CHAIN B TO D. PDB 4CZX CHAIN A WAS USED AS A REFERENCE MODEL FOR CHAINS A AND C. DENSITY FOR THE PAN2 CS1 RESIDUES 322-351 CHAINS A,C COULD NOT BE MODELLED. THE FOLLOWING RESIDUES WERE DISORDERED, CHAIN B 369-374, 561-563, 646-656, CHAIN D 370-375, 558-560, 646- -656. THE FOLLOWING RESIDUES WERE TRUNCATED AT CB, CHAIN A 4, 161, 316, 318, 321, CHAIN B 234, 375, 557, 564, CHAIN C 316, 318, 321, CHAIN D 308, 376, 557, 561, 563, 564.
RfactorNum. reflection% reflection
Rfree0.2629 1670 5 %
Rwork0.2211 --
obs0.2233 33120 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 140.2 Å2
Refinement stepCycle: LAST / Resolution: 3.4→48.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11562 0 88 0 11650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411931
X-RAY DIFFRACTIONf_angle_d0.95816194
X-RAY DIFFRACTIONf_dihedral_angle_d14.3594350
X-RAY DIFFRACTIONf_chiral_restr0.0371801
X-RAY DIFFRACTIONf_plane_restr0.0052074
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4001-3.50010.43791360.38832550X-RAY DIFFRACTION96
3.5001-3.6130.42891500.32352580X-RAY DIFFRACTION100
3.613-3.74210.35581310.30792643X-RAY DIFFRACTION100
3.7421-3.89190.30731380.27452581X-RAY DIFFRACTION99
3.8919-4.06890.2871410.25552630X-RAY DIFFRACTION100
4.0689-4.28330.3381390.2352634X-RAY DIFFRACTION100
4.2833-4.55150.27711380.22772593X-RAY DIFFRACTION99
4.5515-4.90270.2661370.22452625X-RAY DIFFRACTION100
4.9027-5.39550.24111400.19992632X-RAY DIFFRACTION100
5.3955-6.17490.25061400.22222652X-RAY DIFFRACTION100
6.1749-7.77460.28681380.2112645X-RAY DIFFRACTION100
7.7746-48.74560.17631420.15882685X-RAY DIFFRACTION100

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