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- PDB-4d0k: Complex of Chaetomium thermophilum PAN2 (WD40-CS1) with PAN3 (C-term) -

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Basic information

Entry
Database: PDB / ID: 4d0k
TitleComplex of Chaetomium thermophilum PAN2 (WD40-CS1) with PAN3 (C-term)
Components
  • A-SPECIFIC RIBONUCLEASE SUBUNIT PAN2
  • PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN3-LIKE PROTEIN
KeywordsGENE REGULATION / WD40 DOMAIN / 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 / mRNA processing / nucleic acid binding / protein kinase activity / RNA binding / ATP binding / metal ion binding
Similarity search - Function
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 ...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. / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Papain-like cysteine peptidase superfamily / Helix Hairpins / Ribonuclease H superfamily / Ribonuclease H-like superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PAN2-PAN3 deadenylation complex subunit PAN3 / PAN2-PAN3 deadenylation complex catalytic subunit PAN2
Similarity search - Component
Biological speciesCHAETOMIUM THERMOPHILUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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 28, 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: A-SPECIFIC RIBONUCLEASE SUBUNIT PAN2
B: PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN3-LIKE PROTEIN
C: PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN3-LIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)82,4413
Polymers82,4413
Non-polymers00
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-30.9 kcal/mol
Surface area23850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.414, 93.568, 110.676
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.2537, -0.6872, 0.6807), (-0.6834, -0.3708, -0.6289), (0.6846, -0.6248, -0.3755)
Vector: 52.8656, 3.9086, -53.6111)

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Components

#1: Protein A-SPECIFIC RIBONUCLEASE SUBUNIT PAN2 / PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN2 / PAB1P-DEPENDENT POLY(A)-NUCLEASE / PAN ...PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN2 / PAB1P-DEPENDENT POLY(A)-NUCLEASE / PAN DEADENYLATION COMPLEX CATALYTIC SUBUNIT 2


Mass: 51366.246 Da / Num. of mol.: 1 / Fragment: WD40 DOMAIN AND CS1, RESIDUES 1-457
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHAETOMIUM THERMOPHILUM (fungus) / Strain: DSM 1495 / Plasmid: PETMCN (PNYC) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: G0SAK8, poly(A)-specific ribonuclease
#2: Protein PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN3-LIKE PROTEIN / PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN3 / PAB1P-DEPENDENT POLY(A)-NUCLEASE / PAN ...PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN3 / PAB1P-DEPENDENT POLY(A)-NUCLEASE / PAN DEADENYLATION COMPLEX SUBUNIT 3 / A-SPECIFIC RIBONUCLEASE SUBUNIT PAN3


Mass: 15537.467 Da / Num. of mol.: 2 / Fragment: C-TERM, RESIDUES 448-555
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHAETOMIUM THERMOPHILUM (fungus) / Strain: DSM 1495 / Plasmid: PETMCN (PNEA) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: G0S0Y3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE 3 N-TERMINAL RESIDUES OF CHAIN A REMAIN FROM THE PURIFICATION TAG THE 27 N-TERMINAL RESIDUES OF ...THE 3 N-TERMINAL RESIDUES OF CHAIN A REMAIN FROM THE PURIFICATION TAG THE 27 N-TERMINAL RESIDUES OF CHAINS B AND C 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 Å3/Da / Density % sol: 59.6 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1M KCL, 0.1M HEPES PH7.5, 15% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00004
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2014 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.89→47.63 Å / Num. obs: 60515 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 36.2 Å2 / Rsym value: 0.04 / Net I/σ(I): 23.4
Reflection shellResolution: 1.89→2 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 2.48 / Rsym value: 0.71 / % possible all: 95.7

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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 ENTRY 4CZX

4czx


Resolution: 1.89→43.97 Å / SU ML: 0.19 / σ(F): 1.36 / Phase error: 23.26 / Stereochemistry target values: ML
Details: CHAIN A RESIDUES 346-457 WERE PROBABLY DEGRADED BEFORE CRYSTALLIZATION OR ARE DISORDERED. THE FOLLOWING RESIDUES WERE DISORDERED, CHAIN A -2-0, 19-20, 207-214, 329-333, 340, CHAIN B 448-450. ...Details: CHAIN A RESIDUES 346-457 WERE PROBABLY DEGRADED BEFORE CRYSTALLIZATION OR ARE DISORDERED. THE FOLLOWING RESIDUES WERE DISORDERED, CHAIN A -2-0, 19-20, 207-214, 329-333, 340, CHAIN B 448-450. THE FOLLOWING RESIDUES WERE TRUNCATED AT CB CHAIN A 1, 18, 21, 215, 216, 334. THE FOLLOWING RESIDUES WERE REFINED WITH DOUBLE CONFORMATIONS, CHAIN A 28, 42, 77, 298, CHAIN B 531.
RfactorNum. reflection% reflection
Rfree0.2157 3035 5 %
Rwork0.187 --
obs0.1884 60498 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45 Å2
Refinement stepCycle: LAST / Resolution: 1.89→43.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4312 0 0 237 4549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044433
X-RAY DIFFRACTIONf_angle_d0.8666010
X-RAY DIFFRACTIONf_dihedral_angle_d12.111649
X-RAY DIFFRACTIONf_chiral_restr0.033669
X-RAY DIFFRACTIONf_plane_restr0.004773
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8893-1.91880.36061160.35362208X-RAY DIFFRACTION85
1.9188-1.95030.30951360.28132624X-RAY DIFFRACTION100
1.9503-1.98390.27861330.24582557X-RAY DIFFRACTION100
1.9839-2.020.27761300.23372607X-RAY DIFFRACTION100
2.02-2.05880.2491470.23472591X-RAY DIFFRACTION100
2.0588-2.10080.23821510.22842593X-RAY DIFFRACTION100
2.1008-2.14650.24661310.2122576X-RAY DIFFRACTION100
2.1465-2.19640.23631410.1972633X-RAY DIFFRACTION100
2.1964-2.25140.26261390.20812604X-RAY DIFFRACTION100
2.2514-2.31220.2481350.19812607X-RAY DIFFRACTION100
2.3122-2.38030.24741370.20092586X-RAY DIFFRACTION100
2.3803-2.45710.25521380.19892639X-RAY DIFFRACTION100
2.4571-2.54490.22941400.19832605X-RAY DIFFRACTION100
2.5449-2.64680.25731370.19852641X-RAY DIFFRACTION100
2.6468-2.76720.21371360.19772615X-RAY DIFFRACTION100
2.7672-2.91310.20911360.1952630X-RAY DIFFRACTION100
2.9131-3.09560.23931410.20192640X-RAY DIFFRACTION100
3.0956-3.33450.20961370.20132642X-RAY DIFFRACTION100
3.3345-3.66990.17731410.17842658X-RAY DIFFRACTION100
3.6699-4.20060.19491420.16512680X-RAY DIFFRACTION100
4.2006-5.29090.18271420.14242703X-RAY DIFFRACTION100
5.2909-43.9810.20951490.18342824X-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)
10.8721-0.0773-0.1970.8801-0.32540.777-0.0405-0.12180.1432-0.26580.0524-0.11180.02690.0426-0.05450.2283-0.05730.0020.258-0.00860.21440.106921.8283-37.8767
21.73260.2894-0.29571.9725-0.23131.9649-0.0715-0.0258-0.06380.4560.14610.2558-0.5014-0.05440.0712-0.0412-0.0451-0.02150.0019-0.05490.0418-1.707311.6972-5.8863
30.7958-0.59110.20471.7193-0.0761.46270.06240.1521-0.1821-0.3572-0.04790.07040.21370.03680.26090.3735-0.02270.08090.2892-0.00790.291910.481220.0916-53.1176
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN B
2X-RAY DIFFRACTION2CHAIN A
3X-RAY DIFFRACTION3CHAIN C

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