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- PDB-2po1: Crystal structure of the P. abyssi exosome RNase PH ring complexe... -

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Basic information

Entry
Database: PDB / ID: 2po1
TitleCrystal structure of the P. abyssi exosome RNase PH ring complexed with a single stranded 10-mer poly(A) RNA
Components
  • 10-mer poly(A)
  • Probable exosome complex exonuclease 1
  • Probable exosome complex exonuclease 2
Keywordshydrolase/hydrolase/RNA / RNase PH / hydrolase-hydrolase-RNA COMPLEX
Function / homology
Function and homology information


exosome (RNase complex) / RNA catabolic process / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / cytoplasm
Similarity search - Function
Exosome complex component Rrp41 / Exosome complex component Rrp42, archaea / GHMP Kinase, N-terminal domain / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily / 3' exoribonuclease family, domain 1 / Ribosomal Protein S5; domain 2 ...Exosome complex component Rrp41 / Exosome complex component Rrp42, archaea / GHMP Kinase, N-terminal domain / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily / 3' exoribonuclease family, domain 1 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / Exosome complex component Rrp42 / Exosome complex component Rrp41
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsNavarro, M.V.A.S. / Guimaraes, B.G.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Insights into the mechanism of progressive RNA degradation by the archaeal exosome.
Authors: Navarro, M.V.A.S. / Oliveira, C.C. / Zanchin, N.I. / Guimaraes, B.G.
History
DepositionApr 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

Downloads & links

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Assembly

Deposited unit
C: 10-mer poly(A)
A: Probable exosome complex exonuclease 1
B: Probable exosome complex exonuclease 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8278
Polymers61,2363
Non-polymers5915
Water5,549308
1
C: 10-mer poly(A)
A: Probable exosome complex exonuclease 1
B: Probable exosome complex exonuclease 2
hetero molecules

C: 10-mer poly(A)
A: Probable exosome complex exonuclease 1
B: Probable exosome complex exonuclease 2
hetero molecules

C: 10-mer poly(A)
A: Probable exosome complex exonuclease 1
B: Probable exosome complex exonuclease 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,48124
Polymers183,7099
Non-polymers1,77315
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area29630 Å2
ΔGint-234.7 kcal/mol
Surface area55550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.555, 93.555, 125.951
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
DetailsThe biological assembly is a hexamer generated from the heterodimer in the asymmetric unit by the operations: -y, x-y-1, z and -x+y+1, -x, z

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Components

#1: RNA chain 10-mer poly(A)


Mass: 3247.100 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein Probable exosome complex exonuclease 1


Mass: 27720.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Gene: Rrp41 / Plasmid: pET29 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9V119, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#3: Protein Probable exosome complex exonuclease 2


Mass: 30268.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Gene: Rrp42 / Plasmid: pAE / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9V118, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O

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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: 2.61 Å3/Da / Density % sol: 52.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M Bis-Tris, 45% MPD and 0.1 M LiCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1Bis-TrisBis-tris methane11
2MPD11
3LiC11
4Bis-TrisBis-tris methane12
5MPD12
6LiC12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.427 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 10, 2006 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.427 Å / Relative weight: 1
ReflectionResolution: 1.94→46.78 Å / Num. all: 47831 / Num. obs: 46981 / % possible obs: 98.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 11 % / Biso Wilson estimate: 23.6 Å2 / Rsym value: 0.109 / Net I/σ(I): 14.9
Reflection shellResolution: 1.94→2.06 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 6859 / Rsym value: 0.627 / % possible all: 90.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PNZ

2pnz


Resolution: 1.94→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / SU B: 9.473 / SU ML: 0.122 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.151 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24243 2374 5.1 %RANDOM
Rwork0.18738 ---
all0.19016 45299 --
obs0.19016 44547 98.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.413 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.94→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3915 154 0 348 4417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0224185
X-RAY DIFFRACTIONr_angle_refined_deg2.0652.0555696
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5475508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.95624.759166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.82715756
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1211529
X-RAY DIFFRACTIONr_chiral_restr0.1320.2668
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023001
X-RAY DIFFRACTIONr_nbd_refined0.230.22465
X-RAY DIFFRACTIONr_nbtor_refined0.3280.22890
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2452
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.2149
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.229
X-RAY DIFFRACTIONr_mcbond_it1.1011.52579
X-RAY DIFFRACTIONr_mcangle_it1.55924085
X-RAY DIFFRACTIONr_scbond_it2.62131805
X-RAY DIFFRACTIONr_scangle_it3.9384.51608
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 140 -
Rwork0.255 2736 -
obs-2876 83.22 %
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)
11.6837-0.4363-0.14962.4940.06541.58980.0005-0.0080.00450.07470.01630.2260.0306-0.4854-0.0168-0.22520.00410.02160.01320.0005-0.022917.783-24.1781-25.2061
21.41660.01790.07821.6848-0.26532.1715-0.02310.0912-0.0876-0.13360.00970.07590.3265-0.22840.0134-0.0388-0.0946-0.0009-0.1641-0.0211-0.126632.5447-51.2099-32.2068
36.6674.0336-0.4016.8143-1.23318.66530.19421.4345-0.0277-0.6442-0.0979-0.55560.49491.6621-0.09630.2-0.03390.18360.0183-0.04510.177836.8147-20.3249-33.6047
40.6746-0.4447-0.04711.2830.01730.56240.00360.0425-0.0317-0.03710.0010.16520.1881-0.2539-0.0045-0.0406-0.0895-0.01460.036-0.0140.022326.8504-40.997-29.3623
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AB9 - 2449 - 244
2X-RAY DIFFRACTION2BC8 - 27411 - 277
3X-RAY DIFFRACTION3CA3951
4X-RAY DIFFRACTION3CA3984
5X-RAY DIFFRACTION3CA400 - 4046 - 10
6X-RAY DIFFRACTION4A - CJ - I284 - 4091 - 5

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