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- PDB-3l7z: Crystal structure of the S. solfataricus archaeal exosome -

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Basic information

Entry
Database: PDB / ID: 3l7z
TitleCrystal structure of the S. solfataricus archaeal exosome
Components
  • Probable exosome complex RNA-binding protein 1
  • Probable exosome complex exonuclease 1
  • Probable exosome complex exonuclease 2
Keywordshydrolase/RNA binding protein / Exosome / asymmetry / RNA processing / RNA degradation / conformation flexibility / thermal motion / hydrolase-RNA binding protein complex
Function / homology
Function and homology information


CUT catabolic process / cytoplasmic exosome (RNase complex) / U4 snRNA 3'-end processing / poly(A)-dependent snoRNA 3'-end processing / exosome (RNase complex) / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / intracellular organelle / rRNA catabolic process / mRNA 3'-UTR AU-rich region binding / poly(A) binding ...CUT catabolic process / cytoplasmic exosome (RNase complex) / U4 snRNA 3'-end processing / poly(A)-dependent snoRNA 3'-end processing / exosome (RNase complex) / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / intracellular organelle / rRNA catabolic process / mRNA 3'-UTR AU-rich region binding / poly(A) binding / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / RNA binding / cytoplasm
Similarity search - Function
: / Exosome RNA binding protein RRP4 N-terminal domain / Exosome complex component Rrp4 / Exosome complex component Rrp41 / Exosome complex component Rrp42, archaea / : / KH domain / Exosome complex RNA-binding protein 1/RRP40/RRP4 / GHMP Kinase, N-terminal domain / : ...: / Exosome RNA binding protein RRP4 N-terminal domain / Exosome complex component Rrp4 / Exosome complex component Rrp41 / Exosome complex component Rrp42, archaea / : / KH domain / Exosome complex RNA-binding protein 1/RRP40/RRP4 / GHMP Kinase, N-terminal domain / : / : / K Homology domain, type 1 / 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 / K Homology domain, type 1 / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Ribosomal Protein S8; Chain: A, domain 1 / K Homology domain, type 1 superfamily / Ribosomal Protein S5; domain 2 / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Exosome complex component Rrp42 / Exosome complex component Rrp41 / Exosome complex component Rrp4
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.41 Å
AuthorsLu, C. / Ding, F. / Ke, A.
CitationJournal: Plos One / Year: 2010
Title: Crystal structure of the S. solfataricus archaeal exosome reveals conformational flexibility in the RNA-binding ring.
Authors: Lu, C. / Ding, F. / Ke, A.
History
DepositionDec 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable exosome complex exonuclease 2
B: Probable exosome complex exonuclease 1
C: Probable exosome complex RNA-binding protein 1
D: Probable exosome complex exonuclease 2
E: Probable exosome complex exonuclease 1
F: Probable exosome complex RNA-binding protein 1
G: Probable exosome complex exonuclease 2
H: Probable exosome complex exonuclease 1
I: Probable exosome complex RNA-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,37512
Polymers255,0879
Non-polymers2883
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31120 Å2
ΔGint-190 kcal/mol
Surface area81970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.122, 145.484, 97.245
Angle α, β, γ (deg.)90.000, 93.790, 90.000
Int Tables number5
Space group name H-MC121
Detailsbiological unit is the same as asymmetric unit.

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Components

#1: Protein Probable exosome complex exonuclease 2


Mass: 29803.236 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: C20_023, Rrp41/42/4, SSO0732 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9UXC0, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: Protein Probable exosome complex exonuclease 1


Mass: 27195.432 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: SSO0735 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9UXC2, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#3: Protein Probable exosome complex RNA-binding protein 1


Mass: 28030.188 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: C20_026, SSO0736 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UXC4
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
Has protein modificationY

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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: 2.09 Å3/Da / Density % sol: 41.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 200 mM Mg(Ac)2, and 25 mM (NH4)2SO4), pH 8.6, vapor diffusion, hanging drop, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.41→50 Å / % possible obs: 90.4 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.16 / Χ2: 1.549 / Net I/σ(I): 5.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3-3.111.90.47427751.222172.8
3.11-3.2320.3632030.339183.7
3.23-3.382.20.32433130.413185.9
3.38-3.562.30.45133463.987187.3
3.56-3.782.60.334941.339189.8
3.78-4.072.90.35535754.55193.5
4.07-4.483.40.15137550.839197.3
4.48-5.133.50.13637221.159196.5
5.13-6.463.60.12438040.805198.2
6.46-504.10.07438851.218198.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.4.0066refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→20 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.878 / Occupancy max: 1 / Occupancy min: 1 / SU B: 34.87 / SU ML: 0.347 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.705 / ESU R Free: 0.368 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.289 7505 10.1 %RANDOM
Rwork0.263 ---
obs0.266 74262 92.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 197.14 Å2 / Biso mean: 56.59 Å2 / Biso min: 12.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å2-1.47 Å2
2---0.6 Å20 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 2.41→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16378 0 15 0 16393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02216701
X-RAY DIFFRACTIONr_angle_refined_deg1.6211.99322659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.52352113
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.39724.678667
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.658152966
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7941599
X-RAY DIFFRACTIONr_chiral_restr0.2210.22668
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112289
X-RAY DIFFRACTIONr_mcbond_it1.8951.510620
X-RAY DIFFRACTIONr_mcangle_it2.756217204
X-RAY DIFFRACTIONr_scbond_it1.9136081
X-RAY DIFFRACTIONr_scangle_it3.3234.55455
LS refinement shellResolution: 2.413→2.475 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 332 -
Rwork0.371 3051 -
all-3383 -
obs--58 %
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)
11.0298-0.38080.16681.0343-0.26470.53550.0787-0.0101-0.13770.0342-0.0974-0.01490.0446-0.12310.0187-0.0091-0.0850.0007-0.01420.01210.014118.7597-14.688714.128
20.99340.36480.12630.9860.49740.33690.1178-0.16510.08380.0937-0.22320.19560.0498-0.00590.1054-0.0595-0.08940.05320.0418-0.0136-0.00069.64764.306428.7766
33.54021.47860.17872.4817-0.37490.30290.1583-0.16420.2090.0862-0.16940.3973-0.25770.02050.01110.02280.0198-0.0476-0.10490.03730.051614.687636.057220.7018
40.84170.0506-0.74571.24640.69981.3604-0.0475-0.08790.01240.22670.1882-0.26630.21110.1553-0.1407-0.04770.049-0.1202-0.0248-0.02660.066966.1425-4.140924.7637
51.332-0.30470.58130.72220.16150.97670.0020.0136-0.17830.09540.0033-0.1540.0383-0.0819-0.0053-0.0513-0.0161-0.0135-0.0945-0.02170.08850.9561-14.83127.4732
61.3532-0.4485-0.05820.9694-0.03560.3217-0.01240.1387-0.0167-0.141-0.07840.0434-0.0893-0.0050.0909-0.03670.0079-0.049-0.0731-0.00840.024433.63283.8535-15.1205
71.19820.82740.42341.87860.11851.20450.1861-0.23090.14530.2041-0.25920.08960.2024-0.22460.07310.0244-0.13810.05010.0936-0.0441-0.152129.775315.278650.6905
81.11150.1745-0.05420.585-0.40792.88280.1082-0.06510.00030.08550.0085-0.0845-0.03140.1253-0.11670.0501-0.0872-0.0273-0.0165-0.0175-0.111955.244818.552545.9247
91.8787-0.2018-0.50230.935-0.71140.77560.56030.27450.26380.0113-0.26140.0051-0.07760.3673-0.29890.0741-0.07250.0747-0.07410.0822-0.148365.485834.125518.9593
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 271
2X-RAY DIFFRACTION2B7 - 238
3X-RAY DIFFRACTION3C7 - 228
4X-RAY DIFFRACTION4D1 - 271
5X-RAY DIFFRACTION5E2 - 238
6X-RAY DIFFRACTION6F10 - 241
7X-RAY DIFFRACTION7G1 - 270
8X-RAY DIFFRACTION8H5 - 238
9X-RAY DIFFRACTION9I8 - 226

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