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- PDB-4ba2: Archaeal exosome (Rrp4-Rrp41(D182A)-Rrp42) bound to inorganic pho... -

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Basic information

Entry
Database: PDB / ID: 4ba2
TitleArchaeal exosome (Rrp4-Rrp41(D182A)-Rrp42) bound to inorganic phosphate
Components
  • (PROBABLE EXOSOME COMPLEX EXONUCLEASE ...) x 2
  • 5'-R(*AP*AP*AP*AP)-3'
  • PROBABLE EXOSOME COMPLEX RNA-BINDING PROTEIN 1
KeywordsHYDROLASE/RNA / HYDROLASE-RNA COMPLEX / ARCHAEA / RNA DEGRADATION / PHOSPHOROLYTIC REACTION MECHANISM
Function / homology
Function and homology information


exosome (RNase complex) / CUT catabolic process / cytoplasmic exosome (RNase complex) / U4 snRNA 3'-end processing / poly(A)-dependent snoRNA 3'-end processing / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA catabolic process / poly(A) binding / mRNA 3'-UTR AU-rich region binding / RNA catabolic process ...exosome (RNase complex) / CUT catabolic process / cytoplasmic exosome (RNase complex) / U4 snRNA 3'-end processing / poly(A)-dependent snoRNA 3'-end processing / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA catabolic process / poly(A) binding / mRNA 3'-UTR AU-rich region binding / RNA catabolic process / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / gene expression / 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 / Ribosomal Protein S8; Chain: A, domain 1 / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / K Homology domain, type 1 superfamily / Ribosomal Protein S5; domain 2 / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / Nucleic acid-binding proteins / S1 domain / 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
PHOSPHATE ION / RNA / 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 / Resolution: 2.501 Å
AuthorsLorentzen, E. / Conti, E.
CitationJournal: Archaea / Year: 2012
Title: Crystal Structure of a 9-Subunit Archaeal Exosome in Pre-Catalytic States of the Phosphorolytic Reaction.
Authors: Lorentzen, E. / Conti, E.
History
DepositionSep 10, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Jan 15, 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_sheet / 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_asym_id / _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_asym_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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "IC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "IC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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
I: PROBABLE EXOSOME COMPLEX RNA-BINDING PROTEIN 1
R: 5'-R(*AP*AP*AP*AP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,1358
Polymers87,6844
Non-polymers4514
Water1,892105
1
A: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2
B: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
I: PROBABLE EXOSOME COMPLEX RNA-BINDING PROTEIN 1
R: 5'-R(*AP*AP*AP*AP)-3'
hetero molecules

A: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2
B: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
I: PROBABLE EXOSOME COMPLEX RNA-BINDING PROTEIN 1
R: 5'-R(*AP*AP*AP*AP)-3'
hetero molecules

A: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2
B: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
I: PROBABLE EXOSOME COMPLEX RNA-BINDING PROTEIN 1
R: 5'-R(*AP*AP*AP*AP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,40624
Polymers263,05212
Non-polymers1,35412
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_454-z-1/2,-x,y-1/21
crystal symmetry operation10_554-y,z+1/2,-x-1/21
Buried area38180 Å2
ΔGint-270.6 kcal/mol
Surface area79410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.830, 134.830, 134.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11I-1232-

PO4

21I-1232-

PO4

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Components

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PROBABLE EXOSOME COMPLEX EXONUCLEASE ... , 2 types, 2 molecules AB

#1: Protein PROBABLE EXOSOME COMPLEX EXONUCLEASE 2 / RRP42


Mass: 30422.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / References: UniProt: Q9UXC0
#2: Protein PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 / RRP41


Mass: 27764.125 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / References: UniProt: Q9UXC2

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Protein / RNA chain , 2 types, 2 molecules IR

#3: Protein PROBABLE EXOSOME COMPLEX RNA-BINDING PROTEIN 1 / RRP4


Mass: 28225.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / References: UniProt: Q9UXC4
#4: RNA chain 5'-R(*AP*AP*AP*AP)-3'


Mass: 1271.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SULFOLOBUS SOLFATARICUS (archaea)

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Non-polymers , 4 types, 109 molecules

#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsD182A MUTATION

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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: 2.6 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 8 / Details: 40% PEG 400, 50 MM TRIS-HCL PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97995
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 29, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97995 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 28497 / % possible obs: 1 % / Observed criterion σ(I): -2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 14.5
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2.9 / % possible all: 1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8_1069)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JE6

2je6


Resolution: 2.501→38.922 Å / SU ML: 0.42 / σ(F): 1.38 / Phase error: 27.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2589 1424 5 %
Rwork0.1854 --
obs0.189 28497 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.501→38.922 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5418 88 27 105 5638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085701
X-RAY DIFFRACTIONf_angle_d1.1327784
X-RAY DIFFRACTIONf_dihedral_angle_d15.1992116
X-RAY DIFFRACTIONf_chiral_restr0.07929
X-RAY DIFFRACTIONf_plane_restr0.004981
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5007-2.59010.36961410.30632673X-RAY DIFFRACTION100
2.5901-2.69380.34731410.27992678X-RAY DIFFRACTION100
2.6938-2.81630.33741420.25712693X-RAY DIFFRACTION100
2.8163-2.96470.33931400.23472669X-RAY DIFFRACTION100
2.9647-3.15040.30251420.2152692X-RAY DIFFRACTION100
3.1504-3.39350.27411420.18262691X-RAY DIFFRACTION100
3.3935-3.73480.23271420.15262705X-RAY DIFFRACTION100
3.7348-4.27460.2351430.14252705X-RAY DIFFRACTION100
4.2746-5.38330.22681440.14352738X-RAY DIFFRACTION100
5.3833-38.92680.21061470.18132829X-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)
12.6287-1.32950.87132.8418-1.07852.735-0.01260.07860.0977-0.1856-0.1208-0.1221-0.08310.19780.13450.3229-0.0558-0.04210.3692-0.02770.2902-21.27552.584-9.8058
22.05930.06850.04812.25710.56292.15660.1542-0.1357-0.20470.0783-0.0295-0.02370.3172-0.0415-0.11670.3419-0.0246-0.07860.33080.03780.3922-29.24128.7615-2.5752
31.1324-1.11110.08624.86330.4641.91220.00690.3639-0.0489-0.8382-0.0597-0.04520.42090.12970.09510.50470.16390.20890.85320.12610.7145-7.760644.2838-47.7714
41.4-0.25511.16382.50310.02921.2041-0.38410.66081.05080.06040.0939-0.84220.050.14220.09040.57060.18250.05021.130.24751.10725.163742.4343-37.997
51.10840.9143-1.31321.7806-0.82321.61920.2553-0.66420.57080.31580.0079-0.7335-0.50650.7458-0.1320.4431-0.19140.03361.0070.00521.35129.049450.8117-29.3919
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID -1:275)
2X-RAY DIFFRACTION2(CHAIN B AND RESID 8:241)
3X-RAY DIFFRACTION3(CHAIN I AND RESID 6:141)
4X-RAY DIFFRACTION4(CHAIN I AND RESID 142:194)
5X-RAY DIFFRACTION5(CHAIN I AND RESID 195:231)

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