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- PDB-2ja9: Structure of the N-terminal deletion of yeast exosome component Rrp40 -

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Basic information

Entry
Database: PDB / ID: 2ja9
TitleStructure of the N-terminal deletion of yeast exosome component Rrp40
ComponentsEXOSOME COMPLEX EXONUCLEASE RRP40
KeywordsRNA BINDING PROTEIN / RNA-BINDING PROTEIN / RNA / EXOSOME / NUCLEASE / S1 DOMAIN / KH DOMAIN / HYDROLASE / RNA-BINDING / EXONUCLEASE / NUCLEAR PROTEIN / RRNA PROCESSING / NUCLEIC-ACID BINDING
Function / homology
Function and homology information


Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / mRNA decay by 3' to 5' exoribonuclease / cytoplasmic exosome (RNase complex) / TRAMP-dependent tRNA surveillance pathway / CUT catabolic process / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / : / poly(A)-dependent snoRNA 3'-end processing ...Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / mRNA decay by 3' to 5' exoribonuclease / cytoplasmic exosome (RNase complex) / TRAMP-dependent tRNA surveillance pathway / CUT catabolic process / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / : / poly(A)-dependent snoRNA 3'-end processing / exosome (RNase complex) / nuclear 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) / : / RNA catabolic process / Major pathway of rRNA processing in the nucleolus and cytosol / RNA processing / manganese ion binding / nucleolus / RNA binding / nucleus
Similarity search - Function
Exosome complex exonuclease Rrp40, N-terminal / Exosome complex exonuclease Rrp40 N-terminal domain / Rrp40, S1 domain / : / Exosome complex component RRP40, S1 domain / Exosome complex RNA-binding protein 1/RRP40/RRP4 / KH domain / K Homology domain, type 1 / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 ...Exosome complex exonuclease Rrp40, N-terminal / Exosome complex exonuclease Rrp40 N-terminal domain / Rrp40, S1 domain / : / Exosome complex component RRP40, S1 domain / Exosome complex RNA-binding protein 1/RRP40/RRP4 / KH domain / K Homology domain, type 1 / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 / K Homology domain, type 1 superfamily / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Exosome complex component RRP40
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsOddone, A. / Lorentzen, E. / Basquin, J. / Gasch, A. / Rybin, V. / Conti, E. / Sattler, M.
CitationJournal: Embo Rep. / Year: 2007
Title: Structural and Biochemical Characterization of the Yeast Exosome Component Rrp40
Authors: Oddone, A. / Lorentzen, E. / Basquin, J. / Gasch, A. / Rybin, V. / Conti, E. / Sattler, M.
History
DepositionNov 24, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EXOSOME COMPLEX EXONUCLEASE RRP40


Theoretical massNumber of molelcules
Total (without water)19,6081
Polymers19,6081
Non-polymers00
Water1,72996
1
A: EXOSOME COMPLEX EXONUCLEASE RRP40

A: EXOSOME COMPLEX EXONUCLEASE RRP40


Theoretical massNumber of molelcules
Total (without water)39,2152
Polymers39,2152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation37_544y+1/4,x-1/4,-z-1/41
MethodPQS
Unit cell
Length a, b, c (Å)153.510, 153.510, 153.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132

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Components

#1: Protein EXOSOME COMPLEX EXONUCLEASE RRP40 / RRP40 / RIBOSOMAL RNA-PROCESSING PROTEIN 40


Mass: 19607.514 Da / Num. of mol.: 1 / Fragment: RESIDUES 62-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q08285, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE IS A DISCREPANCY IN RESIDUE 160 OF THE SEQUENCE (F IN THE UNIPROT SEQUENCE, L IN OUR SEQUENCE) ...THERE IS A DISCREPANCY IN RESIDUE 160 OF THE SEQUENCE (F IN THE UNIPROT SEQUENCE, L IN OUR SEQUENCE). WE BELIEVE THIS IS A MISTAKE IN THE DATABASE, AS WE HAVE CLONED THE PROTEIN FROM THREE DIFFERENT YEAST SOURCES, AND ALWAYS GOT LEU INSTEAD OF PHE AT POSITION 160.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 65.6 %
Crystal growDetails: 20% (W/V) PEG 3350,200 MM NA2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 15115 / % possible obs: 99 % / Redundancy: 45 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 34
Reflection shellHighest resolution: 2.2 Å / Redundancy: 36 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 8.9 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→14.91 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.951 / SU B: 8.48 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.206 796 5 %RANDOM
Rwork0.189 ---
obs0.19 15115 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.22 Å2
Refinement stepCycle: LAST / Resolution: 2.2→14.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1338 0 0 96 1434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221390
X-RAY DIFFRACTIONr_bond_other_d0.0010.021264
X-RAY DIFFRACTIONr_angle_refined_deg0.9971.9471889
X-RAY DIFFRACTIONr_angle_other_deg0.7132939
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7325181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.60924.84464
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19115233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.937157
X-RAY DIFFRACTIONr_chiral_restr0.060.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021577
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02289
X-RAY DIFFRACTIONr_nbd_refined0.1830.2262
X-RAY DIFFRACTIONr_nbd_other0.1570.21213
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2700
X-RAY DIFFRACTIONr_nbtor_other0.0760.2858
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.276
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2280.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6541.51150
X-RAY DIFFRACTIONr_mcbond_other0.0661.5361
X-RAY DIFFRACTIONr_mcangle_it0.71421417
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.0053594
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.4824.5468
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 57 -
Rwork0.223 1083 -
obs--100 %

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