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- PDB-2nn6: Structure of the human RNA exosome composed of Rrp41, Rrp45, Rrp4... -

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Basic information

Entry
Database: PDB / ID: 2nn6
TitleStructure of the human RNA exosome composed of Rrp41, Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, and Rrp40
Components
  • (Exosome complex exonuclease ...) x 6
  • 3'-5' exoribonuclease CSL4 homolog
  • Exosome component 6
  • Polymyositis/scleroderma autoantigen 1
KeywordsHYDROLASE/TRANSFERASE / RNA / exosome / PM/Scl / exoribonuclease / phosphorolytic / ribonuclease / HYDROLASE-TRANSFERASE COMPLEX
Function / homology
Function and homology information


DNA deamination / nucleolar exosome (RNase complex) / CUT catabolic process / cytoplasmic exosome (RNase complex) / U1 snRNA 3'-end processing / U5 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / mRNA decay by 3' to 5' exoribonuclease / exosome (RNase complex) / U4 snRNA 3'-end processing ...DNA deamination / nucleolar exosome (RNase complex) / CUT catabolic process / cytoplasmic exosome (RNase complex) / U1 snRNA 3'-end processing / U5 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / mRNA decay by 3' to 5' exoribonuclease / exosome (RNase complex) / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / 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) / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / ATF4 activates genes in response to endoplasmic reticulum stress / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / positive regulation of isotype switching / histone mRNA catabolic process / nuclear mRNA surveillance / rRNA catabolic process / 7S RNA binding / mRNA 3'-UTR AU-rich region binding / isotype switching / RNA catabolic process / KSRP (KHSRP) binds and destabilizes mRNA / maturation of 5.8S rRNA / nuclear chromosome / mRNA catabolic process / nuclear-transcribed mRNA catabolic process / Major pathway of rRNA processing in the nucleolus and cytosol / RNA processing / euchromatin / fibrillar center / rRNA processing / chromosome / positive regulation of cell growth / 3'-5'-RNA exonuclease activity / defense response to virus / RNA polymerase II-specific DNA-binding transcription factor binding / immune response / intracellular membrane-bounded organelle / nucleolus / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Exosome complex component Rrp43 / : / Mammalian exosome complex component RRP40, N-terminal / Exosome complex component RRP45 / Rrp40, S1 domain / : / Exosome complex component RRP40, S1 domain / Exosome complex component CSL4, C-terminal / Exosome complex component, N-terminal domain / Exosome complex component Csl4 ...Exosome complex component Rrp43 / : / Mammalian exosome complex component RRP40, N-terminal / Exosome complex component RRP45 / Rrp40, S1 domain / : / Exosome complex component RRP40, S1 domain / Exosome complex component CSL4, C-terminal / Exosome complex component, N-terminal domain / Exosome complex component Csl4 / Exosome component EXOSC1/CSL4 / Exosome complex exonuclease RRP4 N-terminal region / RRP4, S1 domain / : / 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 / 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
Exosome complex component RRP45 / Exosome complex component RRP4 / Exosome complex component RRP42 / Exosome complex component MTR3 / Exosome complex component RRP45 / Exosome complex component RRP43 / Exosome complex component RRP41 / Exosome complex component RRP46 / Exosome complex component RRP40 / Exosome complex component CSL4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.35 Å
AuthorsLima, C.D.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
Title: Reconstitution, activities, and structure of the eukaryotic RNA exosome.
Authors: Liu, Q. / Greimann, J.C. / Lima, C.D.
History
DepositionOct 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 999 SEQUENCE IN THE C-TERMINAL REGION OF CHAIN "A", 303-456, ONLY THIRTY EIGHT RESIDUES WERE VISIBLE ... SEQUENCE IN THE C-TERMINAL REGION OF CHAIN "A", 303-456, ONLY THIRTY EIGHT RESIDUES WERE VISIBLE IN ELECTRON DENSITY. THE SEQUENCE NUMBERING 412-449 OF THESE 38 RESIDUES IN CHAIN A IS RANDOM, AND THESE RESIDUES ARE ASSIGNED AS "UNK" (UNKNOWN AMINO ACIDS). THE SEQUENCE ALIGNMENT IS UNKNOWN IN THIS REGION. THE SEQUENCE IN THIS DISORDERED REGION (RESIDUES 303-456) IS: IDTSDVEEKAEEIIAEAEPPSEVVSTPVLWTPGTAQIGEGVENSWGD LEDSEKEDDEGGGDQAIILDGIKMDTGVEVSDIGSQELGFHHVGQTG LEFLTSDAPIILSDSEEEEMIILEPDKNPKKIRTQTTSAKQEKAPSK KPVKRRKKKRAAN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polymyositis/scleroderma autoantigen 1
B: Exosome complex exonuclease RRP41
C: Exosome complex exonuclease RRP43
D: Exosome complex exonuclease RRP46
E: Exosome complex exonuclease RRP42
F: Exosome component 6
G: Exosome complex exonuclease RRP40
H: Exosome complex exonuclease RRP4
I: 3'-5' exoribonuclease CSL4 homolog


Theoretical massNumber of molelcules
Total (without water)272,6669
Polymers272,6669
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26920 Å2
ΔGint-116 kcal/mol
Surface area98680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)307.800, 307.800, 307.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number207
Space group name H-MP432

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Components

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Protein , 3 types, 3 molecules AFI

#1: Protein Polymyositis/scleroderma autoantigen 1 / Ribosomal RNA-processing protein 45 / Rrp45 / PM/Scl-75


Mass: 39405.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: placental cDNA (Ambion, Inc) / Gene: PMSCL1 / Plasmid: pETDuet-1 (Novagen) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus-RIL / References: UniProt: Q86Y41, UniProt: Q06265*PLUS
#6: Protein Exosome component 6 / Mtr3


Mass: 28267.127 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: placental cDNA (Ambion, Inc) / Gene: EXOSC6 / Plasmid: pRSFDuet-1 (Novagen) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: Q5RKV6
#9: Protein 3'-5' exoribonuclease CSL4 homolog / Exosome component 1


Mass: 23097.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: placental cDNA (Ambion, Inc) / Gene: EXOSC1, CSL4 / Plasmid: pRSFDuet-1 (Novagen) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus-RIL
References: UniProt: Q9Y3B2, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters

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Exosome complex exonuclease ... , 6 types, 6 molecules BCDEGH

#2: Protein Exosome complex exonuclease RRP41 / Ribosomal RNA-processing protein 41 / Exosome component 4 / p12A


Mass: 26831.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: placental cDNA (Ambion, Inc) / Gene: EXOSC4, RRP41, SKI6 / Plasmid: pETDuet-1 (Novagen) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus-RIL
References: UniProt: Q9NPD3, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#3: Protein Exosome complex exonuclease RRP43 / Ribosomal RNA-processing protein 43 / Exosome component 8 / p9 / Opa-interacting protein 2 / OIP2


Mass: 30285.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: placental cDNA (Ambion, Inc) / Gene: EXOSC8, OIP2, RRP43 / Plasmid: pSMT3 (Smt3 fusion) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus-RIL
References: UniProt: Q96B26, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#4: Protein Exosome complex exonuclease RRP46 / Ribosomal RNA-processing protein 46 / Exosome component 5 / p12B / Chronic myelogenous leukemia ...Ribosomal RNA-processing protein 46 / Exosome component 5 / p12B / Chronic myelogenous leukemia tumor antigen 28


Mass: 25480.213 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: placental cDNA (Ambion, Inc) / Gene: EXOSC5, CML28, RRP46 / Plasmid: pSMT3 (Smt3-fusion) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus-RIL
References: UniProt: Q9NQT4, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#5: Protein Exosome complex exonuclease RRP42 / Ribosomal RNA-processing protein 42 / Exosome component 7 / p8


Mass: 33479.121 Da / Num. of mol.: 1 / Mutation: L274V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: placental cDNA (Ambion, Inc) / Gene: EXOSC7, KIAA0116, RRP42 / Plasmid: pRSFDuet-1 (Novagen) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star
References: UniProt: Q15024, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#7: Protein Exosome complex exonuclease RRP40 / Ribosomal RNA-processing protein 40 / Exosome component 3 / p10


Mass: 31227.881 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: placental cDNA (Ambion, Inc) / Gene: EXOSC3, RRP40 / Plasmid: pRSFDuet-1 (Novagen) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus-RIL
References: UniProt: Q9NQT5, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#8: Protein Exosome complex exonuclease RRP4 / Ribosomal RNA-processing protein 4 / Exosome component 2


Mass: 34590.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: placental cDNA (Ambion, Inc) / Gene: EXOSC2, RRP4 / Plasmid: pRSFDuet-1 (Novagen) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus-RIL
References: UniProt: Q13868, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters

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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: 4.45 Å3/Da / Density % sol: 72.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 4.5-8% w/v PEG4000, 0.1M Sodium citrate, 1 mM TCEP, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9809 Å / Relative weight: 1
ReflectionResolution: 3.35→35 Å / Num. all: 69964 / Num. obs: 69964 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 38.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.5
Reflection shellResolution: 3.35→3.47 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.6 / Num. unique all: 6999 / % possible all: 95.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQUANTUMdata collection
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIRAS / Resolution: 3.35→14.98 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 59512279.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: BULK SOLVENT MODEL USED CNS version 1.2 grid search used
RfactorNum. reflection% reflectionSelection details
Rfree0.344 3465 5 %RANDOM
Rwork0.291 ---
obs0.291 69115 97.7 %-
all-69115 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.5031 Å2 / ksol: 0.26 e/Å3
Displacement parametersBiso mean: 119.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.74 Å0.63 Å
Luzzati d res low-6 Å
Luzzati sigma a1.35 Å0.98 Å
Refinement stepCycle: LAST / Resolution: 3.35→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16858 0 0 0 16858
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_mcbond_it3.042.5
X-RAY DIFFRACTIONc_mcangle_it5.263.5
X-RAY DIFFRACTIONc_scbond_it5.364.5
X-RAY DIFFRACTIONc_scangle_it8.25.5
LS refinement shellResolution: 3.35→3.47 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.398 336 5.2 %
Rwork0.349 6167 -
obs--93.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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