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- PDB-6mat: Cryo-EM structure of the essential ribosome assembly AAA-ATPase Rix7 -

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Basic information

Entry
Database: PDB / ID: 6mat
TitleCryo-EM structure of the essential ribosome assembly AAA-ATPase Rix7
Components
  • Rix7 mutant
  • unknown protein
KeywordsRIBOSOMAL PROTEIN / AAA-ATPase
Function / homologyAAA+ ATPase domain / ATPase, AAA-type, core / ATPase, AAA-type, conserved site / P-loop containing nucleoside triphosphate hydrolase / ATPase family associated with various cellular activities (AAA) / AAA-protein family signature. / ATP binding / Uncharacterized protein
Function and homology information
Specimen sourceChaetomium thermophilum (fungus)
Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.5 Å resolution
AuthorsLo, Y.H. / Sobhany, M. / Hsu, A.L. / Ford, B.L. / Krahn, J.M. / Borgnia, M.J. / Stanley, R.E.
CitationJournal: Nat Commun / Year: 2019
Title: Cryo-EM structure of the essential ribosome assembly AAA-ATPase Rix7.
Authors: Yu-Hua Lo / Mack Sobhany / Allen L Hsu / Brittany L Ford / Juno M Krahn / Mario J Borgnia / Robin E Stanley
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 28, 2018 / Release: Feb 6, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Feb 6, 2019Structure modelrepositoryInitial release
1.1Feb 13, 2019Structure modelData collection / Database referencescitation / citation_author_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

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Assembly

Deposited unit
A: Rix7 mutant
B: Rix7 mutant
C: Rix7 mutant
D: Rix7 mutant
E: Rix7 mutant
F: Rix7 mutant
G: unknown protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)544,40418
Polyers538,8257
Non-polymers5,57911
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)53540
ΔGint (kcal/M)-187
Surface area (Å2)162790

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Components

#1: Protein/peptide
Rix7 mutant


Mass: 89418.266 Da / Num. of mol.: 6 / Mutation: E303Q/E602Q
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0002840 / Production host: Escherichia coli (E. coli) / References: UniProt: G0RZG1
#2: Protein/peptide unknown protein


Mass: 2315.846 Da / Num. of mol.: 1
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 11 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: AAA-ATPase Rix7 / Type: RIBOSOME / Entity ID: 1, 2 / Source: RECOMBINANT
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: C-flat-1.2/1.3 4C
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 / Nominal defocus max: -2700 nm / Nominal defocus min: -1200 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
4CTFFIND4.1.10CTF correction
7Coot0.8.9.1model fitting
11RELION2.1.0classification
12RELION2.1.03D reconstruction
13CNS1.3model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 64386 / Symmetry type: POINT
Atomic model buildingDetails: 5C18 was used for reference restraints in refinement
Atomic model buildingPDB-ID: 5FTK
Least-squares processHighest resolution: 4.5 Å

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