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- EMDB-9063: Cryo-EM structure of the essential ribosome assembly AAA-ATPase Rix7 -

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Basic information

Entry
Database: EMDB / ID: EMD-9063
TitleCryo-EM structure of the essential ribosome assembly AAA-ATPase Rix7
Map data
Sample
  • Complex: AAA-ATPase Rix7
    • Protein or peptide: Rix7 mutant
    • Protein or peptide: unknown protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsAAA-ATPase / RIBOSOMAL PROTEIN
Function / homology
Function and homology information


preribosome binding / ribosome biogenesis / ATP hydrolysis activity / RNA binding / ATP binding / nucleus
Similarity search - Function
AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
AAA+ ATPase domain-containing protein
Similarity search - Component
Biological speciesChaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) / Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsLo YH / Sobhany M / Hsu AL / Ford BL / Krahn JM / Borgnia MJ / Stanley RE
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ZIA ES103247 United States
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 /
Abstract: Rix7 is an essential type II AAA-ATPase required for the formation of the large ribosomal subunit. Rix7 has been proposed to utilize the power of ATP hydrolysis to drive the removal of assembly ...Rix7 is an essential type II AAA-ATPase required for the formation of the large ribosomal subunit. Rix7 has been proposed to utilize the power of ATP hydrolysis to drive the removal of assembly factors from pre-60S particles, but the mechanism of release is unknown. Rix7's mammalian homolog, NVL2 has been linked to cancer and mental illness disorders, highlighting the need to understand the molecular mechanisms of this essential machine. Here we report the cryo-EM reconstruction of the tandem AAA domains of Rix7 which form an asymmetric stacked homohexameric ring. We trapped Rix7 with a polypeptide in the central channel, revealing Rix7's role as a molecular unfoldase. The structure establishes that type II AAA-ATPases lacking the aromatic-hydrophobic motif within the first AAA domain can engage a substrate throughout the entire central channel. The structure also reveals that Rix7 contains unique post-α7 insertions within both AAA domains important for Rix7 function.
History
DepositionAug 28, 2018-
Header (metadata) releaseSep 12, 2018-
Map releaseFeb 6, 2019-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0796
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0796
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6mat
  • Surface level: 0.0796
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9063.png

Downloads & links

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Map

FileDownload / File: emd_9063.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 192 pix.
= 266.88 Å		1.39 Å/pix.
x 192 pix.
= 266.88 Å		1.39 Å/pix.
x 192 pix.
= 266.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0796 / Movie #1: 0.0796
Minimum - Maximum-0.14773183 - 0.31063178
Average (Standard dev.)0.0005223646 (±0.017758228)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 266.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z266.880266.880266.880
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.1480.3110.001

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Supplemental data

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Sample components

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Entire : AAA-ATPase Rix7

EntireName: AAA-ATPase Rix7
Components
  • Complex: AAA-ATPase Rix7
    • Protein or peptide: Rix7 mutant
    • Protein or peptide: unknown protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: AAA-ATPase Rix7

SupramoleculeName: AAA-ATPase Rix7 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)

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Macromolecule #1: Rix7 mutant

MacromoleculeName: Rix7 mutant / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 89.418266 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSRRPTLRLG LDRDVYNIVL NLEQQGTDEN GKRPRLTVDY VYDTIKRSNS SLARQKKRML EDSIERVLAV RKEQAKAEEE TDSDDLIEA QERERERQKA AQAQRDANLL NRQIAKSWGF ASSPGAKAAD GEKGTDTGSI ATPAPATPAV AENMAADTPT T STGPVLPA ...String:
MSRRPTLRLG LDRDVYNIVL NLEQQGTDEN GKRPRLTVDY VYDTIKRSNS SLARQKKRML EDSIERVLAV RKEQAKAEEE TDSDDLIEA QERERERQKA AQAQRDANLL NRQIAKSWGF ASSPGAKAAD GEKGTDTGSI ATPAPATPAV AENMAADTPT T STGPVLPA SSTDRQPNGE PRPKKRKAAP KEIDRTPPTK VSILDIAGVD DTLQRLLKEV WFPLRGGEAC EKMGYRYDNG VL LHGPSGC GKTTLAHAIA GSIGVAFIPV SAPSVIGGTS GESEKNIRDV FDEAIRLAPC LIFLDQIDAI AGRRESANKG MES RIVAEI MNGMDRIRQN TPLGKNVVVL AATNRPEFLD PAIRRRFSVE IDMGMPSERA REQILRSLTR DLSLADDINF KELA KMTPG YVGSDLQYVV KAAVSESFQA NIDSLLAQAR AKHPADHLAN VSQPQRDWLL LEAHRDEEVS WPSTKITMEQ FRKAV SLVQ PASKREGFST IPDTTWSHVG ALEDVRKKLE MSIIGPIKNP ELFTRVGIKP AAGILLWGPP GCGKTLVAKA VANESK ANF ISIKGPELLN KYVGESERAV RQLFSRAKSS APCILFFDQM DALVPRRDDS LSDASARVVN TLLTELDGVG DRSGIYV IG ATNRPDMIDE AIRRPGRLGT SIYVGLPSAE DRVKILKTLY RNTVKAPKKR EGTNGEDVDM TDAAAEQQHQ GTTDADLE K VALDLRCTGF SGADLGNLMQ AAAQACLERV YTQRQQKRKE GGSVAEEEEI EPVITMEDWE KALNEVKPSV KDPEKYMHS GFAAALEHHH HHH

UniProtKB: AAA+ ATPase domain-containing protein

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Macromolecule #2: unknown protein

MacromoleculeName: unknown protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 2.315846 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 11 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridModel: C-flat-1.2/1.3 4C / Material: COPPER
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: -2.7 µm / Nominal defocus min: -1.2 µm / Nominal magnification: 59000
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5ftk

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1.0) / Number images used: 64386
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5ftk


Chain - Source name: PDB / Chain - Initial model type: experimental model
Details5C18 was used for reference restraints in refinement
Output model

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

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