+Open data
-Basic information
Entry | Database: PDB / ID: 6az0 | ||||||||||||||||||||||||
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Title | Mitochondrial ATPase Protease YME1 | ||||||||||||||||||||||||
Components |
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Keywords | HYDROLASE / Mitochondrial / ATPase / Protease | ||||||||||||||||||||||||
Function / homology | Function and homology information ATP-dependent peptidase activity / metalloendopeptidase activity / ATP hydrolysis activity / mitochondrion / proteolysis / ATP binding / membrane Similarity search - Function | ||||||||||||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Escherichia coli (E. coli) | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||||||||||||||||||||
Authors | Puchades, C. / Rampello, A.J. / Shin, M. / Giuliano, C. / Wiseman, R.L. / Glynn, S.E. / Lander, G.C. | ||||||||||||||||||||||||
Funding support | United States, 7items
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Citation | Journal: Science / Year: 2017 Title: Structure of the mitochondrial inner membrane AAA+ protease YME1 gives insight into substrate processing. Authors: Cristina Puchades / Anthony J Rampello / Mia Shin / Christopher J Giuliano / R Luke Wiseman / Steven E Glynn / Gabriel C Lander / Abstract: We present an atomic model of a substrate-bound inner mitochondrial membrane AAA+ quality control protease in yeast, YME1. Our ~3.4-angstrom cryo-electron microscopy structure reveals how the ...We present an atomic model of a substrate-bound inner mitochondrial membrane AAA+ quality control protease in yeast, YME1. Our ~3.4-angstrom cryo-electron microscopy structure reveals how the adenosine triphosphatases (ATPases) form a closed spiral staircase encircling an unfolded substrate, directing it toward the flat, symmetric protease ring. Three coexisting nucleotide states allosterically induce distinct positioning of tyrosines in the central channel, resulting in substrate engagement and translocation to the negatively charged proteolytic chamber. This tight coordination by a network of conserved residues defines a sequential, around-the-ring adenosine triphosphate hydrolysis cycle that results in stepwise substrate translocation. A hingelike linker accommodates the large-scale nucleotide-driven motions of the ATPase spiral relative to the planar proteolytic base. The translocation mechanism is likely conserved for other AAA+ ATPases. | ||||||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6az0.cif.gz | 2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6az0.ent.gz | 1.8 MB | Display | PDB format |
PDBx/mmJSON format | 6az0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6az0_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6az0_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 6az0_validation.xml.gz | 302 KB | Display | |
Data in CIF | 6az0_validation.cif.gz | 456.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/6az0 ftp://data.pdbj.org/pub/pdb/validation_reports/az/6az0 | HTTPS FTP |
-Related structure data
Related structure data | 7023MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Number of models | 5 |
-Components
-Protein / Protein/peptide , 2 types, 7 molecules ABCDEFG
#1: Protein | Mass: 48025.758 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: Walker B mutant Source: (gene. exp.) Saccharomyces cerevisiae (strain RM11-1a) (yeast) Strain: RM11-1a / Gene: SCRG_02514 / Production host: Escherichia coli (E. coli) / References: UniProt: B3LL85 #2: Protein/peptide | | Mass: 869.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: unknown polypeptide / Source: (natural) Escherichia coli (E. coli) |
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-Non-polymers , 4 types, 15 molecules
#3: Chemical | ChemComp-ATP / #4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-ADP / | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: YME1 ATPase Protease Walker B mutant bound to substrate Type: COMPLEX Details: YME1 Walker B mutant was recombinantly expressed in E. coli, solved in presence of ATP with unknown bound substrate. Entity ID: #1-#2 / Source: RECOMBINANT | |||||||||||||||||||||||||||||||||||
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Molecular weight | Value: 0.295 MDa / Experimental value: NO | |||||||||||||||||||||||||||||||||||
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) | |||||||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | |||||||||||||||||||||||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||||||||||||
Specimen support | Details: Gatan Solarus Plasma Cleaner / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Details: Data collected using Leginon |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 29000 X / Calibrated magnification: 51500 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm / Calibrated defocus min: 1200 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 70 K / Temperature (min): 70 K |
Image recording | Average exposure time: 7 sec. / Electron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 6098 Details: Images collected in counting mode at 5 frames per second. |
Image scans | Sampling size: 5 µm / Width: 3710 / Height: 3838 / Movie frames/image: 35 / Used frames/image: 1-35 |
-Processing
Software | Name: PHENIX / Version: 1.10.1_2155: / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | |||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2285499 Details: Particles picked automatically with FindEM template picking | |||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 62917 / Algorithm: BACK PROJECTION / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 100 / Protocol: AB INITIO MODEL / Space: REAL | |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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