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- EMDB-7023: Mitochondrial ATPase Protease YME1 -

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Basic information

Entry
Database: EMDB / ID: EMD-7023
TitleMitochondrial ATPase Protease YME1
Map datasharpened map
Sample
  • Complex: YME1 ATPase Protease Walker B mutant bound to substrate
    • Protein or peptide: Mitochondrial inner membrane i-AAA protease supercomplex subunit YME1
    • Protein or peptide: poly(UNK)
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsMitochondrial / ATPase / Protease / HYDROLASE
Function / homology
Function and homology information


ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / mitochondrion organization / metalloendopeptidase activity / mitochondrial inner membrane / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
: / Yme1-like, N-terminal / Peptidase, FtsH / Peptidase M41 / Peptidase M41-like / Peptidase family M41 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. ...: / Yme1-like, N-terminal / Peptidase, FtsH / Peptidase M41 / Peptidase M41-like / Peptidase family M41 / 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 speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain RM11-1a) (yeast) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsPuchades C / Rampello AJ
Funding support United States, 7 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)DP2EB020402 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008468 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS095892 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM115898 United States
American Heart Association United States
National Institutes of Health/Office of the DirectorS10OD021634 United States
pew United States
CitationJournal: 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
DepositionSep 9, 2017-
Header (metadata) releaseNov 15, 2017-
Map releaseNov 15, 2017-
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: 0.08
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6az0
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7023.png

Downloads & links

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Map

FileDownload / File: emd_7023.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 150 pix.
= 154.5 Å		1.03 Å/pix.
x 150 pix.
= 154.5 Å		1.03 Å/pix.
x 150 pix.
= 154.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08 / Movie #1: 0.08
Minimum - Maximum-0.18468148 - 0.34974062
Average (Standard dev.)0.0019727424 (±0.025994394)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 154.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z150150150
origin x/y/z0.0000.0000.000
length x/y/z154.500154.500154.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS150150150
D min/max/mean-0.1850.3500.002

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Supplemental data

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Additional map: focused refinement of step subunit, unsharpened

Fileemd_7023_additional_1.map
Annotationfocused refinement of step subunit, unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: focused refinement of step subunit, sharpened

Fileemd_7023_additional_2.map
Annotationfocused refinement of step subunit, sharpened
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened map

Fileemd_7023_additional_3.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: focused refinement of step subunit, half map 2

Fileemd_7023_half_map_1.map
Annotationfocused refinement of step subunit, half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: focused refinement of step subunit, half map 1

Fileemd_7023_half_map_2.map
Annotationfocused refinement of step subunit, half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : YME1 ATPase Protease Walker B mutant bound to substrate

EntireName: YME1 ATPase Protease Walker B mutant bound to substrate
Components
  • Complex: YME1 ATPase Protease Walker B mutant bound to substrate
    • Protein or peptide: Mitochondrial inner membrane i-AAA protease supercomplex subunit YME1
    • Protein or peptide: poly(UNK)
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: YME1 ATPase Protease Walker B mutant bound to substrate

SupramoleculeName: YME1 ATPase Protease Walker B mutant bound to substrate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: YME1 Walker B mutant was recombinantly expressed in E. coli, solved in presence of ATP with unknown bound substrate.
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 295 KDa

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Macromolecule #1: Mitochondrial inner membrane i-AAA protease supercomplex subunit YME1

MacromoleculeName: Mitochondrial inner membrane i-AAA protease supercomplex subunit YME1
type: protein_or_peptide / ID: 1 / Details: Walker B mutant / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain RM11-1a) (yeast) / Strain: RM11-1a
Molecular weightTheoretical: 48.025758 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: KFDDVCGCDE ARAELEEIVD FLKDPTKYES LGGKLPKGVL LTGPPGTGKT LLARATAGEA GVDFFFMSGS EFDEVYVGVG AKRIRDLFA QARSRAPAII FIDQLDAIGG KRNPKDQAYA KQTLNQLLVE LDGFSQTSGI IIIGATNFPE ALDKALTRPG R FDKVVNVD ...String:
KFDDVCGCDE ARAELEEIVD FLKDPTKYES LGGKLPKGVL LTGPPGTGKT LLARATAGEA GVDFFFMSGS EFDEVYVGVG AKRIRDLFA QARSRAPAII FIDQLDAIGG KRNPKDQAYA KQTLNQLLVE LDGFSQTSGI IIIGATNFPE ALDKALTRPG R FDKVVNVD LPDVRGRADI LKHHMKKITL ADNVDPTIIA RGTPGLSGAE LANLVNQAAV YACQKNAVSV DMSHFEWAKD KI LMGAERK TMVLTDAARK ATAFHEAGHA IMAKYTNGAT PLYKATILPR GRALGITFQL PEMDKVDITK RECQARLDVC MGG KIAEEL IYGKDNTTSG CGSDLQSATG TARAMVTQYG MSDDVGPVNL SEEWESWSNK IRDIADNEVI ELLKDSEERA RRLL TKKNV ELHRLAQGLI EYETLDAHEI EQVCKGEKLA KLKT

UniProtKB: AAA+ ATPase domain-containing protein

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Macromolecule #2: poly(UNK)

MacromoleculeName: poly(UNK) / type: protein_or_peptide / ID: 2 / Details: unknown polypeptide / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 869.063 Da
SequenceString:
(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: 4 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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
Component:
ConcentrationFormulaName
25.0 mMHEPESHEPES
100.0 mMKClpotassium chloride
5.0 mMMgCl2magnesium chloride
1.0 mMDTTdithiothreitol
1.0 mMATPadenosine triphosphate
0.05 %LMNGLauryl Maltose Neopentyl Glycol
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 6 sec. / Pretreatment - Atmosphere: OTHER / Details: Gatan Solarus Plasma Cleaner
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 70.0 K / Max: 70.0 K
DetailsData collected using Leginon
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 1-35 / Number grids imaged: 3 / Number real images: 6098 / Average exposure time: 7.0 sec. / Average electron dose: 60.0 e/Å2
Details: Images collected in counting mode at 5 frames per second.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 1.2 µm / Calibrated magnification: 51500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2285499
Details: Particles picked automatically with FindEM template picking
Startup modelType of model: INSILICO MODEL
In silico model: common lines model generated from negative stain data
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 62917
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4) / Details: RELION 1.4
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4) / Details: RELION 1.4
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 100
Output model

PDB-6az0:
Mitochondrial ATPase Protease YME1

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