[English] 日本語
Yorodumi
- EMDB-7023: Mitochondrial ATPase Protease YME1 -

+
Open data


ID or keywords:

Loading...

-
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 / metalloendopeptidase activity / ATP binding / membrane
Similarity search - Function
Peptidase M41 / Peptidase, FtsH / 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 ...Peptidase M41 / Peptidase, FtsH / 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 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

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.08
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6az0
  • Surface level: 0.08
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7023.png

Downloads & links

-
Map

FileDownload / File: emd_7023.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Voxel sizeX=Y=Z: 1.03 Å
Density
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

-
Supplemental data

-
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)

-
Additional map: focused refinement of step subunit, sharpened

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

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: unsharpened map

Fileemd_7023_additional_3.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
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)

-
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)

-
Half map: half map 1

Fileemd_7023_half_map_3.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 2

Fileemd_7023_half_map_4.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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

-
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 domain-containing protein

-
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)

-
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 / Adenosine triphosphate

-
Macromolecule #4: ZINC ION

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

-
Macromolecule #5: MAGNESIUM ION

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

-
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 / Adenosine diphosphate

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
25.0 mMHEPESHEPES
100.0 mMKClpotassium chloride
5.0 mMMgCl2magnesium chloride
1.0 mMDTTdithiothreitol
1.0 mMATPAdenosine triphosphateadenosine 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

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
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 FIELDBright-field microscopy / 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
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.
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
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
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
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
FSC plot (resolution estimation)

-
Atomic model buiding 1

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

PDB-6az0:
Mitochondrial ATPase Protease YME1

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more