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- PDB-6az0: Mitochondrial ATPase Protease YME1 -

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Basic information

Entry
Database: PDB / ID: 6az0
TitleMitochondrial ATPase Protease YME1
Components
  • Mitochondrial inner membrane i-AAA protease supercomplex subunit YME1
  • poly(UNK)
KeywordsHYDROLASE / Mitochondrial / ATPase / Protease
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 / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Helicase, Ruva Protein; domain 3 ...Peptidase M41 / Peptidase, FtsH / Peptidase M41-like / Peptidase family M41 / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / AAA domain-containing protein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsPuchades, C. / Rampello, A.J. / Shin, M. / Giuliano, C. / Wiseman, R.L. / Glynn, S.E. / Lander, G.C.
Funding support United States, 7items
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, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Author supporting evidence / Other / Category: cell / pdbx_audit_support
Item: _cell.Z_PDB / _cell.length_a ..._cell.Z_PDB / _cell.length_a / _cell.length_b / _cell.length_c / _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: Mitochondrial inner membrane i-AAA protease supercomplex subunit YME1
B: Mitochondrial inner membrane i-AAA protease supercomplex subunit YME1
C: Mitochondrial inner membrane i-AAA protease supercomplex subunit YME1
D: Mitochondrial inner membrane i-AAA protease supercomplex subunit YME1
E: Mitochondrial inner membrane i-AAA protease supercomplex subunit YME1
F: Mitochondrial inner membrane i-AAA protease supercomplex subunit YME1
G: poly(UNK)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)291,96922
Polymers289,0247
Non-polymers2,94615
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38950 Å2
ΔGint-407 kcal/mol
Surface area109300 Å2
Number of models5

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Components

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Protein / Protein/peptide , 2 types, 7 molecules ABCDEFG

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


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 poly(UNK)


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 / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 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
Molecular weightValue: 0.295 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHEPESHEPES1
2100 mMpotassium chlorideKCl1
35 mMmagnesium chlorideMgCl21
41 mMdithiothreitolDTT1
51 mMadenosine triphosphateATPAdenosine triphosphate1
60.05 %Lauryl Maltose Neopentyl GlycolLMNG1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Gatan Solarus Plasma Cleaner / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Details: Data collected using Leginon
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / 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 holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 70 K / Temperature (min): 70 K
Image recordingAverage 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 scansSampling size: 5 µm / Width: 3710 / Height: 3838 / Movie frames/image: 35 / Used frames/image: 1-35

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1FindEMparticle selectionimplemented in Appion
2Leginon3.2image acquisitionLeginon used for data collection
4RELION1.4CTF correction
10RELION1.4initial Euler assignment
11RELION1.4final Euler assignment
13RELION1.43D reconstruction
14Rosetta3.5model refinement
15PHENIX1.9model refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 2285499
Details: Particles picked automatically with FindEM template picking
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 62917 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingB value: 100 / Protocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0120505
ELECTRON MICROSCOPYf_angle_d0.97327661
ELECTRON MICROSCOPYf_dihedral_angle_d7.1917272
ELECTRON MICROSCOPYf_chiral_restr0.0553151
ELECTRON MICROSCOPYf_plane_restr0.0063618

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