6AZ0

Mitochondrial ATPase Protease YME1

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Structure of the mitochondrial inner membrane AAA+ protease YME1 gives insight into substrate processing.

Puchades, C., Rampello, A.J., Shin, M., Giuliano, C.J., Wiseman, R.L., Glynn, S.E., Lander, G.C.

(2017) Science 358

  • DOI: https://doi.org/10.1126/science.aao0464
  • Primary Citation of Related Structures:  
    6AZ0

  • PubMed 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 adenosine triphosphatases (ATPases) form a closed spiral staircase encircling an unfolded substrate, directing it toward the flat, symmetric protease ring ...

    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.

    Organizational Affiliation: 

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute HZ 175, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. glander@scripps.edu steven.glynn@stonybrook.edu.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial inner membrane i-AAA protease supercomplex subunit YME1
A, B, C, D, E, F
A, B, C, D, E, F
439Saccharomyces cerevisiae RM11-1aMutation(s): 0 
Gene Names: SCRG_02514
UniProt
Find proteins for B3LL85 (Saccharomyces cerevisiae (strain RM11-1a))
Explore B3LL85 
Go to UniProtKB:  B3LL85
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3LL85
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
poly(UNK)G10Escherichia coliMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP
Download Ideal Coordinates CCD File 
H [auth A],
K [auth B],
N [auth C],
S [auth D]		ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N		 Ligand Interaction
ADP
Query on ADP
Download Ideal Coordinates CCD File 
T [auth E]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
I [auth A],
L [auth B],
O [auth C],
Q [auth D],
U [auth E],
I [auth A],
L [auth B],
O [auth C],
Q [auth D],
U [auth E],
V [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
J [auth A],
M [auth B],
P [auth C],
R [auth D]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4
MODEL REFINEMENTRosetta3.5
MODEL REFINEMENTPHENIX1.9

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)United StatesDP2EB020402
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM008468
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01NS095892
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM115898
American Heart AssociationUnited States--
National Institutes of Health/Office of the DirectorUnited StatesS10OD021634
pewUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-15
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Author supporting evidence, Other
  • Version 1.2: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.3: 2019-12-18
    Changes: Other