6NYY

human m-AAA protease AFG3L2, substrate-bound

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Unique Structural Features of the Mitochondrial AAA+ Protease AFG3L2 Reveal the Molecular Basis for Activity in Health and Disease.

Puchades, C., Ding, B., Song, A., Wiseman, R.L., Lander, G.C., Glynn, S.E.

(2019) Mol Cell 75: 1073

  • DOI: 10.1016/j.molcel.2019.06.016
  • Primary Citation of Related Structures:  
    6NYY

  • PubMed Abstract: 

    • Mitochondrial AAA+ quality-control proteases regulate diverse aspects of mitochondrial biology through specialized protein degradation, but the underlying mechanisms of these enzymes remain poorly defined. The mitochondrial AAA+ protease AFG3L2 is of particular interest, as genetic mutations localized throughout AFG3L2 are linked to diverse neurodegenerative disorders ...

    Mitochondrial AAA+ quality-control proteases regulate diverse aspects of mitochondrial biology through specialized protein degradation, but the underlying mechanisms of these enzymes remain poorly defined. The mitochondrial AAA+ protease AFG3L2 is of particular interest, as genetic mutations localized throughout AFG3L2 are linked to diverse neurodegenerative disorders. However, a lack of structural data has limited our understanding of how mutations impact enzymatic function. Here, we used cryoelectron microscopy (cryo-EM) to determine a substrate-bound structure of the catalytic core of human AFG3L2. This structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins. Many disease-relevant mutations localize to these unique structural features of AFG3L2 and distinctly influence its activity and stability. Our results provide a molecular basis for neurological phenotypes associated with different AFG3L2 mutations and establish a structural framework to understand how different members of the AAA+ superfamily achieve specialized biological functions.

    Organizational Affiliation: 

    Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA. Electronic address: steven.glynn@stonybrook.edu.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AFG3-like protein 2
A, B, C, D, E, F
A, B, C, D, E, F
529Homo sapiensMutation(s): 0 
Gene Names: AFG3L2
EC: 3.4.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y4W6 (Homo sapiens)
Explore Q9Y4W6 
Go to UniProtKB:  Q9Y4W6
PHAROS:  Q9Y4W6
GTEx:  ENSG00000141385 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y4W6
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SubstrateG, H, I, J11Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP
Download Ideal Coordinates CCD File 
L [auth B],
Q [auth C],
R [auth D]		PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N		 Ligand Interaction
ADP
Query on ADP
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U [auth E]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
ZN
Query on ZN
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K [auth A],
N [auth B],
P [auth C],
T [auth D],
V [auth E],
K [auth A],
N [auth B],
P [auth C],
T [auth D],
V [auth E],
W [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
M [auth B],
O [auth C],
S [auth D]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR21 AG061697 01

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2019-08-07
    Changes: Data collection, Database references
  • Version 1.2: 2019-09-18
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.4: 2019-12-18
    Changes: Other