6CNL | pdb_00006cnl

Crystal Structure of H105A PGAM5 Dodecamer

• PDB DOI: https://doi.org/10.2210/pdb6CNL/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-03-08 Released: 2019-02-13 
• Deposition Author(s): Ruiz, K., Agnew, C., Jura, N.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.264 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Functional role of PGAM5 multimeric assemblies and their polymerization into filaments.

Ruiz, K., Thaker, T.M., Agnew, C., Miller-Vedam, L., Trenker, R., Herrera, C., Ingaramo, M., Toso, D., Frost, A., Jura, N.

(2019) Nat Commun 10: 531-531

• PubMed: 30705304 
• DOI: https://doi.org/10.1038/s41467-019-08393-w
• Primary Citation Related Structures: 
  6CNI, 6CNL


• PubMed Abstract: 
  

  PGAM5 is a mitochondrial protein phosphatase whose genetic ablation in mice results in mitochondria-related disorders, including neurodegeneration. Functions of PGAM5 include regulation of mitophagy, cell death, metabolism and aging. However, mechanisms regulating PGAM5 activation and signaling are poorly understood. Using electron cryo-microscopy, we show that PGAM5 forms dodecamers in solution. We also present a crystal structure of PGAM5 that reveals the determinants of dodecamer formation. Furthermore, we observe PGAM5 dodecamer assembly into filaments both in vitro and in cells. We find that PGAM5 oligomerization into a dodecamer is not only essential for catalytic activation, but this form also plays a structural role on mitochondrial membranes, which is independent of phosphatase activity. Together, these findings suggest that modulation of the oligomerization of PGAM5 may be a regulatory switch of potential therapeutic interest.

---

Organizational Affiliation: 
• Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA.
Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, 94158, USA.
Tetrad Graduate Program, University of California San Francisco, San Francisco, CA, 94158, USA.
Calico Life Sciences, South San Francisco, CA, 94080, USA.
California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA, 94720, USA.
Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA. [e-mail].
Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D6  (Explore in 3D)
Global Stoichiometry: Hetero 24-mer - A12B12 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 24-mer - A12B1C1D1E1F1G1H1I1J1K1L1M1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 325.84 kDa 
• Atom Count: 18,873 
• Modeled Residue Count: 2,379 
• Deposited Residue Count: 2,844 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein phosphatase PGAM5, mitochondrial	A, B [auth C], C [auth L], D [auth J], E [auth F], F [auth H], G [auth K], H [auth D], I [auth B], J [auth I], K [auth G], L [auth E]	223	Homo sapiens	Mutation(s): 1  Gene Names: PGAM5 EC: 3.1.3.16
UniProt & NIH Common Fund Data Resources
Find proteins for Q96HS1 (Homo sapiens) Explore Q96HS1  Go to UniProtKB:  Q96HS1
PHAROS:  Q96HS1 GTEx:  ENSG00000247077

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PGAM5 Multimerization Motif Peptide	M, N [auth O], O [auth X], P [auth V], Q [auth R], R [auth T], S [auth W], T [auth P], U [auth N], V [auth U], W [auth S], X [auth Q]	14	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	AA [auth C], AB [auth E], BA [auth C], BB [auth E], CA [auth C], CB [auth P], DA [auth C], EA [auth L], FA [auth L], GA [auth J], HA [auth J], IA [auth F], JA [auth F], KA [auth F], LA [auth F], MA [auth H], NA [auth H], OA [auth K], PA [auth D], QA [auth D], RA [auth D], SA [auth B], TA [auth B], UA [auth I], VA [auth I], WA [auth I], XA [auth G], Y [auth A], YA [auth G], Z [auth C], ZA [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.264 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.372	α = 90
b = 242.538	β = 90
c = 272.458	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-02-13 
Deposition Author(s): Ruiz, K., Agnew, C., Jura, N.

Revision History  

• Version 1.0: 2019-02-13
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description