6OPC

Cdc48 Hexamer in a complex with substrate and Shp1(Ubx Domain)

• PDB DOI: https://doi.org/10.2210/pdb6OPC/pdb
• EM Map EMD-20149: EMDB EMDataResource

• Classification: MOTOR PROTEIN
• Organism(s): Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2019-04-24 Released: 2019-07-10 
• Deposition Author(s): Cooney, I., Han, H., Stewart, M., Carson, R.H., Hansen, D., Price, J.C., Hill, C.P., Shen, P.S.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of the Cdc48 segregase in the act of unfolding an authentic substrate.

Cooney, I., Han, H., Stewart, M.G., Carson, R.H., Hansen, D.T., Iwasa, J.H., Price, J.C., Hill, C.P., Shen, P.S.

(2019) Science 365: 502-505

• PubMed: 31249134 
• DOI: https://doi.org/10.1126/science.aax0486
• Primary Citation of Related Structures:  
  6OMB, 6OPC


• PubMed Abstract: 
  

  The cellular machine Cdc48 functions in multiple biological pathways by segregating its protein substrates from a variety of stable environments such as organelles or multi-subunit complexes. Despite extensive studies, the mechanism of Cdc48 has remained obscure, and its reported structures are inconsistent with models of substrate translocation proposed for other AAA+ ATPases (adenosine triphosphatases). Here, we report a 3.7-angstrom-resolution structure of Cdc48 in complex with an adaptor protein and a native substrate. Cdc48 engages substrate by adopting a helical configuration of substrate-binding residues that extends through the central pore of both of the ATPase rings. These findings indicate a unified hand-over-hand mechanism of protein translocation by Cdc48 and other AAA+ ATPases.

---

Organizational Affiliation: 

Department of Biochemistry, 15 N. Medical Drive East, University of Utah, Salt Lake City, UT 84112, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 8-mer - A6B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A5B1C1D1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 606.57 kDa 
• Atom Count: 30,015 
• Modelled Residue Count: 4,477 
• Deposited Residue Count: 5,455 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division control protein 48	A, B, C, D, E, F	835	Saccharomyces cerevisiae	Mutation(s): 0  EC: 3.6.4.6
UniProt
Find proteins for P25694 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25694  Go to UniProtKB:  P25694

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Substrate bound to the central pore of the Cdc48 hexamer	G	22	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
UBX domain-containing protein 1	H [auth Z]	423	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P34223 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P34223  Go to UniProtKB:  P34223

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	AA [auth D], DA [auth D], GA [auth E], HA [auth E], I [auth A], L [auth A], O [auth B], Q [auth B], U [auth C], X [auth C]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
BEF	BA [auth D], EA [auth D], J [auth A], M [auth A], R [auth B], T [auth C], V [auth C], Y [auth C]	BERYLLIUM TRIFLUORIDE ION Be F3 OGIAHMCCNXDTIE-UHFFFAOYSA-K
MG	CA [auth D], FA [auth D], K [auth A], N [auth A], P [auth B], S [auth B], W [auth C], Z [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-07-10 
Deposition Author(s): Cooney, I., Han, H., Stewart, M., Carson, R.H., Hansen, D., Price, J.C., Hill, C.P., Shen, P.S.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	P50GM082545

Revision History  

• Version 1.0: 2019-07-10
  Type: Initial release
  
• Version 1.1: 2019-08-14
  Changes: Data collection, Database references
• Version 1.2: 2019-12-18
  Changes: Author supporting evidence
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references, Derived calculations