6CHS | pdb_00006chs

Cdc48-Npl4 complex in the presence of ATP-gamma-S

• PDB DOI: https://doi.org/10.2210/pdb6CHS/pdb
• EM Map EMD-7476: EMDB EMDataResource

• Classification: MOTOR PROTEIN
• Organism(s): Thermochaetoides thermophila DSM 1495
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-02-22 Released: 2018-07-04 
• Deposition Author(s): Kim, K.H., Bodnar, N.O., Walz, T., Rapoport, T.A.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of the Cdc48 ATPase with its ubiquitin-binding cofactor Ufd1-Npl4.

Bodnar, N.O., Kim, K.H., Ji, Z., Wales, T.E., Svetlov, V., Nudler, E., Engen, J.R., Walz, T., Rapoport, T.A.

(2018) Nat Struct Mol Biol 25: 616-622

• PubMed: 29967539 
• DOI: https://doi.org/10.1038/s41594-018-0085-x
• Primary Citation Related Structures: 
  6CDD, 6CHS


• PubMed Abstract: 
  

  Many polyubiquitinated proteins are extracted from membranes or complexes by the conserved ATPase Cdc48 (in yeast; p97 or VCP in mammals) before proteasomal degradation. Each Cdc48 hexamer contains two stacked ATPase rings (D1 and D2) and six N-terminal (N) domains. Cdc48 binds various cofactors, including the Ufd1-Npl4 heterodimer. Here, we report structures of the Cdc48-Ufd1-Npl4 complex from Chaetomium thermophilum. Npl4 interacts through its UBX-like domain with a Cdc48 N domain, and it uses two Zn ²⁺ -finger domains to anchor the enzymatically inactive Mpr1-Pad1 N-terminal (MPN) domain, homologous to domains found in several isopeptidases, to the top of the D1 ATPase ring. The MPN domain of Npl4 is located above Cdc48's central pore, a position similar to the MPN domain from deubiquitinase Rpn11 in the proteasome. Our results indicate that Npl4 is unique among Cdc48 cofactors and suggest a mechanism for binding and translocation of polyubiquitinated substrates into the ATPase.

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Organizational Affiliation: 
• Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
Laboratory of Molecular Electron Microscopy, the Rockefeller University, New York, NY, USA.
Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA.
Howard Hughes Medical Institute and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.
Laboratory of Molecular Electron Microscopy, the Rockefeller University, New York, NY, USA. [e-mail].
Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, Boston, MA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A6B1 Local Symmetry: Cyclic - C6  (Explore in 3D)
Local Stoichiometry: Homo 6-mer - A6 

Local Symmetry: Cyclic - C6  (Explore in 3D)
Local Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration, cross-linking

Macromolecule Content 

• Total Structure Weight: 623.18 kDa 
• Atom Count: 29,502 
• Modeled Residue Count: 3,760 
• Deposited Residue Count: 5,573 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Npl4	A	659	Thermochaetoides thermophila DSM 1495	Mutation(s): 0  Gene Names: CTHT_0009420
UniProt
Find proteins for G0S0B4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0S0B4  Go to UniProtKB:  G0S0B4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative cell division control protein	B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], G [auth F]	819	Thermochaetoides thermophila DSM 1495	Mutation(s): 0  Gene Names: CTHT_0027280
UniProt
Find proteins for G0S6Y2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0S6Y2  Go to UniProtKB:  G0S6Y2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AGS	AA [auth E], DA [auth F], EA [auth F], J [auth H], K [auth H], N [auth I], O [auth I], R [auth J], S [auth J], V [auth D], W [auth D], Z [auth E]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C10 H16 N5 O12 P3 S NLTUCYMLOPLUHL-KQYNXXCUSA-N
ZN	H [auth A], I [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	BA [auth E], CA [auth E], FA [auth F], GA [auth F], L [auth H], M [auth H], P [auth I], Q [auth I], T [auth J], U [auth J], X [auth D], Y [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-07-04 
Deposition Author(s): Kim, K.H., Bodnar, N.O., Walz, T., Rapoport, T.A.

Revision History  

• Version 1.0: 2018-07-04
  Type: Initial release
  
• Version 1.1: 2018-07-18
  Changes: Data collection, Database references
• Version 1.2: 2018-07-25
  Changes: Data collection, Database references
• Version 1.3: 2019-12-18
  Changes: Other
• Version 1.4: 2024-03-13
  Changes: Data collection, Database references, Derived calculations