6CDD | pdb_00006cdd

Npl4 zinc finger and MPN domains (Chaetomium thermophilum)

• PDB DOI: https://doi.org/10.2210/pdb6CDD/pdb

• Classification: PROTEIN BINDING
• Organism(s): Thermochaetoides thermophila DSM 1495
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-02-08 Released: 2018-07-04 
• Deposition Author(s): Bodnar, N.O., Rapoport, T.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 
  0.229 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

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: Monomer - A1 

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

Biological Assembly Evidence: microscopy

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 107.49 kDa 
• Atom Count: 7,515 
• Modeled Residue Count: 915 
• Deposited Residue Count: 948 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Npl4 zinc finger	A, B	474	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], E [auth B], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free:  0.229 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Diffraction Data: https://doi.org/10.15785/SBGRID/565

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.858	α = 90
b = 72.221	β = 96.714
c = 193.543	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHENIX	refinement
PHENIX	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM052586
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32GM007753
Howard Hughes Medical Institute (HHMI)	United States	--

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: 2019-11-20
  Changes: Author supporting evidence
• Version 1.4: 2024-03-13
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-04-03
  Changes: Refinement description