6OA9

Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP

PDB DOI: https://doi.org/10.2210/pdb6OA9/pdb
EM Map EMD-0665: EMDB EMDataResource

Classification: MOTOR PROTEIN
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-03-15 Released: 2019-07-03
Deposition Author(s): Twomey, E.C., Ji, Z., Wales, T.E., Bodnar, N.O., Engen, J.R., Rapoport, T.A.
Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.90 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

Substrate processing by the Cdc48 ATPase complex is initiated by ubiquitin unfolding.

Twomey, E.C., Ji, Z., Wales, T.E., Bodnar, N.O., Ficarro, S.B., Marto, J.A., Engen, J.R., Rapoport, T.A.

(2019) Science 365

PubMed: 31249135 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/science.aax1033
Primary Citation of Related Structures:
6OA9, 6OAA, 6OAB

PubMed Abstract:
The Cdc48 adenosine triphosphatase (ATPase) (p97 or valosin-containing protein in mammals) and its cofactor Ufd1/Npl4 extract polyubiquitinated proteins from membranes or macromolecular complexes for subsequent degradation by the proteasome. How Cdc48 processes its diverse and often well-folded substrates is unclear. Here, we report cryo-electron microscopy structures of the Cdc48 ATPase in complex with Ufd1/Npl4 and polyubiquitinated substrate. The structures show that the Cdc48 complex initiates substrate processing by unfolding a ubiquitin molecule. The unfolded ubiquitin molecule binds to Npl4 and projects its N-terminal segment through both hexameric ATPase rings. Pore loops of the second ring form a staircase that acts as a conveyer belt to move the polypeptide through the central pore. Inducing the unfolding of ubiquitin allows the Cdc48 ATPase complex to process a broad range of substrates.

Organizational Affiliation

Department of Cell Biology, Harvard Medical School, and Howard Hughes Medical Institute, 240 Longwood Avenue, Boston, MA 02115, USA.

Macromolecule Content

Total Structure Weight: 649.33 kDa
Atom Count: 29,006
Modelled Residue Count: 3,718
Deposited Residue Count: 5,818
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division control protein 48	A, B, C, D, E A, B, C, D, E, F	835	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: CDC48, YDL126C EC: 3.6.4.6
UniProt
Find proteins for P25694 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25694 Go to UniProtKB: P25694
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25694
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	G [auth K], H, I [auth J]	76	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: RPL40A, UBI1, YIL148W
UniProt
Find proteins for P0CH08 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CH08 Go to UniProtKB: P0CH08
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0CH08
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear protein localization protein 4	J [auth G]	580	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: NPL4, HRD4, YBR170C, YBR1231
UniProt
Find proteins for P33755 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P33755 Go to UniProtKB: P33755
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P33755
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain S [auth E] SDF format, chain T [auth F] MOL2 format, chain K [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth E] MOL2 format, chain T [auth F]	K [auth A] L [auth B] M [auth C] N [auth C] O [auth C] K [auth A], L [auth B], M [auth C], N [auth C], O [auth C], P [auth D], Q [auth D], S [auth E], T [auth F]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain S [auth E] Focus chain T [auth F] Interactions & Density Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain S [auth E] Focus chain T [auth F]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain R [auth E] MOL2 format, chain R [auth E]	R [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain R [auth E] Interactions & Density Focus chain R [auth E]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain U [auth G] SDF format, chain V [auth G] MOL2 format, chain U [auth G] MOL2 format, chain V [auth G]	U [auth G], V [auth G]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain U [auth G] Focus chain V [auth G] Interactions & Density Focus chain U [auth G] Focus chain V [auth G]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-07-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--
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