PXD045179

PXD045179 is an original dataset announced via ProteomeXchange.

Title	A Non-symmetrical p97 Conformation Favors Ufd1/Npl4 Recruitment
Description	p97/Cdc48 is a hexameric AAA ATPase in which each monomer consists of an N-terminal domain (NTD) and two ATPase domains (D1 and D2), which cooperate in substrate recruitment and processing. In vitro experiments and cryo-EM structures of p97 and its cofactor, Ufd1/Npl4 (UN), revealed mechanistic insights regarding substrate processing. Yet, dynamics and the intermediate structures of the related ATPase cycle upon UN binding remain unresolved. Using novel mutations, we captured two discrete functional conformations associated with specific nucleotide states: a functional conformation in which D1 protomers are ATP bound, while the D2 subunits are in the ADP state. A configuration that is presumably required for the initial substrate engagement with the D2 pore. We also report on a heterologous nucleotide state within the D1 ring in which only 2NTDs are in the “up” ATP state. Based on the elevated affinity and structural insights, we propose that this conformation favors UN binding. Further analysis suggests that p97-UN complex formation entails a two-state mechanism. Initially, UN binds p97's non-symmetrical conformation (2NTDs in an "up" state), this association promotes a structural transition upon which five NTDs shift to an "up" state and are poised to bind ATP. The UBXL domain of Npl4 selectively binds p97's downed NTD demonstrating a new conformation that may introduce directionality to incoming substrate.
HostingRepository	PRIDE
AnnounceDate	2024-05-16
AnnouncementXML	Submission_2024-05-16_10:41:08.792.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Michal Arie
SpeciesList	scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2023-09-06 23:52:30	ID requested
⏵ 1	2024-05-16 10:41:09	announced

Dataset with its publication pending

submitter keyword: ATPase, XL LC-MS/MS,p97/VCP

Ami Navon
contact affiliation	Department of Immunology and Regenerative Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
contact email	ami.navon@weizmann.ac.il
lab head
Michal Arie
contact affiliation	Department of Immunology and Regenerative Biology, The Weizmann Institiute of Science
contact email	michalarie2@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD045179
     1. Label: PRIDE project
     2. Name: A Non-symmetrical p97 Conformation Favors Ufd1/Npl4 Recruitment