PXD071146

PXD071146 is an original dataset announced via ProteomeXchange.

Title	Oligomeric assemblies of plant biotin carboxylase revealed by cryo-EM and cross-linking
Description	Acetyl-CoA carboxylase (ACCase) initiates de novo fatty acid synthesis in plastids, yet no experimental structure has been available for any plastid biotin carboxylase (BC) subunit. Here, we report the first cryo-EM structures of BC from Thlaspi arvense (pennycress), a developing oilseed crop. Purified recombinant BC predominantly formed a dimer, resolved at 2.85 Å, with architecture highly similar to bacterial heteromeric ACCase BCs. Rare tetrameric particles (<1%) yielded an ~8 Å reconstruction revealing a distinct “kissing” interface between A domains that differs from previously described BCCP-induced tetramers. Bioinformatic comparison with bacterial homologs and normal mode analysis identified a highly dynamic B-domain lid whose motions are consistent with nucleotide-dependent opening and closure. Consistently, lysine acetylation mapping showed strong reactivity in the exposed B-domain, supporting intrinsic mobility. Crosslinking mass spectrometry at higher BC concentration captured dimer–dimer interactions that could not be explained by the symmetric cryo-EM tetramer. Crosslink-guided modeling instead supported an asymmetric dimer of dimers with rotated, translated, and tilted orientations that partially restrict lid opening. These results provide the first structural framework for a plastid BC and reveal multiple oligomeric architectures, including an asymmetric assembly that may underlie higher-order organization observed in plant chloroplasts.
HostingRepository	PRIDE
AnnounceDate	2026-04-02
AnnouncementXML	Submission_2026-04-02_03:15:26.587.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Gabriel Lemes Jorge
SpeciesList	scientific name: Thlaspi arvense; NCBI TaxID: NEWT:13288;
ModificationList	acetylated residue; monohydroxylated residue
Instrument	timsTOF Pro 2; LTQ Orbitrap XL

Revision	Datetime	Status	ChangeLog Entry
0	2025-11-24 13:46:57	ID requested
1	2026-03-30 16:08:00	announced
⏵ 2	2026-04-02 03:15:27	announced	2026-04-02: Updated project metadata.

10.1042/BCJ20250372;

submitter keyword: Oligomerization dynamics, Thlaspi arvense (pennycress),Plastid fatty acid synthesis

Steven R. Van Doren
contact affiliation	Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA; Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
contact email	vandorens@missouri.edu
lab head
Gabriel Lemes Jorge
contact affiliation	University of Missouri
contact email	glj2d5@umsystem.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD071146
     1. Label: PRIDE project
     2. Name: Oligomeric assemblies of plant biotin carboxylase revealed by cryo-EM and cross-linking