8B01 | pdb_00008b01

Cryo-EM structure of the Tripartite ATP-independent Periplasmic (TRAP) transporter SiaQM from Photobacterium profundum in a nanodisc


Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
BF_UNCLASSIFIEDe8b01B1 A: alpha complex topologyX: dicarboxylate/sodium symporter (From Topology)H: dicarboxylate/sodium symporter (From Topology)T: dicarboxylate/sodium symporterF: F_UNCLASSIFIEDECOD (1.6)
CF_UNCLASSIFIEDe8b01C1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: F_UNCLASSIFIEDECOD (1.6)

SAbDab Antibody Annotation SAbDab Database Homepage

ChainChain ClassChain SubclassChain TypeAntigen Name(s) Provenance Source
Heavy ChainIGHV1 -putative trap-type c4-dicarboxylate transport system, largepermease component | putative trap-type c4-dicarboxylate transport system, smallpermease component SAbDab (2025-06-13)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF04290Tripartite ATP-independent periplasmic transporters, DctQ component (DctQ)Tripartite ATP-independent periplasmic transporters, DctQ componentThis entry includes tripartite ATP-independent periplasmic (TRAP) transporters which are substrate-binding protein (SBP)-dependent secondary transporters ubiquitous prokaryotes [1]. They are comprised of an SBP of the DctP or TAXI families and two in ...This entry includes tripartite ATP-independent periplasmic (TRAP) transporters which are substrate-binding protein (SBP)-dependent secondary transporters ubiquitous prokaryotes [1]. They are comprised of an SBP of the DctP or TAXI families and two integral membrane proteins of unequal sizes that form the DctQ and DctM protein families (the small and large membrane components respectively) [1-3]. This entry represents the DctQ component and its homologues, which consists of five transmembrane segments. In SiaT, a protein involved in sialic acid uptake [4], this entry represents the N-terminal five transmembrane segments.
Domain
PF06808Tripartite ATP-independent periplasmic transporter, DctM component (DctM)Tripartite ATP-independent periplasmic transporter, DctM componentThis entry represents the transmembrane segments from a diverse range of transporter proteins from the tripartite ATP-independent periplasmic (TRAP) transport system, in which the driving force for solute accumulation is an electrochemical ion gradie ...This entry represents the transmembrane segments from a diverse range of transporter proteins from the tripartite ATP-independent periplasmic (TRAP) transport system, in which the driving force for solute accumulation is an electrochemical ion gradient and not ATP hydrolysis [3-5]. The first TRAP transporter to be characterised was the high-affinity C4-dicarboxylate transport (Dct) system from Rhodobacter capsulatus which consists of ESR (DctP) and small (DctQ) and large (DctM) integral membrane proteins [4]. In general, C4-dicarboxylate transport systems allow C4-dicarboxylates like succinate, fumarate, and malate to be taken up [1]. This entry also includes SiaM (involved in sialic acid uptake) [6] and YiaN (involved in the uptake of 2,3-diketo-L-gulonate) [2].
Domain