8B01

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

External Resource: Annotation

Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: mpstruc

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	PF06808	e8b01B1	A: alpha complex topology	X: dicarboxylate/sodium symporter (From Topology)	H: dicarboxylate/sodium symporter (From Topology)	T: dicarboxylate/sodium symporter	F: PF06808	ECOD (1.6)
C	PF07686	e8b01C1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C	Heavy Chain	IGHV1	-	putative trap-type c4-dicarboxylate transport system, largepermease component \| putative trap-type c4-dicarboxylate transport system, smallpermease component	SAbDab (2024-05-31)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF04290	Tripartite ATP-independent periplasmic transporters, DctQ component (DctQ)	Tripartite ATP-independent periplasmic transporters, DctQ component	-	Family
B	PF06808	Tripartite ATP-independent periplasmic transporter, DctM component (DctM)	Tripartite ATP-independent periplasmic transporter, DctM component	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Putative TRAP-type C4-dicarboxylate transport system, small permease component	transporter activity transmembrane transporter activity	organic acid transport localization organic anion transport carboxylic acid transport transport organic substance transport dicarboxylic acid transport C4-dicarboxylate transport establishment of localization	cell periphery plasma membrane membrane cellular anatomical entity
B	Putative TRAP-type C4-dicarboxylate transport system, large permease component	transporter activity transmembrane transporter activity	-	cell periphery plasma membrane membrane cellular anatomical entity
C	Megabody c7HopQ	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR007387	TRAP transporter, small membrane protein DctQ	Family
B	IPR010656	TRAP C4-dicarboxylate transport system permease DctM subunit	Domain
B	IPR004681	TRAP transporter large membrane protein DctM	Family
C	IPR040838	SabA, N-terminal extracellular adhesion domain	Domain
C	IPR002718	Outer membrane protein, Helicobacter	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C	OPM	Transmembrane	Alpha-helical polytopic	Ion transporter superfamily	TRAP transporter

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Tripartite ATP-independent periplasmic (TRAP) protein family	SiaQM TRAP transporter in amphipol

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.