8DKM | pdb_00008dkm

Cryo-EM structure of cystine-bound cystinosin in a lumen-open state

External Resource: Annotation

Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
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	PHF5	e8dkmB1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PHF5	ECOD (develop294)
A	PHF5	e8dkmA1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PHF5	ECOD (develop294)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B	Light Chain	IGKV15	Kappa	isoform 2 of cystinosin	SAbDab (2026-03-20)
A	Heavy Chain	IGHV5	-	isoform 2 of cystinosin	SAbDab (2026-03-20)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth P]	PF04193	PQ loop repeat (PQ-loop)	PQ loop repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth P]	Isoform 2 of Cystinosin	monoatomic cation transmembrane transporter activity proton transmembrane transporter activity solute:monoatomic cation symporter activity active transmembrane transporter activity solute:proton symporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity symporter activity secondary active transmembrane transporter activity L-amino acid transmembrane transporter activity amino acid transmembrane transporter activity L-cystine transmembrane transporter activity sulfur amino acid transmembrane transporter activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity solute:monoatomic cation symporter activity active transmembrane transporter activity solute:proton symporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity symporter activity secondary active transmembrane transporter activity L-amino acid transmembrane transporter activity amino acid transmembrane transporter activity L-cystine transmembrane transporter activity sulfur amino acid transmembrane transporter activity sulfur compound transmembrane transporter activity carboxylic acid transmembrane transporter activity modified amino acid transmembrane transporter activity	developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development nucleoside phosphate metabolic process ribose phosphate metabolic process purine nucleoside triphosphate metabolic process ATP metabolic process developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development nucleoside phosphate metabolic process ribose phosphate metabolic process purine nucleoside triphosphate metabolic process ATP metabolic process carbohydrate derivative metabolic process primary metabolic process nucleotide metabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process ribonucleotide metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process nucleoside triphosphate metabolic process purine ribonucleotide metabolic process phosphorus metabolic process sensory organ development eye development visual system development camera-type eye development sensory system development lens development in camera-type eye localization transport monoatomic ion transport establishment of localization establishment of protein localization protein transport macromolecule localization intracellular protein localization cellular response to stimulus TOR signaling regulation of biological process regulation of signaling regulation of cellular process response to stimulus regulation of TOR signaling signaling biological regulation regulation of signal transduction intracellular signal transduction cell communication regulation of intracellular signal transduction regulation of response to stimulus regulation of cell communication regulation of TORC1 signaling signal transduction TORC1 signaling system process nervous system process cognition response to light stimulus learning learning or memory visual learning visual behavior associative learning behavior response to radiation response to abiotic stimulus pigment metabolic process pigment biosynthetic process melanin metabolic process secondary metabolic process biosynthetic process secondary metabolite biosynthetic process phenol-containing compound metabolic process phenol-containing compound biosynthetic process melanin biosynthetic process glutathione metabolic process modified amino acid metabolic process sulfur compound metabolic process transmembrane transport amino acid metabolic process long-term memory memory positive regulation of cell communication positive regulation of signal transduction positive regulation of biological process positive regulation of TORC1 signaling positive regulation of response to stimulus positive regulation of TOR signaling positive regulation of cellular process positive regulation of intracellular signal transduction positive regulation of signaling nitrogen compound transport organic anion transport carboxylic acid transport L-cystine transport neutral amino acid transport L-amino acid transport organic acid transport amino acid transport sulfur amino acid transport sulfur compound transport modified amino acid transport regulation of biosynthetic process regulation of melanin biosynthetic process regulation of secondary metabolite biosynthetic process regulation of secondary metabolic process regulation of metabolic process adult walking behavior adult locomotory behavior adult behavior locomotory behavior walking behavior grooming behavior	membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle extracellular exosome extracellular vesicle membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cell periphery plasma membrane membrane lytic vacuole vacuole lysosome vacuolar membrane lytic vacuole membrane bounding membrane of organelle lysosomal membrane organelle membrane endosome endomembrane system late endosome chitosome cytoplasmic vesicle membrane vesicle membrane melanosome membrane pigment granule membrane
B	Fab 3H5 Kappa chain	-	-	-
A	Fab 3H5 Heavy Chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth P]	IPR005282	Lysosomal cystine transporter	Family
C [auth P]	IPR006603	PQ-loop repeat	Repeat

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth P]	Pharos: O60931	cystinosis juvenile nephropathic cystinosis ocular cystinosis nephropathic cystinosis Fanconi renotubular syndrome astrocytic tumor CYSTINOSIS, ATYPICAL NEPHROPATHIC (disorder) glioblastoma atypical teratoid rhabdoid tumor inborn errors of metabolism lysosomal storage disease intellectual disability malignant ependymoma renal tubular acidosis

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
C [auth P]	OPM	Transmembrane	Alpha-helical polytopic	PQ-loop transporters	Lysosomal cystine transporter

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
C [auth P]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
C [auth P]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	SWEET and semiSWEET Transporters, and Their Relatives	Cystinosin cystine transporter, lumen-open state

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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.