7WLD | pdb_00007wld

Cryo-EM structure of the human glycosylphosphatidylinositol transamidase complex at 2.53 Angstrom resolution

External Resource: Annotation

Domain Annotation: ECOD Classification
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: MemProtMD
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 [auth K]	Peptidase_M2	e7wldK01	A: a/b three-layered sandwiches	X: Rossmann-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Peptidase_M2	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth G]	PF04114	Gaa1-like, GPI transamidase component (Gaa1)	Gaa1-like, GPI transamidase component	-	Family
B [auth K]	PF01650	Peptidase C13 family (Peptidase_C13)	Peptidase C13 family	-	Family
C [auth S]	PF10510	Phosphatidylinositol-glycan biosynthesis class S protein (PIG-S)	Phosphatidylinositol-glycan biosynthesis class S protein	-	Family
D [auth T]	PF04113	Gpi16 subunit, GPI transamidase component (Gpi16)	Gpi16 subunit, GPI transamidase component	-	Family
E [auth U]	PF06728	GPI transamidase subunit PIG-U (PIG-U)	GPI transamidase subunit PIG-U	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth G]	Glycosylphosphatidylinositol anchor attachment 1 protein	binding lipid binding phospholipid binding GPI anchor binding glycolipid binding carbohydrate derivative binding	maintenance of protein location cellular localization maintenance of location maintenance of location in cell localization maintenance of protein localization in endoplasmic reticulum maintenance of protein location in cell macromolecule localization protein localization to organelle cellular process maintenance of protein localization in organelle intracellular protein localization protein localization to endoplasmic reticulum protein retention in ER lumen maintenance of protein location cellular localization maintenance of location maintenance of location in cell localization maintenance of protein localization in endoplasmic reticulum maintenance of protein location in cell macromolecule localization protein localization to organelle cellular process maintenance of protein localization in organelle intracellular protein localization protein localization to endoplasmic reticulum protein retention in ER lumen glycolipid metabolic process glycerophospholipid metabolic process carbohydrate derivative metabolic process lipid biosynthetic process GPI anchor biosynthetic process GPI anchor metabolic process protein maturation phospholipid metabolic process GPI anchored protein biosynthesis phosphate-containing compound metabolic process protein metabolic process phosphorus metabolic process carbohydrate derivative biosynthetic process glycerophospholipid biosynthetic process liposaccharide metabolic process primary metabolic process glycolipid biosynthetic process gene expression macromolecule biosynthetic process phospholipid biosynthetic process biosynthetic process glycerolipid biosynthetic process organophosphate metabolic process organophosphate biosynthetic process glycerolipid metabolic process metabolic process macromolecule metabolic process lipid metabolic process attachment of GPI anchor to protein	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane protein-containing complex caspase complex membrane protein complex GPI-anchor transamidase complex transferase complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane protein-containing complex caspase complex membrane protein complex GPI-anchor transamidase complex transferase complex endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endopeptidase complex endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane catalytic complex organelle subcompartment peptidase complex endoplasmic reticulum organelle membrane centrosome microtubule organizing center cytoskeleton membraneless organelle intracellular membraneless organelle microtubule cytoskeleton cytosol
B [auth K]	GPI-anchor transamidase	cysteine-type peptidase activity transferase activity, transferring nitrogenous groups peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity transferase activity catalytic activity GPI-anchor transamidase activity endopeptidase activity	biosynthetic process GPI anchored protein biosynthesis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process protein maturation proteolysis glycolipid metabolic process glycerophospholipid metabolic process carbohydrate derivative metabolic process biosynthetic process GPI anchored protein biosynthesis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process protein maturation proteolysis glycolipid metabolic process glycerophospholipid metabolic process carbohydrate derivative metabolic process lipid biosynthetic process GPI anchor biosynthetic process GPI anchor metabolic process phospholipid metabolic process phosphate-containing compound metabolic process phosphorus metabolic process carbohydrate derivative biosynthetic process glycerophospholipid biosynthetic process liposaccharide metabolic process glycolipid biosynthetic process phospholipid biosynthetic process glycerolipid biosynthetic process organophosphate metabolic process organophosphate biosynthetic process glycerolipid metabolic process lipid metabolic process attachment of GPI anchor to protein	cellular anatomical structure membrane membrane-bounded organelle protein-containing complex intracellular anatomical structure caspase complex membrane protein complex GPI-anchor transamidase complex transferase complex endomembrane system endoplasmic reticulum subcompartment intracellular organelle nuclear outer membrane-endoplasmic reticulum membrane network endopeptidase complex cellular anatomical structure membrane membrane-bounded organelle protein-containing complex intracellular anatomical structure caspase complex membrane protein complex GPI-anchor transamidase complex transferase complex endomembrane system endoplasmic reticulum subcompartment intracellular organelle nuclear outer membrane-endoplasmic reticulum membrane network endopeptidase complex endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane catalytic complex organelle subcompartment peptidase complex intracellular membrane-bounded organelle organelle endoplasmic reticulum cytoplasm organelle membrane
C [auth S]	GPI transamidase component PIG-S	-	biosynthetic process GPI anchored protein biosynthesis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process protein maturation glycolipid metabolic process glycerophospholipid metabolic process carbohydrate derivative metabolic process lipid biosynthetic process biosynthetic process GPI anchored protein biosynthesis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process protein maturation glycolipid metabolic process glycerophospholipid metabolic process carbohydrate derivative metabolic process lipid biosynthetic process GPI anchor biosynthetic process GPI anchor metabolic process phospholipid metabolic process phosphate-containing compound metabolic process phosphorus metabolic process carbohydrate derivative biosynthetic process glycerophospholipid biosynthetic process liposaccharide metabolic process glycolipid biosynthetic process phospholipid biosynthetic process glycerolipid biosynthetic process organophosphate metabolic process organophosphate biosynthetic process glycerolipid metabolic process lipid metabolic process attachment of GPI anchor to protein	cellular anatomical structure membrane membrane-bounded organelle protein-containing complex intracellular anatomical structure caspase complex membrane protein complex GPI-anchor transamidase complex transferase complex endomembrane system endoplasmic reticulum subcompartment intracellular organelle nuclear outer membrane-endoplasmic reticulum membrane network endopeptidase complex cellular anatomical structure membrane membrane-bounded organelle protein-containing complex intracellular anatomical structure caspase complex membrane protein complex GPI-anchor transamidase complex transferase complex endomembrane system endoplasmic reticulum subcompartment intracellular organelle nuclear outer membrane-endoplasmic reticulum membrane network endopeptidase complex endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane catalytic complex organelle subcompartment peptidase complex intracellular membrane-bounded organelle organelle endoplasmic reticulum cytoplasm organelle membrane
D [auth T]	GPI transamidase component PIG-T	binding lipid binding phospholipid binding GPI anchor binding glycolipid binding carbohydrate derivative binding	biosynthetic process GPI anchored protein biosynthesis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process protein maturation developmental process multicellular organismal process cellular developmental process nervous system development biosynthetic process GPI anchored protein biosynthesis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process protein maturation developmental process multicellular organismal process cellular developmental process nervous system development generation of neurons neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development system development neuron apoptotic process apoptotic process cell death programmed cell death glycolipid metabolic process glycerophospholipid metabolic process carbohydrate derivative metabolic process lipid biosynthetic process GPI anchor biosynthetic process GPI anchor metabolic process phospholipid metabolic process phosphate-containing compound metabolic process phosphorus metabolic process carbohydrate derivative biosynthetic process glycerophospholipid biosynthetic process liposaccharide metabolic process glycolipid biosynthetic process phospholipid biosynthetic process glycerolipid biosynthetic process organophosphate metabolic process organophosphate biosynthetic process glycerolipid metabolic process lipid metabolic process attachment of GPI anchor to protein	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure cytoplasmic vesicle organelle intracellular vesicle cytoplasm intracellular membrane-bounded organelle vesicle membrane protein-containing complex caspase complex membrane protein complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure cytoplasmic vesicle organelle intracellular vesicle cytoplasm intracellular membrane-bounded organelle vesicle membrane protein-containing complex caspase complex membrane protein complex GPI-anchor transamidase complex transferase complex endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endopeptidase complex endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane catalytic complex organelle subcompartment peptidase complex endoplasmic reticulum organelle membrane
E [auth U]	Phosphatidylinositol glycan anchor biosynthesis class U protein	binding lipid binding phospholipid binding GPI anchor binding glycolipid binding carbohydrate derivative binding	cellular response to stimulus cell surface receptor signaling pathway via STAT regulation of biological process regulation of signaling regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation regulation of signal transduction cell communication regulation of response to stimulus regulation of receptor signaling pathway via JAK-STAT regulation of cell communication cellular response to stimulus cell surface receptor signaling pathway via STAT regulation of biological process regulation of signaling regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation regulation of signal transduction cell communication regulation of response to stimulus regulation of receptor signaling pathway via JAK-STAT regulation of cell communication cellular process signal transduction regulation of receptor signaling pathway via STAT cell surface receptor signaling pathway via JAK-STAT biosynthetic process GPI anchored protein biosynthesis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process protein maturation glycolipid metabolic process glycerophospholipid metabolic process carbohydrate derivative metabolic process lipid biosynthetic process GPI anchor biosynthetic process GPI anchor metabolic process phospholipid metabolic process phosphate-containing compound metabolic process phosphorus metabolic process carbohydrate derivative biosynthetic process glycerophospholipid biosynthetic process liposaccharide metabolic process glycolipid biosynthetic process phospholipid biosynthetic process glycerolipid biosynthetic process organophosphate metabolic process organophosphate biosynthetic process glycerolipid metabolic process lipid metabolic process attachment of GPI anchor to protein	cell periphery cellular anatomical structure plasma membrane membrane membrane-bounded organelle protein-containing complex intracellular anatomical structure caspase complex membrane protein complex GPI-anchor transamidase complex transferase complex endomembrane system endoplasmic reticulum subcompartment intracellular organelle cell periphery cellular anatomical structure plasma membrane membrane membrane-bounded organelle protein-containing complex intracellular anatomical structure caspase complex membrane protein complex GPI-anchor transamidase complex transferase complex endomembrane system endoplasmic reticulum subcompartment intracellular organelle nuclear outer membrane-endoplasmic reticulum membrane network endopeptidase complex endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane catalytic complex organelle subcompartment peptidase complex intracellular membrane-bounded organelle organelle endoplasmic reticulum cytoplasm organelle membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth G]	IPR007246	GPI transamidase component Gaa1	Family
B [auth K]	IPR028361	GPI-anchor transamidase	Family
B [auth K]	IPR001096	Peptidase C13, legumain	Family
C [auth S]	IPR019540	Phosphatidylinositol-glycan biosynthesis class S protein	Family
D [auth T]	IPR007245	GPI transamidase component PIG-T	Family
E [auth U]	IPR009600	GPI transamidase subunit PIG-U	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth G]	Pharos: O43292	Ataxias, Hereditary intellectual disability bipolar I disorder Friedreich ataxia diabetes mellitus glycosylphosphatidylinositol biosynthesis defect 15
B [auth K]	Pharos: Q92643	adenoma breast cancer glioblastoma ovarian cancer astrocytic tumor diabetes mellitus large cell medulloblastoma plasma cell myeloma atypical teratoid rhabdoid tumor epilepsy oligodendroglioma tuberculosis
C [auth S]	Pharos: Q96S52	epilepsy Malignant neoplasm of breast
D [auth T]	Pharos: Q969N2	multiple congenital anomalies-hypotonia-seizures syndrome 3 acquired paroxysmal nocturnal hemoglobinuria paroxysmal nocturnal hemoglobinuria 2 congenital disorder of glycosylation Epileptic encephalopathy intellectual disability congenital anemia epilepsy
E [auth U]	Pharos: Q9H490	melanoma cutaneous melanoma vascular disease epilepsy ovarian cancer heart disease skin carcinoma

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A [auth G], B [auth K], C [auth S], D [auth T], E [auth U]	OPM	Transmembrane	Alpha-helical polytopic	GPI transamidase complex	GPI transamidase complex

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A [auth G], B [auth K], C [auth S], D [auth T], E [auth U]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A [auth G], B [auth K], C [auth S], D [auth T], E [auth U]	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A [auth G], B [auth K], C [auth S], D [auth T], E [auth U]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Cysteine Proteases	Glycosylphosphatidylinositol (GPI) transamidase complex

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.