9OT6 | pdb_00009ot6

Cryo-EM structure of the PI4KA complex bound to an EFR3 interfering nanobody (F3IN)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E	SCOP2B Superfamily	Hyccin repeat-like	8091061	3002479	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Hyccin repeat-like	8091062	3002479	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Hyccin repeat-like	8091061	3002479	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Hyccin repeat-like	8091062	3002479	SCOP2B (2022-06-29)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C, H	Heavy Chain	IGHV1	-	tetratricopeptide repeat protein 7b \| hyccin	SAbDab (2026-01-09)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D, F	PF13181	Tetratricopeptide repeat (TPR_8)	Tetratricopeptide repeat	-	Repeat
D, F	PF12895	Anaphase-promoting complex, cyclosome, subunit 3 (ANAPC3)	Anaphase-promoting complex, cyclosome, subunit 3	-	Repeat
D, F	PF13424	Tetratricopeptide repeat (TPR_12)	Tetratricopeptide repeat	-	Repeat
A, B	PF00613	Phosphoinositide 3-kinase family, accessory domain (PIK domain) (PI3Ka)	Phosphoinositide 3-kinase family, accessory domain (PIK domain)	-	Repeat
A, B	PF19274	PI4-kinase N-terminal region (PI4K_N)	PI4-kinase N-terminal region	-	Family
A, B	PF00454	Phosphatidylinositol 3- and 4-kinase (PI3_PI4_kinase)	Phosphatidylinositol 3- and 4-kinase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, H	EFR3 interfering Nanobody (F3IN)	-	-	-
D, F	Tetratricopeptide repeat protein 7B	-	localization protein localization to cell periphery cellular localization protein localization to plasma membrane macromolecule localization cellular process intracellular protein localization localization within membrane protein localization to membrane phosphatidylinositol metabolic process glycerophospholipid biosynthetic process glycerophospholipid metabolic process lipid biosynthetic process primary metabolic process localization protein localization to cell periphery cellular localization protein localization to plasma membrane macromolecule localization cellular process intracellular protein localization localization within membrane protein localization to membrane phosphatidylinositol metabolic process glycerophospholipid biosynthetic process glycerophospholipid metabolic process lipid biosynthetic process primary metabolic process phosphatidylinositol phosphate biosynthetic process phospholipid biosynthetic process phosphatidylinositol biosynthetic process phospholipid metabolic process biosynthetic process glycerolipid biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process metabolic process glycerolipid metabolic process phosphorus metabolic process lipid metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane
E, G	Hyccin	-	myelination developmental process multicellular organism development multicellular organismal process axon ensheathment ensheathment of neurons anatomical structure development cellular process nervous system development system development localization protein localization to cell periphery cellular localization protein localization to plasma membrane myelination developmental process multicellular organism development multicellular organismal process axon ensheathment ensheathment of neurons anatomical structure development cellular process nervous system development system development localization protein localization to cell periphery cellular localization protein localization to plasma membrane macromolecule localization intracellular protein localization localization within membrane protein localization to membrane phosphatidylinositol metabolic process glycerophospholipid biosynthetic process glycerophospholipid metabolic process lipid biosynthetic process primary metabolic process phosphatidylinositol phosphate biosynthetic process phospholipid biosynthetic process phosphatidylinositol biosynthetic process phospholipid metabolic process biosynthetic process glycerolipid biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process metabolic process glycerolipid metabolic process phosphorus metabolic process lipid metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane cell projection neuron projection plasma membrane bounded cell projection
A, B	Phosphatidylinositol 4-kinase alpha	1-phosphatidylinositol 4-kinase activity phosphatidylinositol kinase activity kinase activity lipid kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding 1-phosphatidylinositol 4-kinase activity phosphatidylinositol kinase activity kinase activity lipid kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cell adhesion molecule binding cadherin binding protein binding	phosphatidylinositol metabolic process glycerophospholipid biosynthetic process glycerophospholipid metabolic process lipid biosynthetic process primary metabolic process phosphatidylinositol phosphate biosynthetic process phospholipid biosynthetic process phosphatidylinositol biosynthetic process phospholipid metabolic process biosynthetic process glycerolipid biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process phosphatidylinositol metabolic process glycerophospholipid biosynthetic process glycerophospholipid metabolic process lipid biosynthetic process primary metabolic process phosphatidylinositol phosphate biosynthetic process phospholipid biosynthetic process phosphatidylinositol biosynthetic process phospholipid metabolic process biosynthetic process glycerolipid biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process metabolic process cellular process glycerolipid metabolic process phosphorus metabolic process lipid metabolic process biological process involved in interspecies interaction between organisms host-mediated perturbation of viral process modulation of process of another organism host-mediated perturbation of symbiont process cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation signal transduction cell communication intracellular signal transduction phosphatidylinositol-mediated signaling symbiont-mediated perturbation of host membrane symbiont-mediated disruption of host anatomical structure reorganization of cellular membranes to establish viral sites of replication disruption of anatomical structure in another organism symbiont-mediated disruption of host cellular anatomical structure	cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction membrane membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction membrane membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle Golgi-associated vesicle membrane organelle cytoplasm Golgi-associated vesicle vesicle organelle membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytosol cell periphery plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D, F	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily
D, F	IPR045819	Tetratricopeptide repeat protein 7, N-terminal	Domain
D, F	IPR019734	Tetratricopeptide repeat	Repeat
D, F	IPR051722	Endocytosis and PI4K-regulating protein	Family
E, G	IPR018619	Hyccin	Family
A, B	IPR015433	Phosphatidylinositol 3-/4-kinase	Family
A, B	IPR016024	Armadillo-type fold	Homologous Superfamily
A, B	IPR000403	Phosphatidylinositol 3-/4-kinase, catalytic domain	Domain
A, B	IPR001263	Phosphoinositide 3-kinase, accessory (PIK) domain	Domain
A, B	IPR018936	Phosphatidylinositol 3-/4-kinase, conserved site	Conserved Site
A, B	IPR042236	Phosphoinositide 3-kinase, accessory (PIK) domain superfamily	Homologous Superfamily
A, B	IPR036940	Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily	Homologous Superfamily
A, B	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, B	IPR045495	PI4-kinase, N-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D, F	Pharos: Q86TV6	astrocytic tumor exocrine pancreatic carcinoma lung adenocarcinoma malignant pancreatic neoplasm osteosarcoma pancreatic intraductal papillary-mucinous neoplasm primitive neuroectodermal tumor atypical teratoid rhabdoid tumor glioblastoma malignant ependymoma medulloblastoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia subependymal giant cell astrocytoma ductal breast carcinoma in situ astrocytic tumor exocrine pancreatic carcinoma lung adenocarcinoma malignant pancreatic neoplasm osteosarcoma pancreatic intraductal papillary-mucinous neoplasm primitive neuroectodermal tumor atypical teratoid rhabdoid tumor glioblastoma malignant ependymoma medulloblastoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia subependymal giant cell astrocytoma ductal breast carcinoma in situ invasive ductal breast carcinoma malignant glioma oligodendroglioma pancreatic intraductal papillary-mucinous carcinoma pilocytic astrocytoma
E, G	Pharos: Q9BYI3	hypomyelinating leukodystrophy 5 leukodystrophy intellectual disability cataract Mental deficiency pancreatic intraductal papillary-mucinous carcinoma peripheral neuropathy amyotrophic lateral sclerosis Sjogren syndrome breast carcinoma drug dependence substance-related disorder ductal breast carcinoma in situ hereditary spastic paraplegia invasive ductal breast carcinoma hypomyelinating leukodystrophy 5 leukodystrophy intellectual disability cataract Mental deficiency pancreatic intraductal papillary-mucinous carcinoma peripheral neuropathy amyotrophic lateral sclerosis Sjogren syndrome breast carcinoma drug dependence substance-related disorder ductal breast carcinoma in situ hereditary spastic paraplegia invasive ductal breast carcinoma malignant glioma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia atypical teratoid rhabdoid tumor subependymal giant cell astrocytoma substance dependence facioscapulohumeral muscular dystrophy medulloblastoma myopathy ovarian cancer peripheral nervous system disease breast cancer substance abuse ulcerative colitis glioblastoma lung carcinoma
A, B	Pharos: P42356	polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis acute myeloid leukemia atypical teratoid rhabdoid tumor heparin cofactor 2 deficiency malignant ependymoma medulloblastoma osteosarcoma Pick disease primitive neuroectodermal tumor arthrogryposis Cerebellar Hypoplasia hereditary spastic paraplegia malignant glioma neurodegenerative disease ovarian cancer polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis acute myeloid leukemia atypical teratoid rhabdoid tumor heparin cofactor 2 deficiency malignant ependymoma medulloblastoma osteosarcoma Pick disease primitive neuroectodermal tumor arthrogryposis Cerebellar Hypoplasia hereditary spastic paraplegia malignant glioma neurodegenerative disease ovarian cancer pilocytic astrocytoma schizophrenia astrocytic tumor glioblastoma large cell medulloblastoma malignant mesothelioma oligodendroglioma

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.