6SUR | pdb_00006sur

The Rab33B-Atg16L1 crystal structure

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Ras-like P-loop GTPases	8057384	3002022	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ras-like P-loop GTPases	8057384	3002022	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ras-like P-loop GTPases	8057384	3002022	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ras-like P-loop GTPases	8057384	3002022	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ras-like P-loop GTPases	8057384	3002022	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ras-like P-loop GTPases	8057384	3002022	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	Glyco_hydro_42	e6surF1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_42	ECOD (develop294)
E	Glyco_hydro_42	e6surE1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_42	ECOD (develop294)
D	Glyco_hydro_42	e6surD1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_42	ECOD (develop294)
C	Glyco_hydro_42	e6surC1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_42	ECOD (develop294)
B	Glyco_hydro_42	e6surB1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_42	ECOD (develop294)
A	Anticodon_3	e6surA1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Anticodon_3	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF00071	Ras family (Ras)	Ras family	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motili ...	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G [auth I], H [auth J], I [auth K], J [auth L], K [auth M], G [auth I], H [auth J], I [auth K], J [auth L], K [auth M], L [auth N]	Autophagy-related protein 16-1	protein binding binding enzyme binding GTPase binding protein-membrane adaptor activity protein-macromolecule adaptor activity molecular adaptor activity identical protein binding	developmental process corpus callosum development multicellular organismal process head development forebrain development animal organ development brain development nervous system development multicellular organism development central nervous system development anatomical structure development telencephalon development system development cellular developmental process developmental process corpus callosum development multicellular organismal process head development forebrain development animal organ development brain development nervous system development multicellular organism development central nervous system development anatomical structure development telencephalon development system development cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis dendrite development cell differentiation cellular component organization or biogenesis plasma membrane bounded cell projection organization dendrite arborization dendrite morphogenesis cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis neuron projection arborization neuron development cellular process pallium development hippocampus development limbic system development autophagosome assembly catabolic process organelle assembly vacuole organization macroautophagy autophagy autophagosome organization cellular component biogenesis organelle organization cellular component assembly metabolic process process utilizing autophagic mechanism localization establishment of protein localization protein transport transport macromolecule localization intracellular protein localization establishment of localization cellular localization intracellular transport axonal transport axo-dendritic transport establishment of localization in cell microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport microtubule-based movement microtubule-based process biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response xenophagy response to external stimulus response to biotic stimulus defense response to other organism response to stress response to external biotic stimulus microautophagy defense response to virus response to virus regulation of growth regulation of cellular process developmental growth negative regulation of biological process regulation of cell morphogenesis negative regulation of growth negative regulation of dendrite extension regulation of biological process negative regulation of cell growth developmental growth involved in morphogenesis negative regulation of developmental growth regulation of cellular component organization regulation of developmental process cell growth negative regulation of cellular process dendrite extension regulation of anatomical structure morphogenesis neuron projection extension regulation of developmental growth developmental cell growth negative regulation of developmental process growth biological regulation regulation of dendrite extension regulation of cell growth RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process negative stranded viral RNA replication viral genome replication biosynthetic process viral RNA genome replication viral process macromolecule metabolic process positive regulation of autophagy positive regulation of biological process regulation of catabolic process regulation of autophagy positive regulation of catabolic process positive regulation of metabolic process regulation of metabolic process positive regulation of cellular process protein localization to phagophore assembly site	organelle membrane contact site cellular anatomical structure organelle vacuole-isolation membrane contact site membrane-bounded organelle intracellular anatomical structure axoneme ciliary plasm cilium intracellular membraneless organelle plasma membrane bounded cell projection intracellular organelle cell projection cytoskeleton organelle membrane contact site cellular anatomical structure organelle vacuole-isolation membrane contact site membrane-bounded organelle intracellular anatomical structure axoneme ciliary plasm cilium intracellular membraneless organelle plasma membrane bounded cell projection intracellular organelle cell projection cytoskeleton membraneless organelle cytoplasm endosome membrane endolysosome membrane intracellular vesicle lytic vacuole endomembrane system bounding membrane of organelle endolysosome vesicle membrane cytoplasmic vesicle vesicle lysosome vacuolar membrane membrane endosome vacuole intracellular membrane-bounded organelle lytic vacuole membrane cytoplasmic vesicle membrane lysosomal membrane organelle membrane cytosol phagophore assembly site membrane phagophore assembly site sperm midpiece 9+2 motile cilium sperm flagellum motile cilium synapse cell junction glutamatergic synapse protein-containing complex catalytic complex Atg12-Atg5-Atg16 complex transferase complex autophagosome autophagosome membrane axon neuron projection
A, B, C, D, E A, B, C, D, E, F	Ras-related protein Rab-33B	binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding pyrophosphatase activity GTPase activity G protein activity ribonucleoside triphosphate phosphatase activity molecular function regulator activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity cation binding metal ion binding	autophagosome assembly catabolic process organelle assembly vacuole organization macroautophagy autophagy autophagosome organization cellular component biogenesis cellular component organization organelle organization cellular component assembly cellular process metabolic process cellular component organization or biogenesis autophagosome assembly catabolic process organelle assembly vacuole organization macroautophagy autophagy autophagosome organization cellular component biogenesis cellular component organization organelle organization cellular component assembly cellular process metabolic process cellular component organization or biogenesis process utilizing autophagic mechanism regulation of localization regulation of cellular process transport regulation of constitutive secretory pathway negative regulation of biological process negative regulation of transport vesicle-mediated transport localization secretion by cell regulation of secretion by cell negative regulation of secretion negative regulation of exocytosis negative regulation of cellular process negative regulation of secretion by cell regulation of biological process secretion regulation of transport biological regulation export from cell regulation of vesicle-mediated transport establishment of localization regulation of secretion exocytosis constitutive secretory pathway regulation of exocytosis negative regulation of constitutive secretory pathway establishment of protein localization protein transport macromolecule localization intracellular protein localization cellular response to stimulus small GTPase-mediated signal transduction response to stimulus signaling intracellular signal transduction cell communication intracellular signaling cassette Rab protein signal transduction signal transduction Golgi vesicle transport intra-Golgi vesicle-mediated transport developmental process multicellular organism development multicellular organismal process anatomical structure morphogenesis skeletal system development anatomical structure development animal organ development skeletal system morphogenesis animal organ morphogenesis system development protein localization to Golgi apparatus protein localization to organelle regulation of retrograde vesicle-mediated transport, Golgi to ER retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum regulation of cellular component organization regulation of organelle organization regulation of Golgi organization Golgi organization endomembrane system organization protein localization to phagophore assembly site	phagophore assembly site membrane cellular anatomical structure intracellular anatomical structure membrane phagophore assembly site cytoplasm presynapse synapse cell junction membrane-bounded organelle Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system phagophore assembly site membrane cellular anatomical structure intracellular anatomical structure membrane phagophore assembly site cytoplasm presynapse synapse cell junction membrane-bounded organelle Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen Golgi lumen intracellular organelle organelle lumen organelle endosome intracellular vesicle cytoplasmic vesicle vesicle Golgi membrane bounding membrane of organelle organelle membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
G [auth I], H [auth J], I [auth K], J [auth L], K [auth M], G [auth I], H [auth J], I [auth K], J [auth L], K [auth M], L [auth N]	IPR045160	Autophagy-related protein 16	Family
G [auth I], H [auth J], I [auth K], J [auth L], K [auth M], G [auth I], H [auth J], I [auth K], J [auth L], K [auth M], L [auth N]	IPR019775	WD40 repeat, conserved site	Conserved Site
G [auth I], H [auth J], I [auth K], J [auth L], K [auth M], G [auth I], H [auth J], I [auth K], J [auth L], K [auth M], L [auth N]	IPR020472	PAC1/LIS1-like, WD-40 repeat	Repeat
G [auth I], H [auth J], I [auth K], J [auth L], K [auth M], G [auth I], H [auth J], I [auth K], J [auth L], K [auth M], L [auth N]	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
G [auth I], H [auth J], I [auth K], J [auth L], K [auth M], G [auth I], H [auth J], I [auth K], J [auth L], K [auth M], L [auth N]	IPR013923	Autophagy-related protein 16 domain	Domain
G [auth I], H [auth J], I [auth K], J [auth L], K [auth M], G [auth I], H [auth J], I [auth K], J [auth L], K [auth M], L [auth N]	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
G [auth I], H [auth J], I [auth K], J [auth L], K [auth M], G [auth I], H [auth J], I [auth K], J [auth L], K [auth M], L [auth N]	IPR001680	WD40 repeat	Repeat
A, B, C, D, E A, B, C, D, E, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR041822	Rab33A/B	Family
A, B, C, D, E A, B, C, D, E, F	IPR005225	Small GTP-binding domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR001806	Small GTPase	Family

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.