5W9A

The structure of the Trim5alpha Bbox- coiled coil in complex LC3B

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B [auth C]	d5w9ac_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	GABARAP-like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth D]	d5w9ad_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	GABARAP-like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth B]	SCOP2B Superfamily	B-box zinc-binding domain	8062665	3001359	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	B-box zinc-binding domain	8062665	3001359	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	Ubiquitin-like	8038494	3000157	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	Ubiquitin-like	8038494	3000157	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)
D [auth B]	zf-B_box	e5w9aB1	A: few secondary structure elements	X: B-box zinc-binding domain-like	H: B-box zinc-binding domain (From Topology)	T: B-box zinc-binding domain	F: zf-B_box	ECOD (1.6)
A	zf-B_box	e5w9aA1	A: few secondary structure elements	X: B-box zinc-binding domain-like	H: B-box zinc-binding domain (From Topology)	T: B-box zinc-binding domain	F: zf-B_box	ECOD (1.6)
B [auth C]	Atg8	e5w9aC1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Atg8	ECOD (1.6)
C [auth D]	Atg8	e5w9aD1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Atg8	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth C]	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
C [auth D]	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D [auth B]	PF00643	B-box zinc finger (zf-B_box)	B-box zinc finger	-	Domain
B [auth C], C [auth D]	PF02991	Autophagy protein Atg8 ubiquitin like (ATG8)	Autophagy protein Atg8 ubiquitin like	Light chain 3 is proposed to function primarily as a subunit of microtubule associated proteins 1A and 1B and that its expression may regulate microtubule binding activity [1]. Autophagy is generally known as a process involved in the degradation of ...	Light chain 3 is proposed to function primarily as a subunit of microtubule associated proteins 1A and 1B and that its expression may regulate microtubule binding activity [1]. Autophagy is generally known as a process involved in the degradation of bulk cytoplasmic components that are non-specifically sequestered into an autophagosome, where they are sequestered into double-membrane vesicles and delivered to the degradative organelle, the lysosome/vacuole, for breakdown and eventual recycling of the resulting macromolecules. The yeast proteins are involved in the autophagosome, and Atg8 binds Atg19, via its N-terminus and the C-terminus of Atg19.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D [auth B]	Tripartite motif-containing protein 5	molecular transducer activity pattern recognition receptor activity signaling receptor activity aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity identical protein binding protein binding molecular transducer activity pattern recognition receptor activity signaling receptor activity aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity identical protein binding protein binding binding protein homodimerization activity protein dimerization activity kinase binding enzyme binding protein kinase binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	regulation of defense response positive regulation of response to biotic stimulus regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms response to stimulus regulation of response to external stimulus positive regulation of biological process response to biotic stimulus positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of immune response regulation of response to stress response to stress innate immune response regulation of defense response positive regulation of response to biotic stimulus regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms response to stimulus regulation of response to external stimulus positive regulation of biological process response to biotic stimulus positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of immune response regulation of response to stress response to stress innate immune response regulation of immune system process response to external biotic stimulus positive regulation of immune system process regulation of biological process positive regulation of innate immune response defense response immune response response to other organism regulation of innate immune response biological regulation defense response to symbiont response to external stimulus regulation of response to stimulus immune system process defense response to other organism positive regulation of defense response activation of innate immune response regulation of immune response activation of immune response cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction signaling regulation of signal transduction intracellular signal transduction cell communication regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of signaling positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of cell communication regulation of canonical NF-kappaB signal transduction cellular process positive regulation of signaling cellular catabolic process catabolic process cellular metabolic process autophagy metabolic process process utilizing autophagic mechanism positive regulation of DNA-binding transcription factor activity cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process positive regulation of molecular function nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process regulation of molecular function organic cyclic compound metabolic process regulation of gene expression biosynthetic process regulation of DNA-binding transcription factor activity organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process defense response to virus suppression of viral release by host response to virus regulation of lipopolysaccharide-mediated signaling pathway response to organic substance response to lipid cellular response to lipopolysaccharide lipopolysaccharide-mediated signaling pathway cellular response to biotic stimulus response to bacterium cellular response to organic substance cell surface receptor signaling pathway response to oxygen-containing compound cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound cellular response to chemical stimulus response to chemical cellular response to lipid response to molecule of bacterial origin negative regulation of viral life cycle negative regulation of biological process viral life cycle modulation by symbiont of entry into host biological process involved in interaction with host biological process involved in symbiotic interaction regulation of viral entry into host cell regulation of viral life cycle regulation of viral process negative regulation of viral process symbiont entry into host cell viral process symbiont entry into host negative regulation of viral entry into host cell regulation of biological process involved in symbiotic interaction organonitrogen compound metabolic process protein polyubiquitination protein ubiquitination macromolecule modification protein metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal positive regulation of MAPK cascade regulation of MAPK cascade MAPK cascade positive regulation of NF-kappaB transcription factor activity protein K63-linked ubiquitination protein localization regulation of localization cellular localization regulation of protein localization localization regulation of cellular localization cellular macromolecule localization macromolecule localization viral gene expression regulation of viral transcription negative regulation of viral transcription viral transcription negative regulation of viral genome replication viral genome replication regulation of viral genome replication positive regulation of autophagy positive regulation of cellular metabolic process regulation of catabolic process regulation of autophagy positive regulation of catabolic process positive regulation of metabolic process regulation of cellular catabolic process positive regulation of cellular catabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cytoplasmic ribonucleoprotein granule ribonucleoprotein granule intracellular non-membrane-bounded organelle supramolecular complex P-body non-membrane-bounded organelle
B [auth C], C [auth D]	Microtubule-associated proteins 1A/1B light chain 3B	phosphatidylethanolamine binding binding phospholipid binding lipid binding cytoskeletal protein binding microtubule binding protein binding tubulin binding amide binding ceramide binding sphingolipid binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding	cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress cellular process response to starvation cellular response to starvation cellular catabolic process catabolic process macroautophagy cellular metabolic process autophagy cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress cellular process response to starvation cellular response to starvation cellular catabolic process catabolic process macroautophagy cellular metabolic process autophagy metabolic process process utilizing autophagic mechanism cellular component disassembly protein-containing complex organization protein-containing complex disassembly cellular component organization autophagosome maturation cellular component organization or biogenesis cellular response to nitrogen levels cellular response to nitrogen starvation autophagosome assembly organelle assembly vacuole organization autophagosome organization cellular component biogenesis organelle organization cellular component assembly mitophagy organelle disassembly autophagy of mitochondrion mitochondrion organization	cellular anatomical entity endomembrane system membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytoplasmic vesicle intracellular vesicle vesicle vacuole autophagosome cellular anatomical entity endomembrane system membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytoplasmic vesicle intracellular vesicle vesicle vacuole autophagosome vacuolar membrane autophagosome membrane membrane bounding membrane of organelle organelle membrane axoneme ciliary plasm cilium cytoplasmic region plasma membrane bounded cell projection cytoplasm plasma membrane bounded cell projection cell projection cytoskeleton intracellular non-membrane-bounded organelle non-membrane-bounded organelle mitochondrial membrane organelle envelope mitochondrial envelope cytosol polymeric cytoskeletal fiber supramolecular fiber microtubule supramolecular polymer supramolecular complex microtubule cytoskeleton

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D [auth B]	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A, D [auth B]	IPR043136	B30.2/SPRY domain superfamily	Homologous Superfamily
A, D [auth B]	IPR003877	SPRY domain	Domain
A, D [auth B]	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
A, D [auth B]	IPR000315	B-box-type zinc finger	Domain
A, D [auth B]	IPR001870	B30.2/SPRY domain	Domain
A, D [auth B]	IPR027370	Zinc finger, RING-type, eukaryotic	Domain
A, D [auth B]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, D [auth B]	IPR003879	Butyrophylin-like, SPRY domain	Domain
A, D [auth B]	IPR001841	Zinc finger, RING-type	Domain
B [auth C], C [auth D]	IPR004241	Autophagy protein Atg8 ubiquitin-like	Family
B [auth C], C [auth D]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth C], C [auth D]	Pharos: Q9GZQ8	atopic eczema Chemically-Induced Liver Toxicity drug-induced liver injury hepatocellular carcinoma lung cancer pancreatic ductal adenocarcinoma cancer invasive ductal breast carcinoma non-small cell lung carcinoma plasma cell myeloma large cell medulloblastoma ovarian cancer spina bifida

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.