Annotations: 8JG5

Cryo-EM structure of the GI.4 Chiba VLP complexed with the CV-1A1 Fv-clasp

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
E	DNA_topoisoIV	e8jg5E1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
C	TcdA_TcdB_pore	e8jg5C01	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: TcdA_TcdB_pore	ECOD (v294.2)
F	DNA_topoisoIV	e8jg5F1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
D	TcdA_TcdB_pore	e8jg5D01	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: TcdA_TcdB_pore	ECOD (v294.2)
G	DNA_topoisoIV	e8jg5G1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
B	DNA_topoisoIV	e8jg5B1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
A	TcdA_TcdB_pore	e8jg5A01	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: TcdA_TcdB_pore	ECOD (v294.2)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C, E	Heavy Chain	IGHV1	-	vp1	SAbDab (2026-06-05)
D, F	Light Chain	IGLV2	Lambda	vp1	SAbDab (2026-06-05)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, E	PF11629	C terminal SARAH domain of Mst1 (Mst1_SARAH)	C terminal SARAH domain of Mst1	-	Family
D, F	PF11629	C terminal SARAH domain of Mst1 (Mst1_SARAH)	C terminal SARAH domain of Mst1	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, E	VH,SARAH	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 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 catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups enzyme regulator activity protein serine/threonine kinase activator activity kinase activator activity enzyme activator activity molecular function activator activity molecular function regulator activity protein kinase activator activity protein kinase regulator activity kinase regulator activity identical protein binding protein binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding protein serine kinase activity cation binding magnesium ion binding metal ion binding protein homodimerization activity protein dimerization activity protein serine/threonine kinase activity	regulation of protein stability biological regulation regulation of biological quality protein stabilization developmental process multicellular organism development multicellular organismal process central nervous system development anatomical structure development nervous system development system development positive regulation of locomotion regulation of cellular process regulation of cell motility regulation of protein stability biological regulation regulation of biological quality protein stabilization developmental process multicellular organism development multicellular organismal process central nervous system development anatomical structure development nervous system development system development positive regulation of locomotion regulation of cellular process regulation of cell motility regulation of substrate-dependent cell migration, cell attachment to substrate positive regulation of biological process positive regulation of cell migration cell adhesion positive regulation of cell-substrate adhesion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion positive regulation of cellular process regulation of biological process regulation of cell-substrate adhesion positive regulation of cell adhesion regulation of cell adhesion cell-substrate adhesion regulation of locomotion substrate-dependent cell migration substrate-dependent cell migration, cell attachment to substrate cellular process positive regulation of substrate-dependent cell migration, cell attachment to substrate cellular response to stimulus cell surface receptor signaling pathway response to stimulus signaling canonical Wnt signaling pathway cell communication signal transduction Wnt signaling pathway cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein tetramerization protein-containing complex assembly cellular component organization or biogenesis apoptotic process cell death programmed cell death negative regulation of signaling regulation of canonical Wnt signaling pathway negative regulation of biological process regulation of signal transduction negative regulation of cell communication negative regulation of Wnt signaling pathway negative regulation of cellular process regulation of signaling regulation of Wnt signaling pathway negative regulation of response to stimulus negative regulation of signal transduction negative regulation of canonical Wnt signaling pathway regulation of response to stimulus regulation of cell communication positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death positive regulation of apoptotic process regulation of MAPK cascade intracellular signal transduction regulation of intracellular signal transduction intracellular signaling cassette MAPK cascade regulation of growth regulation of developmental growth regulation of developmental process developmental growth negative regulation of developmental process growth organ growth negative regulation of organ growth negative regulation of developmental growth negative regulation of growth regulation of organ growth regulation of multicellular organismal process negative regulation of multicellular organismal process positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process regulation of peptidyl-serine phosphorylation positive regulation of phosphate metabolic process peptidyl-serine modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process peptidyl-serine phosphorylation phosphate-containing compound metabolic process peptidyl-amino acid modification positive regulation of macromolecule metabolic process protein metabolic process positive regulation of protein phosphorylation protein modification process protein phosphorylation phosphorylation regulation of protein metabolic process primary metabolic process regulation of macromolecule metabolic process positive regulation of peptidyl-serine phosphorylation macromolecule modification metabolic process regulation of phosphorylation macromolecule metabolic process regulation of metabolic process cellular developmental process primitive hemopoiesis hemopoiesis animal organ development cell development embryo development embryonic hemopoiesis cell differentiation embryonic organ development establishment of protein localization cellular localization nucleocytoplasmic transport transport nuclear transport intracellular transport protein localization to nucleus establishment of localization localization intercellular transport import into nucleus establishment of protein localization to organelle protein transport establishment of localization in cell macromolecule localization protein localization to organelle protein import into nucleus intracellular protein localization intracellular protein transport embryonic epithelial tube formation chordate embryonic development tube formation epithelial tube formation tube morphogenesis embryo development ending in birth or egg hatching epithelial tube morphogenesis morphogenesis of embryonic epithelium epithelium development neural tube development tube development embryonic morphogenesis morphogenesis of an epithelium tissue development tissue morphogenesis anatomical structure morphogenesis neural tube formation anatomical structure formation involved in morphogenesis extrinsic apoptotic signaling pathway via death domain receptors extrinsic apoptotic signaling pathway apoptotic signaling pathway protein autophosphorylation branching morphogenesis of an epithelial tube angiogenesis blood vessel development blood vessel morphogenesis vasculature development circulatory system development branching involved in blood vessel morphogenesis morphogenesis of a branching structure morphogenesis of a branching epithelium cell morphogenesis fat cell differentiation positive regulation of fat cell differentiation regulation of cell differentiation positive regulation of developmental process positive regulation of cell differentiation regulation of fat cell differentiation negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation regulation of epithelial cell proliferation epithelial cell proliferation negative regulation of epithelial cell proliferation epidermal cell differentiation epidermis development epithelial cell differentiation skin development keratinocyte differentiation positive regulation of epithelial cell apoptotic process regulation of epithelial cell apoptotic process positive regulation of hepatocyte apoptotic process epithelial cell apoptotic process regulation of hepatocyte apoptotic process hepatocyte apoptotic process hippo signaling positive regulation of cell communication positive regulation of signal transduction positive regulation of response to stimulus positive regulation of intracellular signal transduction positive regulation of hippo signaling regulation of hippo signaling positive regulation of signaling heart development endocardium development positive regulation of apoptotic signaling pathway positive regulation of extrinsic apoptotic signaling pathway via death domain receptors positive regulation of extrinsic apoptotic signaling pathway regulation of extrinsic apoptotic signaling pathway regulation of extrinsic apoptotic signaling pathway via death domain receptors regulation of apoptotic signaling pathway cell differentiation involved in embryonic placenta development placenta development reproductive process developmental process involved in reproduction in utero embryonic development embryonic placenta development regulation of cell differentiation involved in embryonic placenta development regulation of reproductive process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen protein-containing complex intracellular membraneless organelle nuclear body membraneless organelle
D, F	VL,SARAH	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 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 catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups enzyme regulator activity protein serine/threonine kinase activator activity kinase activator activity enzyme activator activity molecular function activator activity molecular function regulator activity protein kinase activator activity protein kinase regulator activity kinase regulator activity identical protein binding protein binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding protein serine kinase activity cation binding magnesium ion binding metal ion binding protein homodimerization activity protein dimerization activity protein serine/threonine kinase activity	regulation of protein stability biological regulation regulation of biological quality protein stabilization developmental process multicellular organism development multicellular organismal process central nervous system development anatomical structure development nervous system development system development positive regulation of locomotion regulation of cellular process regulation of cell motility regulation of protein stability biological regulation regulation of biological quality protein stabilization developmental process multicellular organism development multicellular organismal process central nervous system development anatomical structure development nervous system development system development positive regulation of locomotion regulation of cellular process regulation of cell motility regulation of substrate-dependent cell migration, cell attachment to substrate positive regulation of biological process positive regulation of cell migration cell adhesion positive regulation of cell-substrate adhesion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion positive regulation of cellular process regulation of biological process regulation of cell-substrate adhesion positive regulation of cell adhesion regulation of cell adhesion cell-substrate adhesion regulation of locomotion substrate-dependent cell migration substrate-dependent cell migration, cell attachment to substrate cellular process positive regulation of substrate-dependent cell migration, cell attachment to substrate cellular response to stimulus cell surface receptor signaling pathway response to stimulus signaling canonical Wnt signaling pathway cell communication signal transduction Wnt signaling pathway cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein tetramerization protein-containing complex assembly cellular component organization or biogenesis apoptotic process cell death programmed cell death negative regulation of signaling regulation of canonical Wnt signaling pathway negative regulation of biological process regulation of signal transduction negative regulation of cell communication negative regulation of Wnt signaling pathway negative regulation of cellular process regulation of signaling regulation of Wnt signaling pathway negative regulation of response to stimulus negative regulation of signal transduction negative regulation of canonical Wnt signaling pathway regulation of response to stimulus regulation of cell communication positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death positive regulation of apoptotic process regulation of MAPK cascade intracellular signal transduction regulation of intracellular signal transduction intracellular signaling cassette MAPK cascade regulation of growth regulation of developmental growth regulation of developmental process developmental growth negative regulation of developmental process growth organ growth negative regulation of organ growth negative regulation of developmental growth negative regulation of growth regulation of organ growth regulation of multicellular organismal process negative regulation of multicellular organismal process positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process regulation of peptidyl-serine phosphorylation positive regulation of phosphate metabolic process peptidyl-serine modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process peptidyl-serine phosphorylation phosphate-containing compound metabolic process peptidyl-amino acid modification positive regulation of macromolecule metabolic process protein metabolic process positive regulation of protein phosphorylation protein modification process protein phosphorylation phosphorylation regulation of protein metabolic process primary metabolic process regulation of macromolecule metabolic process positive regulation of peptidyl-serine phosphorylation macromolecule modification metabolic process regulation of phosphorylation macromolecule metabolic process regulation of metabolic process cellular developmental process primitive hemopoiesis hemopoiesis animal organ development cell development embryo development embryonic hemopoiesis cell differentiation embryonic organ development establishment of protein localization cellular localization nucleocytoplasmic transport transport nuclear transport intracellular transport protein localization to nucleus establishment of localization localization intercellular transport import into nucleus establishment of protein localization to organelle protein transport establishment of localization in cell macromolecule localization protein localization to organelle protein import into nucleus intracellular protein localization intracellular protein transport embryonic epithelial tube formation chordate embryonic development tube formation epithelial tube formation tube morphogenesis embryo development ending in birth or egg hatching epithelial tube morphogenesis morphogenesis of embryonic epithelium epithelium development neural tube development tube development embryonic morphogenesis morphogenesis of an epithelium tissue development tissue morphogenesis anatomical structure morphogenesis neural tube formation anatomical structure formation involved in morphogenesis extrinsic apoptotic signaling pathway via death domain receptors extrinsic apoptotic signaling pathway apoptotic signaling pathway protein autophosphorylation branching morphogenesis of an epithelial tube angiogenesis blood vessel development blood vessel morphogenesis vasculature development circulatory system development branching involved in blood vessel morphogenesis morphogenesis of a branching structure morphogenesis of a branching epithelium cell morphogenesis fat cell differentiation positive regulation of fat cell differentiation regulation of cell differentiation positive regulation of developmental process positive regulation of cell differentiation regulation of fat cell differentiation negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation regulation of epithelial cell proliferation epithelial cell proliferation negative regulation of epithelial cell proliferation epidermal cell differentiation epidermis development epithelial cell differentiation skin development keratinocyte differentiation positive regulation of epithelial cell apoptotic process regulation of epithelial cell apoptotic process positive regulation of hepatocyte apoptotic process epithelial cell apoptotic process regulation of hepatocyte apoptotic process hepatocyte apoptotic process hippo signaling positive regulation of cell communication positive regulation of signal transduction positive regulation of response to stimulus positive regulation of intracellular signal transduction positive regulation of hippo signaling regulation of hippo signaling positive regulation of signaling heart development endocardium development positive regulation of apoptotic signaling pathway positive regulation of extrinsic apoptotic signaling pathway via death domain receptors positive regulation of extrinsic apoptotic signaling pathway regulation of extrinsic apoptotic signaling pathway regulation of extrinsic apoptotic signaling pathway via death domain receptors regulation of apoptotic signaling pathway cell differentiation involved in embryonic placenta development placenta development reproductive process developmental process involved in reproduction in utero embryonic development embryonic placenta development regulation of cell differentiation involved in embryonic placenta development regulation of reproductive process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen protein-containing complex intracellular membraneless organelle nuclear body membraneless organelle
A, B, G	VP1	-	-	virion component host cellular component host intracellular part cellular anatomical structure host cell cytoplasm host cell part host intracellular region other organism part

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, E	IPR036674	p53-like tetramerisation domain superfamily	Homologous Superfamily
C, E	IPR000719	Protein kinase domain	Domain
C, E	IPR017441	Protein kinase, ATP binding site	Binding Site
C, E	IPR011524	SARAH domain	Domain
C, E	IPR024205	Mst1/2 SARAH domain	Domain
C, E	IPR050629	STE20/SPS1-related Proline-Alanine-rich Kinase	Family
C, E	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
D, F	IPR036674	p53-like tetramerisation domain superfamily	Homologous Superfamily
D, F	IPR000719	Protein kinase domain	Domain
D, F	IPR017441	Protein kinase, ATP binding site	Binding Site
D, F	IPR011524	SARAH domain	Domain
D, F	IPR024205	Mst1/2 SARAH domain	Domain
D, F	IPR050629	STE20/SPS1-related Proline-Alanine-rich Kinase	Family
D, F	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, B, G	IPR029053	Viral coat protein subunit	Homologous Superfamily
A, B, G	IPR004005	Calicivirus coat protein	Domain
A, B, G	IPR013643	Calicivirus coat protein C-terminal	Domain
A, B, G	IPR033703	Picornavirus/Calicivirus coat protein	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, E	: Q13043	combined immunodeficiency due to STK4 deficiency pancreatic intraductal papillary-mucinous carcinoma Pancreatic Neuroendocrine Tumor acute myeloid leukemia gastrointestinal stromal tumor large cell medulloblastoma mast cell leukemia ovarian cancer pancreatic intraductal papillary-mucinous neoplasm psoriasis aggressive systemic mastocytosis cutaneous lupus erythematosus idiopathic pulmonary fibrosis interstitial lung disease lung carcinoma combined immunodeficiency due to STK4 deficiency pancreatic intraductal papillary-mucinous carcinoma Pancreatic Neuroendocrine Tumor acute myeloid leukemia gastrointestinal stromal tumor large cell medulloblastoma mast cell leukemia ovarian cancer pancreatic intraductal papillary-mucinous neoplasm psoriasis aggressive systemic mastocytosis cutaneous lupus erythematosus idiopathic pulmonary fibrosis interstitial lung disease lung carcinoma non-small cell lung carcinoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia renal cell carcinoma bipolar disorder endogenous depression interstitial cystitis invasive ductal breast carcinoma malignant pancreatic neoplasm osteosarcoma
D, F	: Q13043	combined immunodeficiency due to STK4 deficiency pancreatic intraductal papillary-mucinous carcinoma Pancreatic Neuroendocrine Tumor acute myeloid leukemia gastrointestinal stromal tumor large cell medulloblastoma mast cell leukemia ovarian cancer pancreatic intraductal papillary-mucinous neoplasm psoriasis aggressive systemic mastocytosis cutaneous lupus erythematosus idiopathic pulmonary fibrosis interstitial lung disease lung carcinoma combined immunodeficiency due to STK4 deficiency pancreatic intraductal papillary-mucinous carcinoma Pancreatic Neuroendocrine Tumor acute myeloid leukemia gastrointestinal stromal tumor large cell medulloblastoma mast cell leukemia ovarian cancer pancreatic intraductal papillary-mucinous neoplasm psoriasis aggressive systemic mastocytosis cutaneous lupus erythematosus idiopathic pulmonary fibrosis interstitial lung disease lung carcinoma non-small cell lung carcinoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia renal cell carcinoma bipolar disorder endogenous depression interstitial cystitis invasive ductal breast carcinoma malignant pancreatic neoplasm osteosarcoma

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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.