7BQZ

Crystal Structure of Spindlin1 bound to H3(K4me3-K9me3) peptide

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8052901	3000404	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8052900	3000404	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8052902	3000404	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8052900	3000404	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8052902	3000404	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8052901	3000404	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8052901	3000404	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8052900	3000404	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8052902	3000404	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8052902	3000404	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8052901	3000404	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8052900	3000404	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)
C	Spin-Ssty_1	e7bqzC2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Spin-Ssty_1	ECOD (1.6)
C	Spin-Ssty_2	e7bqzC3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Spin-Ssty_2	ECOD (1.6)
C	Spin-Ssty	e7bqzC1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Spin-Ssty	ECOD (1.6)
E	Spin-Ssty_1	e7bqzE3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Spin-Ssty_1	ECOD (1.6)
E	Spin-Ssty_2	e7bqzE1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Spin-Ssty_2	ECOD (1.6)
E	Spin-Ssty	e7bqzE2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Spin-Ssty	ECOD (1.6)
A	Spin-Ssty_1	e7bqzA3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Spin-Ssty_1	ECOD (1.6)
A	Spin-Ssty_2	e7bqzA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Spin-Ssty_2	ECOD (1.6)
A	Spin-Ssty	e7bqzA2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Spin-Ssty	ECOD (1.6)
G	Spin-Ssty_1	e7bqzG1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Spin-Ssty_1	ECOD (1.6)
G	Spin-Ssty_2	e7bqzG3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Spin-Ssty_2	ECOD (1.6)
G	Spin-Ssty	e7bqzG2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Spin-Ssty	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G	PF02513	Spin/Ssty Family (Spin-Ssty)	Spin/Ssty Family	-	Repeat
B, D, F, H	PF00125	Core histone H2A/H2B/H3/H4 (Histone)	Core histone H2A/H2B/H3/H4	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G	Spindlin-1	methylated histone binding protein binding binding modification-dependent protein binding histone binding methylation-dependent protein binding	cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction cell communication positive regulation of response to stimulus positive regulation of Wnt signaling pathway signal transduction Wnt signaling pathway positive regulation of cellular process cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction cell communication positive regulation of response to stimulus positive regulation of Wnt signaling pathway signal transduction Wnt signaling pathway positive regulation of cellular process regulation of biological process regulation of signaling cell surface receptor signaling pathway regulation of Wnt signaling pathway biological regulation regulation of response to stimulus regulation of cell communication cellular process positive regulation of signaling cellular biosynthetic process RNA metabolic process regulation of primary metabolic process regulation of nitrogen compound metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance metabolic process heterocycle metabolic process organic substance biosynthetic process nitrogen compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process cellular metabolic process cellular nitrogen compound metabolic process primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process heterocycle biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process aromatic compound biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process cellular aromatic compound metabolic process sexual reproduction reproductive process multicellular organismal reproductive process gamete generation rRNA transcription rRNA metabolic process ncRNA transcription ncRNA metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of nitrogen compound metabolic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process meiotic cell cycle cell cycle protein-DNA complex organization cellular component organization protein-containing complex organization chromatin organization cellular component organization or biogenesis	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle nuclear membrane membrane endomembrane system organelle envelope nuclear envelope organelle membrane cytoplasm cytosol cytoskeleton spindle microtubule cytoskeleton nucleoplasm
B, D, F, H	H3(K4me3-K9me3) peptide	DNA binding binding organic cyclic compound binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization	extracellular region cellular anatomical entity extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome extracellular region cellular anatomical entity extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome chromatin chromosome intracellular organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G	IPR042567	Spindlin/spermiogenesis-specific domain superfamily	Homologous Superfamily
A, C, E, G	IPR003671	Spindlin/spermiogenesis-specific protein	Family
B, D, F, H	IPR009072	Histone-fold	Homologous Superfamily
B, D, F, H	IPR007125	Histone H2A/H2B/H3	Domain
B, D, F, H	IPR000164	Histone H3/CENP-A	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C, E, G	Pharos: Q9Y657	acute myeloid leukemia cystic fibrosis glioblastoma malignant ependymoma myopathy pancreatic ductal adenocarcinoma amyotrophic lateral sclerosis Duchenne muscular dystrophy juvenile dermatomyositis malignant pancreatic neoplasm osteosarcoma pancreatic intraductal papillary-mucinous neoplasm Becker muscular dystrophy Emery-Dreifuss muscular dystrophy limb-girdle muscular dystrophy acute myeloid leukemia cystic fibrosis glioblastoma malignant ependymoma myopathy pancreatic ductal adenocarcinoma amyotrophic lateral sclerosis Duchenne muscular dystrophy juvenile dermatomyositis malignant pancreatic neoplasm osteosarcoma pancreatic intraductal papillary-mucinous neoplasm Becker muscular dystrophy Emery-Dreifuss muscular dystrophy limb-girdle muscular dystrophy medulloblastoma ovarian cancer sinusitis
B, D, F, H	Pharos: Q71DI3	idiopathic scoliosis

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B, D, F, H	M3L	Parent Component: LYS RESID: AA0074 PSI-MOD : N6,N6,N6-trimethyl-L-lysine MOD:00083

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.