5Y5W | pdb_00005y5w

Crystal structure of human Spindlin1 in complex with a histone H4K20(me3) peptide

External Resource: Annotation

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
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8052900	3000404	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8052902	3000404	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8052901	3000404	SCOP2B (2022-06-29)
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)
B	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8052900	3000404	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8052901	3000404	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8052902	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)
A	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8052901	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)
D	Spin-Ssty_1	e5y5wD1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Spin-Ssty_1	ECOD (1.6)
D	Spin-Ssty_2	e5y5wD2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Spin-Ssty_2	ECOD (1.6)
D	Spin-Ssty	e5y5wD3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Spin-Ssty	ECOD (1.6)
C	Spin-Ssty_1	e5y5wC2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Spin-Ssty_1	ECOD (1.6)
C	Spin-Ssty_2	e5y5wC3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Spin-Ssty_2	ECOD (1.6)
C	Spin-Ssty	e5y5wC1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Spin-Ssty	ECOD (1.6)
B	Spin-Ssty_1	e5y5wB3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Spin-Ssty_1	ECOD (1.6)
B	Spin-Ssty_2	e5y5wB1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Spin-Ssty_2	ECOD (1.6)
B	Spin-Ssty	e5y5wB2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Spin-Ssty	ECOD (1.6)
A	Spin-Ssty_1	e5y5wA2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Spin-Ssty_1	ECOD (1.6)
A	Spin-Ssty_2	e5y5wA3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Spin-Ssty_2	ECOD (1.6)
A	Spin-Ssty	e5y5wA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Spin-Ssty	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.80.10.70	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)	Spindlin/Ssty	CATH (4.3.0)
C	2.80.10.70	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)	Spindlin/Ssty	CATH (4.3.0)
B	2.80.10.70	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)	Spindlin/Ssty	CATH (4.3.0)
A	2.80.10.70	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)	Spindlin/Ssty	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF02513	Spin/Ssty Family (Spin-Ssty)	Spin/Ssty Family	Spindlin (Spin) is a novel maternal transcript present in the unfertilised egg and early embryo [1]. The Y-linked spermiogenesis -specific transcript (Ssty) is also expressed during gametogenesis and forms part of this Pfam family. Members of this f ...	Spindlin (Spin) is a novel maternal transcript present in the unfertilised egg and early embryo [1]. The Y-linked spermiogenesis -specific transcript (Ssty) is also expressed during gametogenesis and forms part of this Pfam family. Members of this family contain three copies of this 50 residue repeat. The repeat is predicted to contain four beta strands.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, F, G	Histone peptide H4K20(me3)	-	-	-
A, B, C, D	Spindlin-1	histone reader activity histone H3 reader activity chromatin-protein adaptor activity histone H3K4me3 reader activity protein-macromolecule adaptor activity molecular adaptor activity	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 RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process sexual reproduction reproductive process multicellular organismal reproductive process gamete generation rRNA transcription rRNA metabolic process positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process localization protein localization to chromatin protein localization to chromosome protein localization to organelle macromolecule localization intracellular protein localization meiotic cell cycle cell cycle negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process retrotransposition heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process transposable element silencing by heterochromatin formation heterochromatin organization transposition regulatory ncRNA-mediated gene silencing negative regulation of gene expression constitutive heterochromatin formation regulatory ncRNA-mediated heterochromatin formation negative regulation of biosynthetic process transposable element silencing by piRNA-mediated DNA methylation negative regulation of macromolecule biosynthetic process DNA methylation-dependent constitutive heterochromatin formation transposable element silencing negative regulation of gene expression, epigenetic gene silencing by piRNA-directed DNA methylation piRNA-mediated heterochromatin formation	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen nuclear membrane membrane endomembrane system organelle envelope nuclear envelope organelle membrane cytoplasm cytosol cytoskeleton spindle microtubule cytoskeleton nucleoplasm chromatin chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR042567	Spindlin/spermiogenesis-specific domain superfamily	Homologous Superfamily
A, B, C, D	IPR003671	Spindlin/spermiogenesis-specific protein	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	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

Protein Modification Annotation

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

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.