4UY4

1.86 A structure of human Spindlin-4 protein in complex with histone H3K4me3 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)
A	SCOP2 Family	Spin/Ssty	8050490	4006921	SCOP2 (2022-06-29)
A	SCOP2 Family	Spin/Ssty	8052893	4006921	SCOP2 (2022-06-29)
A	SCOP2 Family	Spin/Ssty	8052894	4006921	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Tudor/PWWP/MBT domain-like	8052895	3000404	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Tudor/PWWP/MBT domain-like	8052896	3000404	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Tudor/PWWP/MBT domain-like	8052897	3000404	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8052895	3000404	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8052897	3000404	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8052896	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)
A	PF02513	e4uy4A2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF02513	ECOD (1.6)
B	PF02513	e4uy4B2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF02513	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02513	Spin/Ssty Family (Spin-Ssty)	Spin/Ssty Family	-	Repeat
C, D	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, B	SPINDLIN-4	methylated histone binding protein binding binding modification-dependent protein binding histone binding methylation-dependent protein binding	regulation of cellular process cellular biosynthetic process 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 organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of cellular process cellular biosynthetic process 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 organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process cellular metabolic process biological regulation 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 organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process cellular process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process sexual reproduction reproductive process multicellular organismal reproductive process gamete generation	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
C, D	HISTONE H3K4ME3	DNA binding binding organic cyclic compound binding nucleic acid binding cell adhesion molecule binding cadherin binding protein binding protein heterodimerization activity 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 organic substance metabolic process 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 organic substance metabolic process biosynthetic process cellular biosynthetic process cellular metabolic process organic substance biosynthetic process metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process organelle organization telomere organization chromosome organization regulation of cellular process regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of metabolic process	membrane cellular anatomical entity extracellular region 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 membrane cellular anatomical entity extracellular region 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, B	IPR042567	Spindlin/spermiogenesis-specific domain superfamily	Homologous Superfamily
A, B	IPR003671	Spindlin/spermiogenesis-specific protein	Family
C, D	IPR009072	Histone-fold	Homologous Superfamily
C, D	IPR007125	Histone H2A/H2B/H3	Domain
C, D	IPR000164	Histone H3/CENP-A	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q56A73	adrenal cortex carcinoma Crohn disease malignant glioma pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor atypical teratoid rhabdoid tumor glioblastoma malignant pancreatic neoplasm pancreatic intraductal papillary-mucinous neoplasm psoriasis B-cell chronic lymphocytic leukemia large cell medulloblastoma medulloblastoma pilocytic astrocytoma sarcoidosis
C, D	Pharos: P68431	lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma allergic rhinitis ovarian cancer autism spectrum disorder psoriasis cutaneous lupus erythematosus tuberculosis ependymoma gastric carcinoma Glioma of Brain, Familial lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma allergic rhinitis ovarian cancer autism spectrum disorder psoriasis cutaneous lupus erythematosus tuberculosis ependymoma gastric carcinoma Glioma of Brain, Familial hypertensive disorder lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis astrocytoma (excluding glioblastoma) pancreatic intraductal papillary-mucinous carcinoma breast cancer spina bifida cystic fibrosis exocrine pancreatic carcinoma glioma susceptibility 1 invasive ductal breast carcinoma lung cancer malignant glioma medulloblastoma osteosarcoma atypical teratoid rhabdoid tumor pancreatic intraductal papillary-mucinous neoplasm breast carcinoma subependymoma ductal breast carcinoma in situ gastric cancer hepatocellular carcinoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C, D	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 R01GM133198.