5JH5

Structural Basis for the Hierarchical Assembly of the Core of PRC1.1

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	d5jh5b2	All alpha proteins	Skp1 dimerisation domain-like	Skp1 dimerisation domain-like	Skp1 dimerisation domain-like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5jh5b1	Alpha and beta proteins (a+b)	POZ domain	POZ domain	automated matches	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)
B	SCOP2B Superfamily	POZ domain	8035033	3000894	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Skp1 dimerisation domain-like	8038683	3000564	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8055978	3000157	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Putative DNA-binding domain	8055979	3000158	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	LRR_8_3	e5jh5A1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: LRR_8_3	ECOD (1.6)
A	F-box-like_1	e5jh5A2	A: alpha arrays	X: F-box domain (From Topology)	H: F-box domain (From Topology)	T: F-box domain	F: F-box-like_1	ECOD (1.6)
B	Skp1_POZ	e5jh5B1	A: a+b two layers	X: POZ domain (From Topology)	H: POZ domain (From Topology)	T: POZ domain	F: Skp1_POZ	ECOD (1.6)
C	Rad60-SLD	e5jh5C1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Rad60-SLD	ECOD (1.6)
D	PUFD	e5jh5D1	A: alpha arrays	X: HTH	H: HTH	T: Putative DNA-binding domain	F: PUFD	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.710.10	Alpha Beta	2-Layer Sandwich	Potassium Channel Kv1.1	Chain A	CATH (4.3.0)
C	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	PF12937	F-box-like (F-box-like)	F-box-like	This is an F-box-like family.	Domain
B	PF03931	Skp1 family, tetramerisation domain (Skp1_POZ)	Skp1 family, tetramerisation domain	-	Domain
B	PF01466	Skp1 family, dimerisation domain (Skp1)	Skp1 family, dimerisation domain	-	Domain
C	PF16207	RAWUL domain RING finger- and WD40-associated ubiquitin-like (RAWUL)	RAWUL domain RING finger- and WD40-associated ubiquitin-like	The RAWUL domain is found at the C-terminus of poly-comb group RING finger proteins. It is a ubiquitin-like domain [1]. RAWUL binds directly to PUFD, a domain on BCOR proteins (BCL6 corepressor). BCOR has emerged as an important player in developm ...	The RAWUL domain is found at the C-terminus of poly-comb group RING finger proteins. It is a ubiquitin-like domain [1]. RAWUL binds directly to PUFD, a domain on BCOR proteins (BCL6 corepressor). BCOR has emerged as an important player in development and health [2].	Domain
D	PF16553	BCORL-PCGF1-binding domain (PUFD)	BCORL-PCGF1-binding domain	PUFD is the minimal domain at the C-terminus of BCORL (BCL6 corepressor) that is needed for binding and giving specificity to some of the PCGF proteins, polycomb-group RING finger homologues. PUFD binds to the RAWUL (RING finger- and WD40-associated ...	PUFD is the minimal domain at the C-terminus of BCORL (BCL6 corepressor) that is needed for binding and giving specificity to some of the PCGF proteins, polycomb-group RING finger homologues. PUFD binds to the RAWUL (RING finger- and WD40-associated ubiquitin-like) domain of the particular PCGF PCGF1, Pfam:PF16207. Polycomb group proteins form repressive complexes (PRC) that mediate epigenetic modifications of histones. In humans there are many different PCGF homologues whose functions all vary, but the direct binding partner of PCGF1 is BCOR. BCOR has emerged as an important player in development and health [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Lysine-specific demethylase 2B	histone H3K36 demethylase activity catalytic activity, acting on a protein protein demethylase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen histone demethylase activity histone H3K36me/H3K36me2 demethylase activity demethylase activity dioxygenase activity oxidoreductase activity histone H3 demethylase activity histone modifying activity catalytic activity 2-oxoglutarate-dependent dioxygenase activity RNA binding histone H3K36 demethylase activity catalytic activity, acting on a protein protein demethylase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen histone demethylase activity histone H3K36me/H3K36me2 demethylase activity demethylase activity dioxygenase activity oxidoreductase activity histone H3 demethylase activity histone modifying activity catalytic activity 2-oxoglutarate-dependent dioxygenase activity RNA binding binding organic cyclic compound binding rRNA binding nucleic acid binding transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity DNA binding sequence-specific DNA binding double-stranded DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding unmethylated CpG binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	regulation of biological process regulation of growth regulation of cellular process regulation of cellular component organization positive regulation of biological process biological regulation growth positive regulation of cell growth regulation of cell growth cell growth cellular component organization positive regulation of growth cellular process cellular component organization or biogenesis regulation of biological process regulation of growth regulation of cellular process regulation of cellular component organization positive regulation of biological process biological regulation growth positive regulation of cell growth regulation of cell growth cell growth cellular component organization positive regulation of growth cellular process cellular component organization or biogenesis positive regulation of cellular process developmental process multicellular organismal process head development animal organ development brain development nervous system development multicellular organism development central nervous system development midbrain development anatomical structure development system development spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation hindbrain development fourth ventricle development ventricular system development regulation of developmental process regulation of stem cell population maintenance stem cell population maintenance positive regulation of developmental process positive regulation of stem cell population maintenance positive regulation of multicellular organismal process regulation of multicellular organismal process maintenance of cell number lateral ventricle development forebrain development telencephalon development embryonic epithelial tube formation chordate embryonic development tube formation embryo development epithelial tube formation tube morphogenesis primary neural tube formation 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 anatomical structure morphogenesis tissue morphogenesis initiation of neural tube closure neural tube closure neural tube formation anatomical structure formation involved in morphogenesis tube closure neuron apoptotic process negative regulation of neuron apoptotic process negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death regulation of neuron apoptotic process third ventricle development sensory organ development embryonic eye morphogenesis visual system development embryonic camera-type eye development eye morphogenesis animal organ morphogenesis embryonic organ development sensory system development embryonic organ morphogenesis camera-type eye morphogenesis eye development embryonic camera-type eye morphogenesis sensory organ morphogenesis camera-type eye development cellular biosynthetic process RNA metabolic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process cellular metabolic 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 gene expression biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of cellular biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process negative regulation of cell population proliferation negative regulation of neural precursor cell proliferation cell population proliferation regulation of cell population proliferation neural precursor cell proliferation regulation of neural precursor cell proliferation chromatin organization chromatin remodeling midbrain-hindbrain boundary morphogenesis anterior/posterior pattern specification pattern specification process rostrocaudal neural tube patterning regionalization neural tube patterning midbrain-hindbrain boundary development	membrane-bounded organelle intracellular organelle protein-containing complex intracellular anatomical structure organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity PcG protein complex membrane-enclosed lumen nucleolus intracellular organelle lumen organelle lumen membrane-bounded organelle intracellular organelle protein-containing complex intracellular anatomical structure organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity PcG protein complex membrane-enclosed lumen nucleolus intracellular organelle lumen organelle lumen intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle nucleoplasm chromosome
B	S-phase kinase-associated protein 1	ubiquitin ligase complex scaffold activity protein-macromolecule adaptor activity molecular adaptor activity protein binding binding protein domain specific binding cullin family protein binding ubiquitin-like ligase-substrate adaptor activity enzyme-substrate adaptor activity molecular function activator activity molecular function regulator activity beta-catenin binding F-box domain binding	maintenance of protein location protein localization cellular localization maintenance of protein location in nucleus protein localization to nucleus maintenance of location maintenance of location in cell localization maintenance of protein location in cell cellular macromolecule localization macromolecule localization protein localization to organelle cellular process maintenance of protein localization in organelle maintenance of protein location protein localization cellular localization maintenance of protein location in nucleus protein localization to nucleus maintenance of location maintenance of location in cell localization maintenance of protein location in cell cellular macromolecule localization macromolecule localization protein localization to organelle cellular process maintenance of protein localization in organelle protein ubiquitination macromolecule modification metabolic process primary metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal catabolic process proteolysis involved in protein catabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis SCF-dependent proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process regulation of protein modification process regulation of catalytic activity positive regulation of protein metabolic process positive regulation of biological process regulation of protein ubiquitination regulation of transferase activity positive regulation of post-translational protein modification regulation of primary metabolic process regulation of ubiquitin protein ligase activity positive regulation of metabolic process positive regulation of molecular function positive regulation of ubiquitin protein ligase activity positive regulation of protein modification process positive regulation of macromolecule metabolic process regulation of ubiquitin-protein transferase activity regulation of protein modification by small protein conjugation or removal positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of biological process positive regulation of transferase activity regulation of post-translational protein modification regulation of protein metabolic process biological regulation positive regulation of catalytic activity regulation of macromolecule metabolic process positive regulation of ubiquitin-protein transferase activity regulation of molecular function regulation of metabolic process protein polyubiquitination protein K48-linked ubiquitination protein monoubiquitination cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis	membrane-bounded organelle intracellular organelle protein-containing complex intracellular anatomical structure organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity PcG protein complex centrosome microtubule organizing center cytoskeleton intracellular non-membrane-bounded organelle membrane-bounded organelle intracellular organelle protein-containing complex intracellular anatomical structure organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity PcG protein complex centrosome microtubule organizing center cytoskeleton intracellular non-membrane-bounded organelle microtubule cytoskeleton non-membrane-bounded organelle cytoplasm cytosol membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen cullin-RING ubiquitin ligase complex ubiquitin ligase complex catalytic complex SCF ubiquitin ligase complex transferase complex intracellular protein-containing complex Cul7-RING ubiquitin ligase complex
C	Polycomb group RING finger protein 1	cation binding ion binding binding metal ion binding small molecule binding chromatin binding promoter-specific chromatin 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 regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process cellular metabolic 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 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 regulation of gene expression biosynthetic process metabolic process regulation of macromolecule biosynthetic process cellular process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process negative regulation of biological process negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of cellular biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis	membrane-bounded organelle intracellular organelle protein-containing complex intracellular anatomical structure organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity PcG protein complex PRC1 complex ubiquitin ligase complex catalytic complex transferase complex membrane-bounded organelle intracellular organelle protein-containing complex intracellular anatomical structure organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity PcG protein complex PRC1 complex ubiquitin ligase complex catalytic complex transferase complex nuclear ubiquitin ligase complex intracellular protein-containing complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
D	BCL-6 corepressor-like protein 1	transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity	regulation of cellular process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of cellular process regulation of cellular process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription regulation of biological process negative regulation of transcription by RNA polymerase II cellular metabolic process negative regulation of 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 negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular component organization chromatin organization cellular component organization or biogenesis	cell periphery plasma membrane membrane cellular anatomical entity membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle cell periphery plasma membrane membrane cellular anatomical entity membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001965	Zinc finger, PHD-type	Domain
A	IPR001810	F-box domain	Domain
A	IPR003347	JmjC domain	Domain
A	IPR041070	Jumonji, helical domain	Domain
A	IPR041667	Cupin-like domain 8	Domain
A	IPR002857	Zinc finger, CXXC-type	Domain
A	IPR019787	Zinc finger, PHD-finger	Domain
A	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A	IPR050690	JHDM1 Histone Demethylase	Family
A	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
A	IPR006553	Leucine-rich repeat, cysteine-containing subtype	Repeat
B	IPR016073	SKP1 component, POZ domain	Domain
B	IPR001232	S-phase kinase-associated protein 1-like	Family
B	IPR036296	SKP1-like, dimerisation domain superfamily	Homologous Superfamily
B	IPR016072	SKP1 component, dimerisation	Domain
B	IPR011333	SKP1/BTB/POZ domain superfamily	Homologous Superfamily
B	IPR016897	S-phase kinase-associated protein 1	Family
C	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
C	IPR032443	RAWUL domain	Domain
C	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
C	IPR001841	Zinc finger, RING-type	Domain
D	IPR032365	BCL-6 corepressor, PCGF1 binding domain	Domain
D	IPR002110	Ankyrin repeat	Repeat
D	IPR047144	BCL-6 corepressor-like	Family
D	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
D	IPR038227	PCGF Ub-like fold discriminator superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q8NHM5	schizophrenia adrenal cortex carcinoma medulloblastoma bipolar disorder osteosarcoma endogenous depression ovarian cancer
B	Pharos: P63208	allergic rhinitis esophageal adenocarcinoma hypothyroidism medulloblastoma pilocytic astrocytoma subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor glioblastoma large cell medulloblastoma ovarian cancer plasma cell myeloma systemic lupus erythematosus breast cancer Hashimoto thyroiditis malignant glioma allergic rhinitis esophageal adenocarcinoma hypothyroidism medulloblastoma pilocytic astrocytoma subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor glioblastoma large cell medulloblastoma ovarian cancer plasma cell myeloma systemic lupus erythematosus breast cancer Hashimoto thyroiditis malignant glioma pancreatic ductal adenocarcinoma rheumatoid arthritis
C	Pharos: Q9BSM1	atypical teratoid rhabdoid tumor malignant glioma rheumatoid arthritis glioblastoma medulloblastoma large cell medulloblastoma psoriasis
D	Pharos: Q5H9F3	adenoid cystic carcinoma salivary gland adenoid cystic carcinoma kidney Wilms tumor Cytopenia lung adenocarcinoma intellectual disability malignant mesothelioma congenital anemia