29HI

Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO22 SCF ubiquition ligase in complex with NSD2 via UNC10415667

This is a non-PDB format compatible entry.

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000209	biological_process	protein polyubiquitination
A	0004842	molecular_function	ubiquitin-protein transferase activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0006511	biological_process	ubiquitin-dependent protein catabolic process
A	0019005	cellular_component	SCF ubiquitin ligase complex
A	0030018	cellular_component	Z disc
A	0031146	biological_process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
A	0032436	biological_process	positive regulation of proteasomal ubiquitin-dependent protein catabolic process
A	0036211	biological_process	protein modification process
A	0048742	biological_process	regulation of skeletal muscle fiber development
B	0003682	molecular_function	chromatin binding
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0005694	cellular_component	chromosome
B	0005730	cellular_component	nucleolus
B	0005737	cellular_component	cytoplasm
B	0006302	biological_process	double-strand break repair
B	0006338	biological_process	chromatin remodeling
B	0006355	biological_process	regulation of DNA-templated transcription
B	0031981	cellular_component	nuclear lumen
B	0042054	molecular_function	histone methyltransferase activity
B	0042799	molecular_function	histone H4K20 methyltransferase activity
B	0043565	molecular_function	sequence-specific DNA binding
B	0046975	molecular_function	histone H3K36 methyltransferase activity
B	0140938	molecular_function	histone H3 methyltransferase activity
B	0140954	molecular_function	histone H3K36 dimethyltransferase activity
B	0140955	molecular_function	histone H3K36 trimethyltransferase activity
C	0000082	biological_process	G1/S transition of mitotic cell cycle
C	0000151	cellular_component	ubiquitin ligase complex
C	0000209	biological_process	protein polyubiquitination
C	0000785	cellular_component	chromatin
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005737	cellular_component	cytoplasm
C	0005813	cellular_component	centrosome
C	0005829	cellular_component	cytosol
C	0006338	biological_process	chromatin remodeling
C	0006355	biological_process	regulation of DNA-templated transcription
C	0006879	biological_process	intracellular iron ion homeostasis
C	0007346	biological_process	regulation of mitotic cell cycle
C	0008013	molecular_function	beta-catenin binding
C	0010564	biological_process	regulation of cell cycle process
C	0010824	biological_process	regulation of centrosome duplication
C	0014033	biological_process	neural crest cell differentiation
C	0016567	biological_process	protein ubiquitination
C	0019005	cellular_component	SCF ubiquitin ligase complex
C	0019904	molecular_function	protein domain specific binding
C	0030510	biological_process	regulation of BMP signaling pathway
C	0031146	biological_process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
C	0031467	cellular_component	Cul7-RING ubiquitin ligase complex
C	0031507	biological_process	heterochromatin formation
C	0031519	cellular_component	PcG protein complex
C	0032006	biological_process	regulation of TOR signaling
C	0035102	cellular_component	PRC1 complex
C	0042752	biological_process	regulation of circadian rhythm
C	0042981	biological_process	regulation of apoptotic process
C	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
C	0045892	biological_process	negative regulation of DNA-templated transcription
C	0050727	biological_process	regulation of inflammatory response
C	0051124	biological_process	synaptic assembly at neuromuscular junction
C	0051298	biological_process	centrosome duplication
C	0051457	biological_process	maintenance of protein location in nucleus
C	0051726	biological_process	regulation of cell cycle
C	0060173	biological_process	limb development
C	0060271	biological_process	cilium assembly
C	0070936	biological_process	protein K48-linked ubiquitination
C	0097602	molecular_function	cullin family protein binding
C	0140677	molecular_function	molecular function activator activity
C	0160072	molecular_function	ubiquitin ligase complex scaffold activity
C	1901524	biological_process	regulation of mitophagy
C	1904415	biological_process	regulation of xenophagy
C	1990444	molecular_function	F-box domain binding
C	1990756	molecular_function	ubiquitin-like ligase-substrate adaptor activity
C	1990757	molecular_function	ubiquitin ligase activator activity
C	2000001	biological_process	regulation of DNA damage checkpoint
D	0000082	biological_process	G1/S transition of mitotic cell cycle
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005654	cellular_component	nucleoplasm
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0005886	cellular_component	plasma membrane
D	0006355	biological_process	regulation of DNA-templated transcription
D	0006879	biological_process	intracellular iron ion homeostasis
D	0007346	biological_process	regulation of mitotic cell cycle
D	0010564	biological_process	regulation of cell cycle process
D	0010824	biological_process	regulation of centrosome duplication
D	0014033	biological_process	neural crest cell differentiation
D	0016567	biological_process	protein ubiquitination
D	0019005	cellular_component	SCF ubiquitin ligase complex
D	0030510	biological_process	regulation of BMP signaling pathway
D	0031146	biological_process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
D	0031461	cellular_component	cullin-RING ubiquitin ligase complex
D	0031625	molecular_function	ubiquitin protein ligase binding
D	0032006	biological_process	regulation of TOR signaling
D	0034599	biological_process	cellular response to oxidative stress
D	0042752	biological_process	regulation of circadian rhythm
D	0042981	biological_process	regulation of apoptotic process
D	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
D	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
D	0050727	biological_process	regulation of inflammatory response
D	0051298	biological_process	centrosome duplication
D	0051726	biological_process	regulation of cell cycle
D	0060173	biological_process	limb development
D	0060271	biological_process	cilium assembly
D	0070936	biological_process	protein K48-linked ubiquitination
D	0097193	biological_process	intrinsic apoptotic signaling pathway
D	0160072	molecular_function	ubiquitin ligase complex scaffold activity
D	1901524	biological_process	regulation of mitophagy
D	1904415	biological_process	regulation of xenophagy
D	1990452	cellular_component	Parkin-FBXW7-Cul1 ubiquitin ligase complex
D	2000001	biological_process	regulation of DNA damage checkpoint
E	0000082	biological_process	G1/S transition of mitotic cell cycle
E	0000109	cellular_component	nucleotide-excision repair complex
E	0000122	biological_process	negative regulation of transcription by RNA polymerase II
E	0000165	biological_process	MAPK cascade
E	0000209	biological_process	protein polyubiquitination
E	0004842	molecular_function	ubiquitin-protein transferase activity
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005654	cellular_component	nucleoplasm
E	0005737	cellular_component	cytoplasm
E	0005794	cellular_component	Golgi apparatus
E	0005813	cellular_component	centrosome
E	0005829	cellular_component	cytosol
E	0006283	biological_process	transcription-coupled nucleotide-excision repair
E	0006289	biological_process	nucleotide-excision repair
E	0006355	biological_process	regulation of DNA-templated transcription
E	0006511	biological_process	ubiquitin-dependent protein catabolic process
E	0006513	biological_process	protein monoubiquitination
E	0006879	biological_process	intracellular iron ion homeostasis
E	0006974	biological_process	DNA damage response
E	0007283	biological_process	spermatogenesis
E	0007346	biological_process	regulation of mitotic cell cycle
E	0008283	biological_process	cell population proliferation
E	0010506	biological_process	regulation of autophagy
E	0010564	biological_process	regulation of cell cycle process
E	0010824	biological_process	regulation of centrosome duplication
E	0014033	biological_process	neural crest cell differentiation
E	0016485	biological_process	protein processing
E	0016567	biological_process	protein ubiquitination
E	0019005	cellular_component	SCF ubiquitin ligase complex
E	0019788	molecular_function	NEDD8 transferase activity
E	0030174	biological_process	regulation of DNA-templated DNA replication initiation
E	0030510	biological_process	regulation of BMP signaling pathway
E	0031146	biological_process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
E	0031297	biological_process	replication fork processing
E	0031461	cellular_component	cullin-RING ubiquitin ligase complex
E	0031462	cellular_component	Cul2-RING ubiquitin ligase complex
E	0031463	cellular_component	Cul3-RING ubiquitin ligase complex
E	0031464	cellular_component	Cul4A-RING E3 ubiquitin ligase complex
E	0031465	cellular_component	Cul4B-RING E3 ubiquitin ligase complex
E	0031466	cellular_component	Cul5-RING ubiquitin ligase complex
E	0031467	cellular_component	Cul7-RING ubiquitin ligase complex
E	0031625	molecular_function	ubiquitin protein ligase binding
E	0032006	biological_process	regulation of TOR signaling
E	0032436	biological_process	positive regulation of proteasomal ubiquitin-dependent protein catabolic process
E	0032480	biological_process	negative regulation of type I interferon production
E	0032814	biological_process	regulation of natural killer cell activation
E	0034450	molecular_function	ubiquitin-ubiquitin ligase activity
E	0034599	biological_process	cellular response to oxidative stress
E	0034644	biological_process	cellular response to UV
E	0040029	biological_process	epigenetic regulation of gene expression
E	0042110	biological_process	T cell activation
E	0042127	biological_process	regulation of cell population proliferation
E	0042752	biological_process	regulation of circadian rhythm
E	0042770	biological_process	signal transduction in response to DNA damage
E	0042981	biological_process	regulation of apoptotic process
E	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
E	0043124	biological_process	negative regulation of canonical NF-kappaB signal transduction
E	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
E	0043687	biological_process	post-translational protein modification
E	0044314	biological_process	protein K27-linked ubiquitination
E	0045116	biological_process	protein neddylation
E	0045724	biological_process	positive regulation of cilium assembly
E	0045732	biological_process	positive regulation of protein catabolic process
E	0045879	biological_process	negative regulation of smoothened signaling pathway
E	0045995	biological_process	regulation of embryonic development
E	0046627	biological_process	negative regulation of insulin receptor signaling pathway
E	0050727	biological_process	regulation of inflammatory response
E	0051298	biological_process	centrosome duplication
E	0051726	biological_process	regulation of cell cycle
E	0060090	molecular_function	molecular adaptor activity
E	0060173	biological_process	limb development
E	0060271	biological_process	cilium assembly
E	0060964	biological_process	regulation of miRNA-mediated gene silencing
E	0061629	molecular_function	RNA polymerase II-specific DNA-binding transcription factor binding
E	0061630	molecular_function	ubiquitin protein ligase activity
E	0061663	molecular_function	NEDD8 ligase activity
E	0062197	biological_process	cellular response to chemical stress
E	0070534	biological_process	protein K63-linked ubiquitination
E	0070936	biological_process	protein K48-linked ubiquitination
E	0071230	biological_process	cellular response to amino acid stimulus
E	0080008	cellular_component	Cul4-RING E3 ubiquitin ligase complex
E	0080135	biological_process	regulation of cellular response to stress
E	0090090	biological_process	negative regulation of canonical Wnt signaling pathway
E	0090734	cellular_component	site of DNA damage
E	0097602	molecular_function	cullin family protein binding
E	0140627	biological_process	ubiquitin-dependent protein catabolic process via the C-end degron rule pathway
E	0160240	biological_process	RNA polymerase II transcription initiation surveillance
E	0160276	biological_process	negative regulation of beige fat cell differentiation
E	1900076	biological_process	regulation of cellular response to insulin stimulus
E	1901524	biological_process	regulation of mitophagy
E	1901525	biological_process	negative regulation of mitophagy
E	1901987	biological_process	regulation of cell cycle phase transition
E	1902412	biological_process	regulation of mitotic cytokinesis
E	1902499	biological_process	positive regulation of protein autoubiquitination
E	1902883	biological_process	negative regulation of response to oxidative stress
E	1904178	biological_process	negative regulation of adipose tissue development
E	1904263	biological_process	positive regulation of TORC1 signaling
E	1904415	biological_process	regulation of xenophagy
E	1990116	biological_process	ribosome-associated ubiquitin-dependent protein catabolic process
E	2000001	biological_process	regulation of DNA damage checkpoint
E	2000036	biological_process	regulation of stem cell population maintenance
E	2000104	biological_process	negative regulation of DNA-templated DNA replication

Functional Information from PROSITE/UniProt

site_id	PS01256
Number of Residues	28
Details	CULLIN_1 Cullin family signature. IKkcIdiLIEKeYLeRvdgekdtYsYlA

Chain	Residue	Details
D	ILE749-ALA776

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	46
Details	Domain: {"description":"F-box"}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	1
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	64
Details	Domain: {"description":"PWWP 1","evidences":[{"source":"PROSITE-ProRule","id":"PRU00162","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	20
Details	Region: {"description":"Disordered","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	59
Details	Region: {"description":"Interaction with the F-box domain of F-box proteins","evidences":[{"source":"PubMed","id":"35982156","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"7Z8B","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	1
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"20068231","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"21406692","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO1)","evidences":[{"source":"PubMed","id":"25114211","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	60
Details	Domain: {"description":"Cullin neddylation","evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	1
Details	Modified residue: {"description":"Omega-N-methylarginine","evidences":[{"source":"PubMed","id":"24129315","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in NEDD8)","evidences":[{"source":"PubMed","id":"10597293","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15537541","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18805092","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI12
Number of Residues	45
Details	Zinc finger: {"description":"RING-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU00175","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI13
Number of Residues	7
Details	Binding site: {"evidences":[{"source":"PubMed","id":"11961546","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"38605244","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1LDJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1LDK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U6G","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2HYE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3DPL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3DQV","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3RTR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4F52","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4P5O","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8Q7H","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8RHZ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI14
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"11961546","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"38605244","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1LDJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1LDK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U6G","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2HYE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3DPL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3DQV","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3RTR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4F52","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4P5O","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"7Z8B","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8Q7H","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8RHZ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI15
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PubMed","id":"11961546","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"38605244","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1LDJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1LDK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U6G","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2HYE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3DQV","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3RTR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4F52","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4P5O","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8Q7H","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8RHZ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---