Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

9UUQ

Cryo-EM structure of thalidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly

Functional Information from PROSITE/UniProt

site_id	PS00028
Number of Residues	21
Details	ZINC_FINGER_C2H2_1 Zinc finger C2H2 type domain signature. Cnq..CgasFtqkgnllrHicl..H

Chain	Residue	Details
I	CYS148-HIS168

site_id	PS00183
Number of Residues	16
Details	UBC_1 Ubiquitin-conjugating (UBC) active site signature. YHPNInsn.GsICLdiL

Chain	Residue	Details
D	TYR74-LEU89

site_id	PS00299
Number of Residues	26
Details	UBIQUITIN_1 Ubiquitin domain signature. KerVeEkegIPpqqQrLIYsGkqmnD

Chain	Residue	Details
N	LYS27-ASP52
U	LYS27-ASP52

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

Chain	Residue	Details
A	LEU732-ALA759

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in NEDD8)","evidences":[{"source":"PubMed","id":"38316879","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	46
Details	Repeat: {"description":"WD 1","evidences":[{"source":"PubMed","id":"41565821","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"9OTY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9SFM","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	45
Details	Repeat: {"description":"WD 2","evidences":[{"source":"PubMed","id":"41565821","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"9OTY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9SFM","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	51
Details	Repeat: {"description":"WD 3","evidences":[{"source":"PubMed","id":"41565821","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"9OTY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9SFM","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	52
Details	Repeat: {"description":"WD 4","evidences":[{"source":"PubMed","id":"41565821","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"9OTY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9SFM","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	44
Details	Repeat: {"description":"WD 5","evidences":[{"source":"PubMed","id":"41565821","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"9OTY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9SFM","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	46
Details	Repeat: {"description":"WD 7","evidences":[{"source":"PubMed","id":"41565821","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"9OTY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9SFM","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	36
Details	Repeat: {"description":"WD 8","evidences":[{"source":"PubMed","id":"41565821","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"9OTY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9SFM","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	43
Details	Repeat: {"description":"WD 9","evidences":[{"source":"PubMed","id":"41565821","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"9SFM","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	46
Details	Repeat: {"description":"WD 10","evidences":[{"source":"PubMed","id":"41565821","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"9SFM","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	40
Details	Repeat: {"description":"WD 11","evidences":[{"source":"PubMed","id":"41565821","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"9SFM","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	48
Details	Repeat: {"description":"WD 12","evidences":[{"source":"PubMed","id":"41565821","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"9SFM","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	49
Details	Repeat: {"description":"WD 13","evidences":[{"source":"PubMed","id":"41565821","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"9SFM","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI14
Number of Residues	37
Details	Repeat: {"description":"WD 14","evidences":[{"source":"PubMed","id":"41565821","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"9SFM","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI15
Number of Residues	34
Details	Repeat: {"description":"WD 15","evidences":[{"source":"PubMed","id":"41565821","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"9SFM","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI16
Number of Residues	60
Details	Repeat: {"description":"WD 17","evidences":[{"source":"PubMed","id":"41565821","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"9OTY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUL","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI17
Number of Residues	39
Details	Repeat: {"description":"WD 18","evidences":[{"source":"PubMed","id":"41565821","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"9OTY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUL","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI18
Number of Residues	42
Details	Repeat: {"description":"WD 19","evidences":[{"source":"PubMed","id":"41565821","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"9OTY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUL","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI19
Number of Residues	36
Details	Region: {"description":"WD40 beta-propeller C"}

Chain

Residue

Details

site_id	SWS_FT_FI20
Number of Residues	303
Details	Region: {"description":"WD40 beta-propeller B; Interaction with CUL4A"}

Chain

Residue

Details

site_id	SWS_FT_FI21
Number of Residues	1
Details	Modified residue: {"description":"N-acetylserine","evidences":[{"source":"PubMed","id":"19413330","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI22
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_FI23
Number of Residues	1
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"Q9ESW0","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI24
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)","evidences":[{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI25
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"25108355","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"41565821","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4TZ4","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OTY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9SFM","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI26
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"PubMed","id":"25108355","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4TZ4","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI27
Number of Residues	1
Details	Active site: {"description":"Glycyl thioester intermediate","evidences":[{"source":"PROSITE-ProRule","id":"PRU00388","evidenceCode":"ECO:0000255"},{"source":"PROSITE-ProRule","id":"PRU10133","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI28
Number of Residues	22
Details	Zinc finger: {"description":"C2H2-type 2","evidences":[{"source":"PROSITE-ProRule","id":"PRU00042","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI29
Number of Residues	22
Details	Zinc finger: {"description":"C2H2-type 3","evidences":[{"source":"PROSITE-ProRule","id":"PRU00042","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI30
Number of Residues	2
Details	Region: {"description":"Interaction with UBE1C","evidences":[{"source":"PubMed","id":"14690597","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI31
Number of Residues	2
Details	Site: {"description":"Interaction with UBE1C","evidences":[{"source":"PubMed","id":"14690597","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI32
Number of Residues	1
Details	Modified residue: {"description":"(Microbial infection) Deamidated glutamine","evidences":[{"source":"PubMed","id":"20688984","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21903097","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23175788","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23589306","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"26632597","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI33
Number of Residues	1
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"P29595","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI34
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)","evidences":[{"source":"PubMed","id":"38316879","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI35
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_FI36
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_FI37
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

site_id	SWS_FT_FI38
Number of Residues	75
Details	Domain: {"description":"Ubiquitin-like","evidences":[{"source":"PROSITE-ProRule","id":"PRU00214","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI39
Number of Residues	2
Details	Site: {"description":"Interacts with activating enzyme"}

Chain

Residue

Details

site_id	SWS_FT_FI40
Number of Residues	1
Details	Site: {"description":"Essential for function"}

Chain

Residue

Details

site_id	SWS_FT_FI41
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine; by PINK1","evidences":[{"source":"PubMed","id":"24660806","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24751536","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24784582","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25527291","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI42
Number of Residues	1
Details	Modified residue: {"description":"(Microbial infection) ADP-ribosylthreonine","evidences":[{"source":"PubMed","id":"32330457","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI43
Number of Residues	1
Details	Modified residue: {"description":"ADP-ribosylglycine","evidences":[{"source":"PubMed","id":"28525742","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI44
Number of Residues	1
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16443603","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI45
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)"}

Chain

Residue

Details

site_id	SWS_FT_FI46
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16443603","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16543144","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI47
Number of Residues	1
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"15466860","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI48
Number of Residues	1
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16543144","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25752573","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25752577","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"34239127","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI49
Number of Residues	1
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"25752577","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI50
Number of Residues	1
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16543144","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18719106","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)