9V0B

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

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A (A)	Cullin-4A	polymer	775	89368.9	1	UniProt (Q13619) Pfam (PF00888) Pfam (PF26557) Pfam (PF10557)	Homo sapiens (human)	CUL-4A
2	B (B)	DNA damage-binding protein 1	polymer	1140	127097.5	1	UniProt (Q16531) Pfam (PF10433) Pfam (PF23726) Pfam (PF03178)	Homo sapiens (human)	DDB p127 subunit,DNA damage-binding protein a,DDBa,Damage-specific DNA-binding protein 1,HBV X-associated protein 1,XAP-1,UV-damaged DNA-binding factor,UV-damaged DNA-binding protein 1,UV-DDB 1,XPE-binding factor,XPE-BF,Xeroderma pigmentosum group E-complementing protein,XPCe
3	C (C)	Protein cereblon	polymer	427	48874.9	1	UniProt (Q96SW2) Pfam (PF02190) Pfam (PF03226)	Homo sapiens (human)
4	D (D)	Ubiquitin-conjugating enzyme E2 D1	polymer	146	16490.8	1	UniProt (P51668) Pfam (PF00179)	Homo sapiens (human)	(E3-independent) E2 ubiquitin-conjugating enzyme D1,E2 ubiquitin-conjugating enzyme D1,Stimulator of Fe transport,SFT,UBC4/5 homolog,UbcH5,Ubiquitin carrier protein D1,Ubiquitin-conjugating enzyme E2(17)KB 1,Ubiquitin-conjugating enzyme E2-17 kDa 1,Ubiquitin-protein ligase D1
5	E (I)	Zinc finger protein Aiolos	polymer	58	6549.5	1	UniProt (Q9UKT9) Pfam (PF00096)	Homo sapiens (human)	Ikaros family zinc finger protein 3
6	F (N)	NEDD8	polymer	76	8574.0	1	UniProt (Q15843) Pfam (PF00240)	Homo sapiens (human)	Neddylin,Neural precursor cell expressed developmentally down-regulated protein 8,NEDD-8,Ubiquitin-like protein Nedd8
7	G (R)	E3 ubiquitin-protein ligase RBX1, N-terminally processed	polymer	111	12457.1	1	UniProt (P62877) Pfam (PF12678)	Homo sapiens (human)	E3 ubiquitin-protein transferase RBX1,N-terminally processed
8	H (U)	Ubiquitin	polymer	76	8576.8	1	UniProt (P62979) Pfam (PF00240)	Homo sapiens (human)	Donor Ub
9	I, K, L, M, N... (C, I, R)	ZINC ION	non-polymer		65.4	6	Chemie (ZN) PubChem (32051)
10	J (C)	(3S)-3-(5-azanyl-2-methyl-4-oxidanylidene-quinazolin-3-yl)piperidine-2,6-dione	non-polymer		286.3	1	Chemie (835) PubChem (24967954)

Sequence modifications

A: 2 - 759 (UniProt: Q13619)

PDB	External Database	Details
Gly -15	-	expression tag
Pro -14	-	expression tag
Gly -13	-	expression tag
Ser -12	-	expression tag
Gly -11	-	expression tag
Trp -10	-	expression tag
Ser -9	-	expression tag
His -8	-	expression tag
Pro -7	-	expression tag
Gln -6	-	expression tag
Phe -5	-	expression tag
Glu -4	-	expression tag
Lys -3	-	expression tag
Gly -2	-	expression tag
Ser -1	-	expression tag
Gly 0	-	expression tag
Ser 1	-	expression tag

C: 41 - 442 (UniProt: Q96SW2)

PDB	External Database	Details
Gly 16	-	expression tag
Ser 17	-	expression tag
Ser 18	-	expression tag
His 19	-	expression tag
His 20	-	expression tag
His 21	-	expression tag
His 22	-	expression tag
His 23	-	expression tag
His 24	-	expression tag
His 25	-	expression tag
His 26	-	expression tag
Ser 27	-	expression tag
Ser 28	-	expression tag
Gly 29	-	expression tag
Leu 30	-	expression tag
Glu 31	-	expression tag
Val 32	-	expression tag
Leu 33	-	expression tag
Phe 34	-	expression tag
Gln 35	-	expression tag
Gly 36	-	expression tag
Pro 37	-	expression tag
Gly 38	-	expression tag
Ser 39	-	expression tag
Ser 40	-	expression tag

I: 142 - 197 (UniProt: Q9UKT9)

PDB	External Database	Details
Gly 140	-	expression tag
Pro 141	-	expression tag
Cys 166	Lys 166	conflict
Thr 183	Cys 183	conflict

R: 2 - 108 (UniProt: P62877)

PDB	External Database	Details
Gly -2	-	expression tag
Pro -1	-	expression tag
Gly 0	-	expression tag
Ser 1	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	8
	Total formula weight	317989.4
Non-Polymers*	Number of molecules	7
	Total formula weight	678.7
All*	Total formula weight	318668.2

*Water molecules are not included.