9SQ5

Cryo-EM structure of the DDB1deltaB-CRBN-Pomalidomide complex bound to IKZF1(ZF1-ZF2-Helix)

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A (A)	DNA damage-binding protein 1	polymer	864	96425.6	1	UniProt (Q16531)	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
2	B (B)	Protein cereblon	polymer	466	53290.5	1	UniProt (Q96SW2)	Homo sapiens (human)
3	C (C)	Isoform Ik7 of DNA-binding protein Ikaros	polymer	111	12396.9	1	UniProt (Q13422)	Homo sapiens (human)	Ikaros family zinc finger protein 1,Lymphoid transcription factor LyF-1
4	D, F (B, C)	ZINC ION	non-polymer		65.4	2	Chemie (ZN) PubChem (32051)
5	E (B)	S-Pomalidomide	non-polymer		273.2	1	Chemie (Y70) PubChem (9965330)

Sequence modifications

A: 1 - 699 (UniProt: Q16531)

PDB	External Database	Details
Met -27	-	initiating methionine
Gly -26	-	expression tag
Ser -25	-	expression tag
Ser -24	-	expression tag
His -23	-	expression tag
His -22	-	expression tag
His -21	-	expression tag
His -20	-	expression tag
His -19	-	expression tag
His -18	-	expression tag
Ser -17	-	expression tag
Ala -16	-	expression tag
Ala -15	-	expression tag
His -14	-	expression tag
Ile -13	-	expression tag
Val -12	-	expression tag
Met -11	-	expression tag
Val -10	-	expression tag
Asp -9	-	expression tag
Ala -8	-	expression tag
Tyr -7	-	expression tag
Lys -6	-	expression tag
Pro -5	-	expression tag
Thr -4	-	expression tag
Lys -3	-	expression tag
Gly -2	-	expression tag
Gly -1	-	expression tag
Arg 0	-	expression tag

A: 706 - 1140 (UniProt: Q16531)

PDB	External Database	Details
Gly 700	-	linker
Asn 701	-	linker
Gly 702	-	linker
Asn 703	-	linker
Ser 704	-	linker
Gly 705	-	linker

B: 1 - 442 (UniProt: Q96SW2)

PDB	External Database	Details
Met -23	-	initiating methionine
Gly -22	-	expression tag
Ser -21	-	expression tag
Ser -20	-	expression tag
His -19	-	expression tag
His -18	-	expression tag
His -17	-	expression tag
His -16	-	expression tag
His -15	-	expression tag
His -14	-	expression tag
Ser -13	-	expression tag
Ala -12	-	expression tag
Val -11	-	expression tag
Asp -10	-	expression tag
Glu -9	-	expression tag
Asn -8	-	expression tag
Leu -7	-	expression tag
Tyr -6	-	expression tag
Phe -5	-	expression tag
Gln -4	-	expression tag
Gly -3	-	expression tag
Gly -2	-	expression tag
Gly -1	-	expression tag
Arg 0	-	expression tag

C: 141 - 201 (UniProt: Q13422)

PDB	External Database	Details
Met 91	-	initiating methionine
Asp 92	-	expression tag
Trp 93	-	expression tag
Ser 94	-	expression tag
His 95	-	expression tag
Pro 96	-	expression tag
Gln 97	-	expression tag
Phe 98	-	expression tag
Glu 99	-	expression tag
Lys 100	-	expression tag
Ser 101	-	expression tag
Ala 102	-	expression tag
Val 103	-	expression tag
Met 104	-	expression tag
Ser 105	-	expression tag
Gly 106	-	expression tag
Leu 107	-	expression tag
Asn 108	-	expression tag
Asp 109	-	expression tag
Ile 110	-	expression tag
Phe 111	-	expression tag
Glu 112	-	expression tag
Ala 113	-	expression tag
Gln 114	-	expression tag
Lys 115	-	expression tag
Ile 116	-	expression tag
Glu 117	-	expression tag
Trp 118	-	expression tag
His 119	-	expression tag
Glu 120	-	expression tag
Gly 121	-	expression tag
Gly 122	-	expression tag
Gly 123	-	expression tag
Gly 124	-	expression tag
Ser 125	-	expression tag
Gly 126	-	expression tag
Gly 127	-	expression tag
Gly 128	-	expression tag
Gly 129	-	expression tag
Asp 130	-	expression tag
Glu 131	-	expression tag
Asn 132	-	expression tag
Leu 133	-	expression tag
Tyr 134	-	expression tag
Phe 135	-	expression tag
Gln 136	-	expression tag
Gly 137	-	expression tag
Gly 138	-	expression tag
Gly 139	-	expression tag
Arg 140	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	3
	Total formula weight	162113.0
Non-Polymers*	Number of molecules	3
	Total formula weight	404.1
All*	Total formula weight	162517.0

*Water molecules are not included.