9SQ4

Cryo-EM structure of the DDB1deltaB-CRBN-Pomalidomide complex bound to SALL4(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)	Sal-like protein 4	polymer	255	27486.8	1	UniProt (Q9UJQ4)	Homo sapiens (human)	Zinc finger protein 797,Zinc finger protein SALL4
4	D, F, G (B, C)	ZINC ION	non-polymer		65.4	3	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: 361 - 591 (UniProt: Q9UJQ4)

PDB	External Database	Details
Met 337	-	initiating methionine
Asp 338	-	expression tag
Trp 339	-	expression tag
Ser 340	-	expression tag
His 341	-	expression tag
Pro 342	-	expression tag
Gln 343	-	expression tag
Phe 344	-	expression tag
Glu 345	-	expression tag
Lys 346	-	expression tag
Ser 347	-	expression tag
Ala 348	-	expression tag
Val 349	-	expression tag
Asp 350	-	expression tag
Glu 351	-	expression tag
Asn 352	-	expression tag
Leu 353	-	expression tag
Tyr 354	-	expression tag
Phe 355	-	expression tag
Gln 356	-	expression tag
Gly 357	-	expression tag
Gly 358	-	expression tag
Gly 359	-	expression tag
Arg 360	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	3
	Total formula weight	177202.9
Non-Polymers*	Number of molecules	4
	Total formula weight	469.5
All*	Total formula weight	177672.4

*Water molecules are not included.