8TNR

Cryo-EM structure of DDB1dB:CRBN:PT-179:SD40, conformation 2

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	860	96033.9	1	UniProt (Q16531) Pfam (PF10433) 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
2	B (B)	Protein cereblon	polymer	485	55144.6	1	UniProt (Q96SW2) Pfam (PF02190) Pfam (PF03226)	Homo sapiens (human)
3	C (C)	Maltose/maltodextrin-binding periplasmic protein,SD40	polymer	455	50466.0	1	UniProt (P0AEX9) UniProt (Q13422) Pfam (PF01547) Pfam (PF00096)	Escherichia coli
4	D, F (B, C)	ZINC ION	non-polymer		65.4	2	Chemie (ZN)
5	E (B)	2-[(3S)-2,6-dioxopiperidin-3-yl]-5-(morpholin-4-yl)-1H-isoindole-1,3(2H)-dione	non-polymer		343.3	1	Chemie (MIQ)

Sequence modifications

A: 1 - 699 (UniProt: Q16531)

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

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 -42	-	initiating methionine
Asp -41	-	expression tag
Tyr -40	-	expression tag
Lys -39	-	expression tag
Asp -38	-	expression tag
Asp -37	-	expression tag
Asp -36	-	expression tag
Asp -35	-	expression tag
Lys -34	-	expression tag
Ser -33	-	expression tag
Ala -32	-	expression tag
Val -31	-	expression tag
Asp -30	-	expression tag
Glu -29	-	expression tag
Asn -28	-	expression tag
Leu -27	-	expression tag
Tyr -26	-	expression tag
Phe -25	-	expression tag
Gln -24	-	expression tag
Gly -23	-	expression tag
Gly -22	-	expression tag
Gly -21	-	expression tag
Arg -20	-	expression tag
Gly -19	-	expression tag
Gly -18	-	expression tag
Ser -17	-	expression tag
Ala -16	-	expression tag
His -15	-	expression tag
Ile -14	-	expression tag
Val -13	-	expression tag
Met -12	-	expression tag
Val -11	-	expression tag
Asp -10	-	expression tag
Ala -9	-	expression tag
Tyr -8	-	expression tag
Lys -7	-	expression tag
Pro -6	-	expression tag
Thr -5	-	expression tag
Lys -4	-	expression tag
Gly -3	-	expression tag
Gly -2	-	expression tag
Ser -1	-	expression tag
Gly 0	-	expression tag

C: -376 - -7 (UniProt: P0AEX9)

PDB	External Database	Details
Met -404	-	initiating methionine
Gly -403	-	expression tag
Leu -402	-	expression tag
Asn -401	-	expression tag
Asp -400	-	expression tag
Ile -399	-	expression tag
Phe -398	-	expression tag
Glu -397	-	expression tag
Ala -396	-	expression tag
Gln -395	-	expression tag
Lys -394	-	expression tag
Ile -393	-	expression tag
Glu -392	-	expression tag
Trp -391	-	expression tag
His -390	-	expression tag
Glu -389	-	expression tag
Gly -388	-	expression tag
Ser -387	-	expression tag
Ser -386	-	expression tag
His -385	-	expression tag
His -384	-	expression tag
His -383	-	expression tag
His -382	-	expression tag
His -381	-	expression tag
His -380	-	expression tag
Gly -379	-	expression tag
Ser -378	-	expression tag
Ser -377	-	expression tag
Leu -6	-	linker
Glu -5	-	linker
Val -4	-	linker
Leu -3	-	linker
Phe -2	-	linker
Gln -1	-	linker
Gly 0	-	linker
Pro 1	-	linker
Asp 2	-	linker
Tyr 3	-	linker
Lys 4	-	linker
Asp 5	-	linker
Asp 6	-	linker
Asp 7	-	linker
Asp 8	-	linker
Lys 9	-	linker
Ser 10	-	linker
Gly 11	-	linker
Gly 12	-	linker
Gly 13	-	linker
Gly 14	-	linker

C: 15 - 50 (UniProt: Q13422)

PDB	External Database	Details
Leu 15	Arg 143	engineered mutation
Leu 16	Pro 144	engineered mutation
Leu 17	Phe 145	engineered mutation
Phe 18	Gln 146	engineered mutation
Pro 20	Asn 148	engineered mutation
Ile 21	Gln 149	engineered mutation
Phe 24	Ala 152	engineered mutation
Thr 25	Ser 153	engineered mutation
Cys 26	Phe 154	engineered mutation
Arg 27	Thr 155	engineered mutation
Asn 37	Lys 165	engineered mutation
Thr 40	Ser 168	engineered mutation
Leu 44	Pro 172	engineered mutation
Tyr 47	Cys 175	engineered mutation
Tyr 50	Cys 178	engineered mutation

Contents of the asymmetric unit

Polymers	Number of chains	3
	Total formula weight	201644.6
Non-Polymers*	Number of molecules	3
	Total formula weight	474.2
All*	Total formula weight	202118.7

*Water molecules are not included.