9B9H: DDB1- and CUL4-associated factor 1

Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-40333. Determined by X-ray diffraction at 2.06 Å resolution. Released 6 Nov 2024.

Method: X-ray diffraction
Resolution: 2.06 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,279
Mol. weight: 75.99 kDa
Ligands: A1AM2
Released: 6 Nov 2024

Explore 9B9H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9B9H contains 2 α-helices and 56 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 0 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	35-41	7	8
β-strand	48-53	6	9
β-strand	59-64	6	9
β-strand	69-73	5	9
β-strand	79-83	5	9
β-strand	90-95	6	10
β-strand	101-106	6	10
β-strand	110-115	6	10
β-strand	121-126	6	10
β-strand	132-137	6	11
β-strand	143-148	6	11
β-strand	153-157	5	11
β-strand	163-167	5	11
β-strand	174-179	6	12
β-strand	185-190	6	12
β-strand	195-199	5	12
β-strand	205-209	5	12
β-strand	217-222	6	13
β-strand	228-233	6	13
β-strand	237-242	6	13
β-strand	247-252	6	13
β-strand	264-267	4	14
β-strand	273-276	4	14
β-strand	283-287	5	14
β-strand	293-297	5	14
β-strand	304-309	6	8
β-strand	315-320	6	8
β-strand	327-332	6	8

Chain B: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	1080-1087	8	1
β-strand	1096-1101	6	2
β-strand	1107-1112	6	2
β-strand	1116-1121	6	2
β-strand	1127-1132	6	2
β-strand	1138-1143	6	3
β-strand	1149-1154	6	3
β-strand	1161-1165	5	3
β-strand	1171-1176	6	3
β-strand	1181-1184	4	4
β-strand	1191-1196	6	4
β-strand	1199-1204	6	4
β-strand	1210-1214	5	4
β-strand	1229-1230	2	5
β-strand	1236-1239	4	5
β-strand	1242-1245	4	5
β-strand	1250-1254	5	5
β-strand	1265-1266	2	6
β-strand	1272-1275	4	6
β-strand	1278-1281	4	6
β-strand	1287-1290	4	6
α-helix	1292-1294	3
β-strand	1297-1301	5	7
β-strand	1307-1313	7	7
α-helix	1314-1315	2
β-strand	1330-1338	9	7
β-strand	1344-1349	6	7
β-strand	1353-1359	7	1
β-strand	1365-1371	7	1
β-strand	1382-1389	8	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DDB1- and CUL4-associated factor 1	B	protein	338	Homo sapiens	Q9Y4B6 (AlphaFold model)
WD repeat-containing protein 5	A	protein	329	Homo sapiens	P61964 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>9B9H_1 DDB1- and CUL4-associated factor 1 (chains B)
MGSSHHHHHHSSGRENLYFQGSSRASAFRPISVFREANEDESGFTCCAFSARERFLMLGT
CTGQLKLYNVFSGQEEASYNCHNSAITHLEPSRDGSLLLTSATWSQPLSALWGMKSVFDM
KHSFTEDHYVEFSKHSQDRVIGTKGDIAHIYDIQTGNKLLTLFNPDLANNYKRNCATFNP
TDDLVLNDGVLWDVRSAQAIHKFDKFNMNISGVFHPNGLEVIINTEIWDLRTFHLLHTVP
ALDQCRVVFNHTGTVMYGAMLQADDEDDLMEERMKSPFGSSFRTFNATDYKPIATIDVKR
NIFDLCTDTKDCYLAVIENQGSMDALNMDTVCRLYEVG

Sequence of entity 2 (A), FASTA

>9B9H_2 WD repeat-containing protein 5 (chains A)
MHHHHHHSSGRENLYFQGTQSKPTPVKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSA
DKLIKIWGAYDGKFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTL
KGHSNYVFCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNRDGSL
IVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYILAATLDNTLKLWDYSK
GKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGHTDVVI
STACHPTENIIASAALENDKTIKLWKSDC

Ligands and cofactors

ID	Name	Formula	Copies
A1AM2	N-{(1P)-5'-({(17E)-18-[(3P)-4-{[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxop…	C60 H63 Cl2 F6 N9 O10	1

Primary citation

Crystal structures of DCAF1-PROTAC-WDR5 ternary complexes provide insight into DCAF1 substrate specificity. Mabanglo, M.F., Wilson, B., Noureldin, M. et al. Nat Commun (2024) 15:10165-10165. DOI 10.1038/s41467-024-54500-x · PubMed

Other PDB entries of the same protein (UniProt Q9Y4B6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9PLY 1.4 Å, Crystal structure of the human DCAF1 WDR domain in complex with OICR-40156
9BHS 1.43 Å, Crystal structure of the WDR domain of human DCAF1 in complex with OICR-9939 compound
9Y4Q 1.48 Å, Crystal structure of the human DCAF1 WDR domain in complex with OICR-40102
8OOD 1.5 Å, Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 15
9YDG 1.54 Å, Crystal structure of the human DCAF1 WDR domain in complex with OICR-41074
8F8E 1.55 Å, Crystal structure of the WDR domain of human DCAF1 in complex with OICR-8268 compound
9Y76 1.56 Å, Crystal structure of the human DCAF1 WDR domain in complex with OICR-40120
9YV4 1.6 Å, Crystal structure of the human DCAF1 WDR domain in complex with OICR-41109
7SSE 1.62 Å, Crystal structure of the WDR domain of human DCAF1 in complex with CYCA-117-70
9BHR 1.62 Å, Crystal structure of the WDR domain of human DCAF1 in complex with OICR-40155 compound
9D4E 1.7 Å, Crystal structure of the human DCAF1 WDR domain in complex with OICR-41103
4PXW 1.72 Å, Crystal structure of human DCAF1 WD40 repeats (Q1250L)

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