8BB3: Human WDR5 and pVHL:ElonginC:ElonginB

Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with PEG linker (conformation #1). Determined by X-ray diffraction at 1.8 Å resolution. Released 9 Nov 2022.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,513
Mol. weight: 79.91 kDa
Ligands: Q3X, SCN
Released: 9 Nov 2022

Explore 8BB3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8BB3 contains 18 α-helices and 57 β-strands across 4 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 B: 1 helix, 28 β-strands

Element	Residues	Length	Sheet
β-strand	36-41	6	9
β-strand	48-53	6	10
β-strand	59-64	6	10
β-strand	69-73	5	10
β-strand	79-83	5	10
β-strand	90-95	6	11
β-strand	101-106	6	11
β-strand	110-115	6	11
β-strand	121-126	6	11
β-strand	132-137	6	12
β-strand	143-148	6	12
β-strand	153-157	5	12
β-strand	163-167	5	12
β-strand	174-179	6	13
β-strand	185-190	6	13
β-strand	195-199	5	13
β-strand	205-208	4	13
α-helix	215-216	2
β-strand	217-222	6	14
β-strand	228-233	6	14
β-strand	237-242	6	14
β-strand	247-252	6	14
β-strand	264-267	4	15
β-strand	273-277	5	15
β-strand	283-287	5	15
β-strand	293-297	5	15
β-strand	304-309	6	9
β-strand	315-320	6	9
β-strand	327-331	5	9

Chain J: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	1
β-strand	10	1	2
β-strand	12-19	8	1
β-strand	23	1	3
α-helix	24-35	12
α-helix	39-41	3
β-strand	42-46	5	1
β-strand	49-50	2	1
α-helix	51-52	2
β-strand	56	1	3
α-helix	58-60	3
β-strand	68	1	4
β-strand	71	1	4
α-helix	72	1
β-strand	73-79	7	1
β-strand	80-81	2	5
β-strand	84-85	2	5
α-helix	86-88	3
β-strand	90	1	2
α-helix	91-94	4
α-helix	98-100	3

Chain K: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	1
β-strand	28-32	5	1
α-helix	33-36	4
α-helix	40-46	7
β-strand	59-61	3	1
α-helix	67-83	17
α-helix	97-110	14

Chain L: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	71-78	8	6
β-strand	84-89	6	7
β-strand	95-97	3	7
β-strand	101	1	7
β-strand	106-112	7	6
β-strand	116-121	6	7
β-strand	127	1	7
β-strand	129-130	2	6
β-strand	133	1	6
β-strand	136	1	7
β-strand	142	1	8
β-strand	145	1	8
α-helix	146	1
β-strand	147-152	6	6
α-helix	158-169	12
α-helix	172-177	6
α-helix	182-189	8
α-helix	194-207	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Elongin-B	J	protein	104	Homo sapiens	Q15370 (AlphaFold model)
Elongin-C	K	protein	98	Homo sapiens	Q15369 (AlphaFold model)
von Hippel-Lindau disease tumor suppressor	L	protein	162	Homo sapiens	P40337 (AlphaFold model)
WD repeat-containing protein 5	B	protein	321	Homo sapiens	P61964 (AlphaFold model)

Sequence of entity 1 (J), FASTA

>8BB3_1 Elongin-B (chains J)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMK

Sequence of entity 2 (K), FASTA

>8BB3_2 Elongin-C (chains K)
KAMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVC
MYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Sequence of entity 3 (L), FASTA

>8BB3_3 von Hippel-Lindau disease tumor suppressor (chains L)
GSMEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHS
YRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVK
PENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD

Sequence of entity 4 (B), FASTA

>8BB3_4 WD repeat-containing protein 5 (chains B)
MGSSHHHHHHSSGLVPRGSPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWG
AYDGKFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVF
CCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDG
LCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYT
GHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGHTDVVISTACHPTE
NIIASAALENDKTIKLWKSDC

Ligands and cofactors

ID	Name	Formula	Copies
Q3X	~{N}-[5-[4-[2-[2-[2-[2-[3-[[3,3-dimethyl-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-t…	C58 H72 F3 N9 O11 S	1
SCN	Thiocyanate ion	C N S	15

Water and common crystallization additives (P6G, EDO) are not listed.

Primary citation

Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with PEG linker (conformation #1). Kraemer, A., Doelle, A., Knapp, S. et al. To be published.

Other PDB entries of the same protein (UniProt Q15370 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7Z76 1.32 Å, Crystal structure of compound 10 in complex with the bromodomain of human SMARCA2 and…
9GIO 1.49 Å, Crystal structure of the VHL-EloC-EloB complex with a covalent compound bound to C77 of…
7JTO 1.7 Å, Crystal structure of Protac MS33 in complex with the WD repeat-containing protein 5 and…
8BDS 1.72 Å, Ternary complex between VCB, BRD4-BD1 and PROTAC 48
4AJY 1.73 Å, von Hippel-Lindau protein-ElonginB-ElonginC complex, bound to Hif1- alpha peptide
6GMR 1.75 Å, pVHL:EloB:EloC in complex with (4-(1H-pyrrol-1-yl)phenyl)methanol
6HR2 1.76 Å, Crystal structure of PROTAC 2 in complex with the bromodomain of human SMARCA4 and…
7ZLM 1.79 Å, Crystal structure of SOCS2:ElonginB:ElonginC in complex with compound MN551
6I7Q 1.8 Å, Structure of pVHL-elongin B-elongin C (VCB) in complex with hydroxylated-HIF-2alpha…
6GFX 1.83 Å, pVHL:EloB:EloC in complex with modified HIF-1a CODD peptide containing…
1LM8 1.85 Å, Structure of a HIF-1a-pVHL-ElonginB-ElonginC Complex
9D1Z 1.88 Å, Structure of G75Q Ubiquitin bound to KLHDC3-EloB/C

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