8BDS: Elongin-B

Ternary complex between VCB, BRD4-BD1 and PROTAC 48. Determined by X-ray diffraction at 1.72 Å resolution. Released 15 Feb 2023.

Method: X-ray diffraction
Resolution: 1.72 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,297
Mol. weight: 58.32 kDa
Ligands: QIY
Released: 15 Feb 2023

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

Secondary structure: helices and β-sheets

8BDS contains 32 α-helices and 27 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 A: 10 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
α-helix	64-66	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	91-93	3
α-helix	96-100	5
α-helix	101-103	3

Chain B: 5 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	97-99	3
α-helix	100-110	11

Chain C: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	71-78	8	6
α-helix	83	1
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
α-helix	140-141	2
α-helix	145-146	2
β-strand	147-152	6	6
α-helix	158-169	12
α-helix	172-177	6
α-helix	183-189	7
α-helix	194-206	13

Chain D: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	45-49	5
α-helix	61-65	5
α-helix	66-71	6
α-helix	72-75	4
α-helix	81-83	3
α-helix	97-100	4
α-helix	107-115	9
α-helix	122-139	18
α-helix	145-161	17
α-helix	164-167	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Elongin-B	A	protein	104	Homo sapiens	Q15370 (AlphaFold model)
Elongin-C	B	protein	97	Homo sapiens	Q15369 (AlphaFold model)
von Hippel-Lindau disease tumor suppressor	C	protein	162	Homo sapiens	P40337 (AlphaFold model)
Bromodomain-containing protein 4	D	protein	127	Homo sapiens	O60885 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8BDS_1 Elongin-B (chains A)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMK

Sequence of entity 2 (B), FASTA

>8BDS_2 Elongin-C (chains B)
MMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCM
YFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Sequence of entity 3 (C), FASTA

>8BDS_3 von Hippel-Lindau disease tumor suppressor (chains C)
GSMEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHS
YRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVK
PENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD

Sequence of entity 4 (D), FASTA

>8BDS_4 Bromodomain-containing protein 4 (chains D)
SMNPPPPETSNPNKPKRQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKII
KTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKI
NELPTEE

Ligands and cofactors

ID	Name	Formula	Copies
QIY	(2S,4R)-N-[(1S)-1-(4-chlorophenyl)-3-[2-[2-[2-[2-[2-[(9S)-7-(4-chlorophenyl)-4,…	C50 H63 Cl2 N9 O9 S	1

Water and common crystallization additives (EDO, SO4) are not listed.

Primary citation

Systematic Potency and Property Assessment of VHL Ligands and Implications on PROTAC Design. Krieger, J., Sorrell, F.J., Wegener, A.A. et al. ChemMedChem (2023) 18:e202200615-e202200615. DOI 10.1002/cmdc.202200615 · PubMed

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…
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…
8BB3 1.8 Å, Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with PEG linker…
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

Browse structure collections

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