9BOL: Elongin-B

Crystal structure of the complex between VHL, ElonginB, ElonginC, and compound 5. Determined by X-ray diffraction at 1.99 Å resolution. Released 29 May 2024.

Method: X-ray diffraction
Resolution: 1.99 Å
Organism: Homo sapiens
Chains: 6
Atoms: 5,970
Mol. weight: 87.8 kDa
Ligands: A1ARP
Released: 29 May 2024

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

Secondary structure: helices and β-sheets

9BOL contains 39 α-helices and 54 β-strands across 6 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: 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	57-60	4
β-strand	68	1	4
β-strand	71	1	4
α-helix	72	1
β-strand	73-79	7	1
β-strand	80	1	5
β-strand	85	1	5
α-helix	86-87	2
β-strand	90	1	2
α-helix	91-100	10
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	89-92	4
α-helix	97-110	14

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	182-189	8
α-helix	194-208	15

Chain D: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	8
β-strand	10	1	9
β-strand	12-19	8	8
β-strand	23	1	10
α-helix	24-35	12
α-helix	39-41	3
β-strand	42-46	5	8
β-strand	49-50	2	8
α-helix	51-52	2
β-strand	56	1	10
β-strand	68	1	11
β-strand	71	1	11
α-helix	72	1
β-strand	73-79	7	8
β-strand	80-81	2	12
β-strand	84-85	2	12
α-helix	86-88	3
β-strand	90	1	9
α-helix	91-98	8
α-helix	101-103	3

Chain E: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	8
β-strand	28-32	5	8
α-helix	33-36	4
α-helix	40-45	6
β-strand	59-61	3	8
α-helix	67-83	17
α-helix	89-92	4
α-helix	97-99	3
α-helix	100-110	11

Chain F: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	71-78	8	13
α-helix	83	1
β-strand	84-89	6	14
β-strand	95-97	3	14
β-strand	101	1	14
β-strand	106-112	7	13
β-strand	116-121	6	14
β-strand	127	1	14
β-strand	129-130	2	13
β-strand	133	1	13
β-strand	136	1	14
α-helix	145-146	2
β-strand	147-152	6	13
α-helix	158-169	12
α-helix	172-177	6
α-helix	182-189	8
α-helix	194-205	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Elongin-B	A, D	protein	104	Homo sapiens	Q15370 (AlphaFold model)
Elongin-C	B, E	protein	96	Homo sapiens	Q15369 (AlphaFold model)
von Hippel-Lindau disease tumor suppressor	C, F	protein	176	Homo sapiens	P40337 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>9BOL_1 Elongin-B (chains A, D)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMK

Sequence of entity 2 (B, E), FASTA

>9BOL_2 Elongin-C (chains B, E)
MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMY
FTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Sequence of entity 3 (C, F), FASTA

>9BOL_3 von Hippel-Lindau disease tumor suppressor (chains C, F)
MHHHHHHGENLYFQGSMEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQP
YPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYT
LKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD

Ligands and cofactors

ID	Name	Formula	Copies
A1ARP	(4R)-1-[(2S)-2-(4-cyclopropyl-1H-1,2,3-triazol-1-yl)-3,3-dimethylbutanoyl]-4-hy…	C27 H34 N6 O3 S	2

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

Primary citation

Potency-Enhanced Peptidomimetic VHL Ligands with Improved Oral Bioavailability. Wu, H., Murray, J., Ishisoko, N. et al. J Med Chem (2024) 67:8585-8608. DOI 10.1021/acs.jmedchem.3c02203 · 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…
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…
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

Browse structure collections

About this viewer

MolViewer shows 9BOL directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.