6BVB: HIF-2alpha-pVHL-elongin B-elongin C

Crystal structure of HIF-2alpha-pVHL-elongin B-elongin C. Determined by X-ray diffraction at 2.0 Å resolution. Released 1 Aug 2018.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,895
Mol. weight: 44.89 kDa
Released: 1 Aug 2018

Explore 6BVB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6BVB contains 19 α-helices and 26 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: 8 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	3
β-strand	10	1	4
β-strand	12-19	8	3
β-strand	23	1	5
α-helix	24-35	12
α-helix	39-41	3
β-strand	42-46	5	3
β-strand	49-50	2	3
α-helix	51-52	2
β-strand	56	1	5
α-helix	58-60	3
β-strand	68	1	6
β-strand	71	1	6
α-helix	72	1
β-strand	73-79	7	3
β-strand	90	1	4
α-helix	91-96	6
α-helix	98-100	3
α-helix	101-103	3

Chain C: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	3
β-strand	28-32	5	3
α-helix	33-36	4
α-helix	40-45	6
β-strand	58-61	4	3
α-helix	67-83	17
α-helix	89-92	4
α-helix	97-110	14

Chain H: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	532	1	1

Chain V: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	71-78	8	1
α-helix	83	1
β-strand	84-89	6	2
β-strand	95-97	3	2
β-strand	101	1	2
β-strand	106-112	7	1
β-strand	116-121	6	2
β-strand	127	1	2
β-strand	129-130	2	1
β-strand	133	1	1
β-strand	136	1	2
α-helix	145-146	2
β-strand	147-152	6	1
α-helix	158-169	12
α-helix	172-177	6
α-helix	183-189	7
α-helix	194-207	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
von Hippel-Lindau disease tumor suppressor	V	protein	162	Homo sapiens	P40337 (AlphaFold model)
Elongin-B	B	protein	118	Homo sapiens	Q15370 (AlphaFold model)
Elongin-C	C	protein	96	Homo sapiens	Q15369 (AlphaFold model)
Hypoxia-Inducible Factor 2 alpha	H	protein	19	Homo sapiens	Q99814 (AlphaFold model)

Sequence of entity 1 (V), FASTA

>6BVB_1 von Hippel-Lindau disease tumor suppressor (chains V)
GSMEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHS
YRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVK
PENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD

Sequence of entity 2 (B), FASTA

>6BVB_2 Elongin-B (chains B)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ

Sequence of entity 3 (C), FASTA

>6BVB_3 Elongin-C (chains C)
MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMY
FTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Sequence of entity 4 (H), FASTA

>6BVB_4 Hypoxia-Inducible Factor 2 alpha (chains H)
ELDLETLAPYIPMDGEDFL

Primary citation

HIF-2 alpha-pVHL complex reveals broad genotype-phenotype correlations in HIF-2 alpha-driven disease. Tarade, D., Robinson, C.M., Lee, J.E. et al. Nat Commun (2018) 9:3359-3359. DOI 10.1038/s41467-018-05554-1 · PubMed

Other PDB entries of the same protein (UniProt P40337 (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…
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
6ZHC 1.92 Å, PROTAC6 mediated complex of VHL:EloB:EloC and Bcl-xL

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