9BJU

Crystal structure of the complex between VHL, ElonginB, ElonginC, and compound 5

• PDB DOI: https://doi.org/10.2210/pdb9BJU/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-04-25 Released: 2024-05-29 
• Deposition Author(s): Murray, J.M., Wu, H., Fuhrmann, J., Fairbrother, W.J., DiPasquale, A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free: 0.256 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 

Literature

Potency-enhanced peptidomimetic VHL ligands with improved oral bioavailability

Wu, H., Murray, J.M., Ishisoko, N., Frommlet, A., Fairbrother, W.J., Fuhrmann, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 175.29 kDa 
• Atom Count: 11,148 
• Modelled Residue Count: 1,361 
• Deposited Residue Count: 1,524 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-B	A, D, G, J	104	Homo sapiens	Mutation(s): 0  Gene Names: ELOB, TCEB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15370 (Homo sapiens) Explore Q15370  Go to UniProtKB:  Q15370
PHAROS:  Q15370 GTEx:  ENSG00000103363

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-C	B, E, H, K	96	Homo sapiens	Mutation(s): 0  Gene Names: ELOC, TCEB1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15369 (Homo sapiens) Explore Q15369  Go to UniProtKB:  Q15369
PHAROS:  Q15369 GTEx:  ENSG00000154582

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
von Hippel-Lindau disease tumor suppressor	C, L	176	Homo sapiens	Mutation(s): 0  Gene Names: VHL
UniProt & NIH Common Fund Data Resources
Find proteins for P40337 (Homo sapiens) Explore P40337  Go to UniProtKB:  P40337
PHAROS:  P40337 GTEx:  ENSG00000134086

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
von Hippel-Lindau disease tumor suppressor	F, I	176	Homo sapiens	Mutation(s): 0  Gene Names: VHL
UniProt & NIH Common Fund Data Resources
Find proteins for P40337 (Homo sapiens) Explore P40337  Go to UniProtKB:  P40337
PHAROS:  P40337 GTEx:  ENSG00000134086

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE	M [auth W], N [auth X], O [auth Y], P [auth Z]	5	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TFA	Q [auth B], Z [auth K]	trifluoroacetic acid C2 H F3 O2 DTQVDTLACAAQTR-UHFFFAOYSA-N
PEG	R [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
DMS	AA [auth L], W [auth H], X [auth I]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO	S [auth C], Y [auth K]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	T [auth C], U [auth F], V [auth H]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSX	C, L	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS
HYP	M [auth W], N [auth X], O [auth Y], P [auth Z]	L-PEPTIDE LINKING	C5 H9 N O3		PRO
TBG	M [auth W], N [auth X], O [auth Y], P [auth Z]	L-PEPTIDE LINKING	C6 H13 N O2		VAL

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free: 0.256 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 
• Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.297	α = 90
b = 93.297	β = 90
c = 362.757	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-29 
Deposition Author(s): Murray, J.M., Wu, H., Fuhrmann, J., Fairbrother, W.J., DiPasquale, A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-05-29
  Type: Initial release