9RP9 | pdb_00009rp9

Crystal structure of mouse pVHL-ElonginB-ElonginC complex

• PDB DOI: https://doi.org/10.2210/pdb9RP9/pdb

• Classification: LIGASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-06-24 Released: 2025-07-09 
• Deposition Author(s): Blat, A., Biterova, E., Cukier, C.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.222 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of mouse pVHL-ElonginB-ElonginC complex

Blat, A., Biterova, E., Cukier, C.

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

Macromolecule Content 

• Total Structure Weight: 42.7 kDa 
• Atom Count: 2,936 
• Modeled Residue Count: 342 
• Deposited Residue Count: 365 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
von Hippel-Lindau disease tumor suppressor	A	164	Mus musculus	Mutation(s): 0  Gene Names: Vhl, Vhlh
UniProt
Find proteins for P40338 (Mus musculus) Explore P40338  Go to UniProtKB:  P40338

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-B	B	104	Mus musculus	Mutation(s): 0  Gene Names: Elob, Tceb2
UniProt
Find proteins for P62869 (Mus musculus) Explore P62869  Go to UniProtKB:  P62869

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-C	C	97	Mus musculus	Mutation(s): 0  Gene Names: Eloc, Tceb1
UniProt
Find proteins for P83940 (Mus musculus) Explore P83940  Go to UniProtKB:  P83940

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	D [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
IOD	E [auth A], G [auth B], I [auth C]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
PEG	J [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	F [auth A], H [auth B], K [auth C], L [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSX	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.222 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M39RP9

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.48	α = 90
b = 59.78	β = 100.85
c = 91.67	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-09 
Deposition Author(s): Blat, A., Biterova, E., Cukier, C.

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Funding Organization	Location	Grant Number
Other private	Poland	--

Revision History  

• Version 1.0: 2025-07-09
  Type: Initial release