8BE3

Crystal structure of KRasG12V-Nanobody84

• PDB DOI: https://doi.org/10.2210/pdb8BE3/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-10-21 Released: 2023-11-01 
• Deposition Author(s): Fischer, B., Wohlkonig, A., Steyaert, J.
• Funding Organization(s): Research Foundation - Flanders (FWO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.230 
• R-Value Work: 0.201 
• R-Value Observed: 0.202 

Literature

ChILL & DisCO to discover Nanobodies that modulate protein-protein interactions and tune the SOS-Ras nucleotide exchange rate

Fischer, B., Wohlkonig, A., Steyaert, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 71.32 kDa 
• Atom Count: 4,725 
• Modelled Residue Count: 543 
• Deposited Residue Count: 624 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody84	A [auth AA0A], D [auth A00A]	122	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2B of GTPase KRas	B [auth R], C [auth A]	190	Homo sapiens	Mutation(s): 1  Gene Names: KRAS, KRAS2, RASK2 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116-2 (Homo sapiens) Explore P01116-2  Go to UniProtKB:  P01116-2
GTEx:  ENSG00000133703

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	F [auth R], H [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	E [auth R], G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.230 
• R-Value Work: 0.201 
• R-Value Observed: 0.202 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.85	α = 90
b = 130.5	β = 116.25
c = 55.6	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-01 
Deposition Author(s): Fischer, B., Wohlkonig, A., Steyaert, J.

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Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	--

Revision History  

• Version 1.0: 2023-11-01
  Type: Initial release