8BOS | pdb_00008bos

Transition state analogue complex of small G protein and its GAP effector

• PDB DOI: https://doi.org/10.2210/pdb8BOS/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-11-15 Released: 2023-11-29 
• Deposition Author(s): Baumann, P., Jin, Y.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.280 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

A small G protein with MgF3 TSA complex

Baumann, P., Jin, Y.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 57.26 kDa 
• Atom Count: 3,973 
• Modeled Residue Count: 486 
• Deposited Residue Count: 497 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase HRas	A [auth R]	166	Homo sapiens	Mutation(s): 0  Gene Names: HRAS, HRAS1 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01112 (Homo sapiens) Explore P01112  Go to UniProtKB:  P01112
PHAROS:  P01112 GTEx:  ENSG00000174775

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras GTPase-activating protein 1	B [auth G]	331	Homo sapiens	Mutation(s): 0  Gene Names: RASA1, GAP, RASA
UniProt & NIH Common Fund Data Resources
Find proteins for P20936 (Homo sapiens) Explore P20936  Go to UniProtKB:  P20936
PHAROS:  P20936 GTEx:  ENSG00000145715

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP (Subject of Investigation/LOI)	C [auth R]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MGF (Subject of Investigation/LOI)	D [auth R]	TRIFLUOROMAGNESATE F3 Mg GJOMWUHGUQLOAC-UHFFFAOYSA-K
GAI	F [auth G]	GUANIDINE C H5 N3 ZRALSGWEFCBTJO-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	E [auth R]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.280 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.832	α = 90
b = 41.558	β = 109.25
c = 89.674	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Coot	model building
Aimless	data scaling
MOLREP	phasing
xia2	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-29 
Deposition Author(s): Baumann, P., Jin, Y.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	218568/Z/19/Z
Wellcome Trust	United Kingdom	209057/Z/17/Z

Revision History  

• Version 1.0: 2023-11-29
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Structure summary