6SQ2 | pdb_00006sq2

Structure of a phosphomimetic switch 2 variant of Rab8a in complex with the phospho-Rab binding domain of RILPL2

• PDB DOI: https://doi.org/10.2210/pdb6SQ2/pdb

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


• Deposited: 2019-09-03 Released: 2020-09-30 
• Deposition Author(s): Khan, A.R., Waschbusch, D.
• Funding Organization(s): Science Foundation Ireland

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 
  0.202 (Depositor) 
• R-Value Work: 
  0.181 (Depositor) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Structure of a phosphomimetic switch 2 variant of Rab8a in complex with the phospho-Rab binding domain of RILPL2

Khan, A.R., Waschbusch, D.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content 

• Total Structure Weight: 53.84 kDa 
• Atom Count: 3,974 
• Modeled Residue Count: 412 
• Deposited Residue Count: 454 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-8A	A, B	184	Homo sapiens	Mutation(s): 2  Gene Names: RAB8A, MEL, RAB8 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P61006 (Homo sapiens) Explore P61006  Go to UniProtKB:  P61006
PHAROS:  P61006 GTEx:  ENSG00000167461

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RILP-like protein 2	C [auth D], D [auth E]	43	Homo sapiens	Mutation(s): 0  Gene Names: RILPL2, RLP2
UniProt & NIH Common Fund Data Resources
Find proteins for Q969X0 (Homo sapiens) Explore Q969X0  Go to UniProtKB:  Q969X0
PHAROS:  Q969X0 GTEx:  ENSG00000150977

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	E [auth A], G [auth B]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
MG	F [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free:  0.202 (Depositor) 
• R-Value Work:  0.181 (Depositor) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.698	α = 90
b = 71.733	β = 90
c = 116.39	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-09-30 
Deposition Author(s): Khan, A.R., Waschbusch, D.

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Funding Organization	Location	Grant Number
Science Foundation Ireland	Ireland	12/IA/1239

Revision History  

• Version 1.0: 2020-09-30
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description