2E9S | pdb_00002e9s

human neuronal Rab6B in three intermediate forms

• PDB DOI: https://doi.org/10.2210/pdb2E9S/pdb

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


• Deposited: 2007-01-26 Released: 2008-01-29 
• Deposition Author(s): Vellieux, F.M., Tcherniuk, S., Garcia-Saez, I., Kozielski, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.231 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

3D structure of human neuronal Rab6B in three intermediate forms

Vellieux, F.M., Tcherniuk, S., Garcia-Saez, I., Kozielski, F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 60.82 kDa 
• Atom Count: 4,241 
• Modelled Residue Count: 468 
• Deposited Residue Count: 513 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-6B	A, B, C	171	Homo sapiens	Mutation(s): 0  Gene Names: RAB6B EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NRW1 (Homo sapiens) Explore Q9NRW1  Go to UniProtKB:  Q9NRW1
PHAROS:  Q9NRW1 GTEx:  ENSG00000154917

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	F [auth A], H [auth B], I [auth C]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
NO3	D [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
MG	E [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.231 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.808	α = 90
b = 65.185	β = 90
c = 108.672	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-29 
Deposition Author(s): Vellieux, F.M., Tcherniuk, S., Garcia-Saez, I., Kozielski, F.

Revision History  

• Version 1.0: 2008-01-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description