6Y7G | pdb_00006y7g

Structure of the human RAB3C in complex with GDP

• PDB DOI: https://doi.org/10.2210/pdb6Y7G/pdb

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


• Deposited: 2020-02-29 Released: 2021-03-31 
• Deposition Author(s): Diaz-Saez, L., Jung, S., Raux, B., Burgess-Brown, N.A., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Huber, K.V.M., Structural Genomics Consortium (SGC)
• Funding Organization(s): Innovative Medicines Initiative

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.289 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Structure of the human RAB3C in complex with GDP

Diaz-Saez, L., Jung, S., Burgess-Brown, N.A., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Huber, K.V.M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 53.31 kDa 
• Atom Count: 2,874 
• Modeled Residue Count: 324 
• Deposited Residue Count: 454 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-3C	A, B	227	Homo sapiens	Mutation(s): 0  Gene Names: RAB3C EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q96E17 (Homo sapiens) Explore Q96E17  Go to UniProtKB:  Q96E17
PHAROS:  Q96E17 GTEx:  ENSG00000152932

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP (Subject of Investigation/LOI)	C [auth A], F [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
BTB	D [auth A], G [auth B]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N
MG	E [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.289 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.19	α = 86.02
b = 40.434	β = 74.16
c = 66.362	γ = 66.45

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
DIALS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-03-31 
Deposition Author(s): Diaz-Saez, L., Jung, S., Raux, B., Burgess-Brown, N.A., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Huber, K.V.M., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
Innovative Medicines Initiative		--

Revision History  

• Version 1.0: 2021-03-31
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Advisory, Data collection, Database references, Refinement description