6IY1

Structure of human Ras-related protein Rab11

• PDB DOI: https://doi.org/10.2210/pdb6IY1/pdb

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


• Deposited: 2018-12-12 Released: 2019-12-18 
• Deposition Author(s): Ma, P., Li, S., Li, J.
• Funding Organization(s): National Science Foundation (China)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 0.261 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 

Starting Model: experimental

Literature

Structure of human Ras-related protein Rab11

Ma, P., Li, S., Li, J.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 assigned by authors and generated by PISA (software)

Biological Assembly 6  

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

Biological assembly 6 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 114.64 kDa 
• Atom Count: 8,223 
• Modelled Residue Count: 988 
• Deposited Residue Count: 995 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-11A	A, B, C, E	165	Homo sapiens	Mutation(s): 0  Gene Names: RAB11A, RAB11 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P62491 (Homo sapiens) Explore P62491  Go to UniProtKB:  P62491
PHAROS:  P62491 GTEx:  ENSG00000103769

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-11A	D	167	Homo sapiens	Mutation(s): 0  Gene Names: RAB11A, RAB11 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P62491 (Homo sapiens) Explore P62491  Go to UniProtKB:  P62491
PHAROS:  P62491 GTEx:  ENSG00000103769

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-11A	F	168	Homo sapiens	Mutation(s): 0  Gene Names: RAB11A, RAB11 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P62491 (Homo sapiens) Explore P62491  Go to UniProtKB:  P62491
PHAROS:  P62491 GTEx:  ENSG00000103769

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 0.261 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.606	α = 90
b = 150.762	β = 98.46
c = 60.125	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-12-18 
Deposition Author(s): Ma, P., Li, S., Li, J.

---

Funding Organization	Location	Grant Number
National Science Foundation (China)	China	31500632

Revision History  

• Version 1.0: 2019-12-18
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description