Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer - A2 Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 80.36 kDa 
• Atom Count: 5049 
• Modelled Residue Count: 627 
• Deposited Residue Count: 704 
• Unique protein chains: 2

2CFH

Structure of the Bet3-TPC6B core of TRAPP

• DOI: 10.2210/pdb2CFH/pdb

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


• Deposited: 2006-02-21 Released: 2006-07-12 
• Deposition Author(s): Kummel, D., Muller, J.J., Roske, Y., Henke, N., Heinemann, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.269 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 

Literature

Structure of the Bet3-Tpc6B Core of Trapp: Two Tpc6 Paralogs Form Trimeric Complexes with Bet3 and Mum2.

Kummel, D., Muller, J.J., Roske, Y., Henke, N., Heinemann, U.

(2006) J Mol Biol 361: 22

• PubMed: 16828797 
• DOI: 10.1016/j.jmb.2006.06.012
• Primary Citation of Related Structures:  
  2CFH


• PubMed Abstract: 
  

The transport protein particle (TRAPP) complexes are involved in the tethering process at different trafficking steps of vesicle transport. We here present the crystal structure of a human Bet3-Tpc6B heterodimer, which represents a core sub-complex in the assembly of TRAPP. We describe a conserved patch of Tpc6 with uncharged pockets, forming a putative interaction interface for an anchoring moiety at the Golgi. The structural and functional comparison of the two paralogs Tpc6A and Tpc6B, only found in some organisms, indicates redundancy and added complexity of TRAPP architecture and function. Both iso-complexes, Bet3-Tpc6A and Bet3-Tpc6B, are able to recruit Mum2, a further TRAPP subunit, and we identify the alpha1-alpha2 loop regions as a binding site for Mum2. Our study reveals similar stability of the iso-complexes and similar expression patterns of the tpc6 variants in different mouse organs. These findings raise the possibility that the Tpc6 paralogs might contribute to the formation of two distinct TRAPP complexes that differ in function.

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Organizational Affiliation: 

Max-Delbrück Center for Molecular Medicine, Berlin, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 3	A, B	194	Homo sapiens	Mutation(s): 0  Gene Names: TRAPPC3, BET3, CDABP0066
Find proteins for O43617 (Homo sapiens) Explore O43617  Go to UniProtKB:  O43617
NIH Common Fund Data Resources
PHAROS:  O43617 GTEx:  ENSG00000054116

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 6B	C, D	158	Homo sapiens	Mutation(s): 0  Gene Names: TRAPPC6B
Find proteins for Q86SZ2 (Homo sapiens) Explore Q86SZ2  Go to UniProtKB:  Q86SZ2
NIH Common Fund Data Resources
PHAROS:  Q86SZ2 GTEx:  ENSG00000182400

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLM	A, B	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	C,D	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.269 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.45	α = 90
b = 69.59	β = 91.55
c = 144.006	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-02-21 
• Released Date: 2006-07-12 
Deposition Author(s): Kummel, D., Muller, J.J., Roske, Y., Henke, N., Heinemann, U.

Revision History  

• Version 1.0: 2006-07-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2011-10-26
  Changes: Atomic model, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary