2W3C | pdb_00002w3c

Globular head region of the human general vesicular transport factor p115

• PDB DOI: https://doi.org/10.2210/pdb2W3C/pdb

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


• Deposited: 2008-11-11 Released: 2009-03-03 
• Deposition Author(s): Striegl, H., Roske, Y., Kummel, D., Heinemann, U.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 
  0.269 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Literature

Unusual Armadillo Fold in the Human General Vesicular Transport Factor P115

Striegl, H., Roske, Y., Kummel, D., Heinemann, U.

(2009) PLoS One 4: E4656

• PubMed: 19247479 
• DOI: https://doi.org/10.1371/journal.pone.0004656
• Primary Citation Related Structures: 
  2W3C


• PubMed Abstract: 
  

  The golgin family gives identity and structure to the Golgi apparatus and is part of a complex protein network at the Golgi membrane. The golgin p115 is targeted by the GTPase Rab1a, contains a large globular head region and a long region of coiled-coil which forms an extended rod-like structure. p115 serves as vesicle tethering factor and plays an important role at different steps of vesicular transport. Here we present the 2.2 A-resolution X-ray structure of the globular head region of p115. The structure exhibits an armadillo fold that is decorated by elongated loops and carries a C-terminal non-canonical repeat. This terminal repeat folds into the armadillo superhelical groove and allows homodimeric association with important implications for p115 mediated multiple protein interactions and tethering.

---

Organizational Affiliation: 
• Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 64.66 kDa 
• Atom Count: 4,439 
• Modeled Residue Count: 551 
• Deposited Residue Count: 577 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GENERAL VESICULAR TRANSPORT FACTOR P115	A	577	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O60763 (Homo sapiens) Explore O60763  Go to UniProtKB:  O60763
PHAROS:  O60763 GTEx:  ENSG00000138768

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	B [auth A], C [auth A], D [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free:  0.269 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 175.55	α = 90
b = 68.89	β = 108.74
c = 85.75	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-03 
Deposition Author(s): Striegl, H., Roske, Y., Kummel, D., Heinemann, U.

Revision History  

• Version 1.0: 2009-03-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other