3GRL | pdb_00003grl

Crystal Structure of the Monomer of the p115 Tether Globular Head Domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.204 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

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This is version 1.2 of the entry. See complete history

Literature

Structural and functional analysis of the globular head domain of p115 provides insight into membrane tethering.

An, Y.Chen, C.Y.Moyer, B.Rotkiewicz, P.Elsliger, M.A.Godzik, A.Wilson, I.A.Balch, W.E.

(2009) J Mol Biology 391: 26-41

  • DOI: https://doi.org/10.1016/j.jmb.2009.04.062
  • Primary Citation Related Structures: 
    3GQ2, 3GRL

  • PubMed Abstract: 

    Molecular tethers have a central role in the organization of the complex membrane architecture of eukaryotic cells. p115 is a ubiquitous, essential tether involved in vesicle transport and the structural organization of the exocytic pathway. We describe two crystal structures of the N-terminal domain of p115 at 2.0 A resolution. The p115 structures show a novel alpha-solenoid architecture constructed of 12 armadillo-like, tether-repeat, alpha-helical tripod motifs. We find that the H1 TR binds the Rab1 GTPase involved in endoplasmic reticulum to Golgi transport. Mutation of the H1 motif results in the dominant negative inhibition of endoplasmic reticulum to Golgi trafficking. We propose that the H1 helical tripod contributes to the assembly of Rab-dependent complexes responsible for the tether and SNARE-dependent fusion of membranes.


  • Organizational Affiliation
    • Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Macromolecule Content 

  • Total Structure Weight: 72.76 kDa 
  • Atom Count: 5,085 
  • Modeled Residue Count: 601 
  • Deposited Residue Count: 651 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
General vesicular transport factor p115651Bos taurusMutation(s): 0 
Gene Names: USO1VDP
UniProt
Find proteins for P41541 (Bos taurus)
Explore P41541 
Go to UniProtKB:  P41541
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41541
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4

Query on PO4



Download:Ideal Coordinates CCD File
B [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.204 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.629α = 90
b = 174.715β = 90
c = 87.511γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations