5KYW

crystal structure of Sec23 and TANGO1 peptide3 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

TANGO1/cTAGE5 receptor as a polyvalent template for assembly of large COPII coats.

Ma, W.Goldberg, J.

(2016) Proc.Natl.Acad.Sci.USA 113: 10061-10066

  • DOI: 10.1073/pnas.1605916113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The supramolecular cargo procollagen is loaded into coat protein complex II (COPII)-coated carriers at endoplasmic reticulum (ER) exit sites by the receptor molecule TANGO1/cTAGE5. Electron microscopy studies have identified a tubular carrier of suit ...

    The supramolecular cargo procollagen is loaded into coat protein complex II (COPII)-coated carriers at endoplasmic reticulum (ER) exit sites by the receptor molecule TANGO1/cTAGE5. Electron microscopy studies have identified a tubular carrier of suitable dimensions that is molded by a distinctive helical array of the COPII inner coat protein Sec23/24•Sar1; the helical arrangement is absent from canonical COPII-coated small vesicles. In this study, we combined X-ray crystallographic and biochemical analysis to characterize the association of TANGO1/cTAGE5 with COPII proteins. The affinity for Sec23 is concentrated in the proline-rich domains (PRDs) of TANGO1 and cTAGE5, but Sec23 recognizes merely a PPP motif. The PRDs contain repeated PPP motifs separated by proline-rich linkers, so a single TANGO1/cTAGE5 receptor can bind multiple copies of coat protein in a close-packed array. We propose that TANGO1/cTAGE5 promotes the accretion of inner coat proteins to the helical lattice. Furthermore, we show that PPP motifs in the outer coat protein Sec31 also bind to Sec23, suggesting that stepwise COPII coat assembly will ultimately displace TANGO1/cTAGE5 and compartmentalize its operation to the base of the growing COPII tubule.


    Organizational Affiliation

    Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065; Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 goldberj@mskcc.org.,Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065; Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein transport protein Sec23A
A
765Homo sapiensMutation(s): 0 
Gene Names: SEC23A
Find proteins for Q15436 (Homo sapiens)
Go to Gene View: SEC23A
Go to UniProtKB:  Q15436
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein transport protein Sec24D
B
770Homo sapiensMutation(s): 0 
Gene Names: SEC24D (KIAA0755)
Find proteins for O94855 (Homo sapiens)
Go to Gene View: SEC24D
Go to UniProtKB:  O94855
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
TANGO1 peptide3
C
9Homo sapiensMutation(s): 0 
Gene Names: MIA3 (KIAA0268, TANGO)
Find proteins for Q5JRA6 (Homo sapiens)
Go to Gene View: MIA3
Go to UniProtKB:  Q5JRA6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 101.625α = 90.00
b = 141.346β = 90.00
c = 151.878γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-07-22 
  • Released Date: 2016-09-07 
  • Deposition Author(s): Ma, W., Goldberg, J.

Revision History 

  • Version 1.0: 2016-09-07
    Type: Initial release
  • Version 1.1: 2016-09-14
    Type: Database references
  • Version 1.2: 2017-08-23
    Type: Data collection, Database references, Derived calculations