8EGK

Re-refinement of Crystal Structure of NosGet3d, the All4481 protein from Nostoc sp. PCC 7120


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 3IGF


Literature

Structures of Get3d reveal a distinct architecture associated with the emergence of photosynthesis.

Barlow, A.N.Manu, M.S.Saladi, S.M.Tarr, P.T.Yadav, Y.Thinn, A.M.M.Zhu, Y.Laganowsky, A.D.Clemons Jr., W.M.Ramasamy, S.

(2023) J Biol Chem 299: 104752-104752

  • DOI: https://doi.org/10.1016/j.jbc.2023.104752
  • Primary Citation of Related Structures:  
    8EGK, 8ELF

  • PubMed Abstract: 

    Homologs of the protein Get3 have been identified in all domains yet remain to be fully characterized. In the eukaryotic cytoplasm, Get3 delivers tail-anchored (TA) integral membrane proteins, defined by a single transmembrane helix at their C terminus, to the endoplasmic reticulum. While most eukaryotes have a single Get3 gene, plants are notable for having multiple Get3 paralogs. Get3d is conserved across land plants and photosynthetic bacteria and includes a distinctive C-terminal α-crystallin domain. After tracing the evolutionary origin of Get3d, we solve the Arabidopsis thaliana Get3d crystal structure, identify its localization to the chloroplast, and provide evidence for a role in TA protein binding. The structure is identical to that of a cyanobacterial Get3 homolog, which is further refined here. Distinct features of Get3d include an incomplete active site, a "closed" conformation in the apo-state, and a hydrophobic chamber. Both homologs have ATPase activity and are capable of binding TA proteins, supporting a potential role in TA protein targeting. Get3d is first found with the development of photosynthesis and conserved across 1.2 billion years into the chloroplasts of higher plants across the evolution of photosynthesis suggesting a role in the homeostasis of photosynthetic machinery.


  • Organizational Affiliation

    Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
All4481 protein
A, B
374Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 1 
Gene Names: all4481
UniProt
Find proteins for Q8YNT0 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Explore Q8YNT0 
Go to UniProtKB:  Q8YNT0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8YNT0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.17α = 90
b = 55.553β = 98.87
c = 122.363γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SnBphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Office of the DirectorUnited StatesR01GM097572
National Institutes of Health/Office of the DirectorUnited StatesR01GM125063
National Institutes of Health/Office of the DirectorUnited StatesDP1GM105385
Other privateWeston Havens Foundation
National Science Foundation (NSF, United States)United States11444469
National Institutes of Health/Office of the DirectorUnited StatesT32GM07616

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-24
    Type: Initial release
  • Version 1.1: 2023-06-14
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection
  • Version 1.3: 2023-11-15
    Changes: Data collection