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 5YVF | pdb_00005yvf

Crystal structure of BFA1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.261 (Depositor), 0.259 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 
    0.223 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5YVF

This is version 1.2 of the entry. See complete history. 

Literature

Nucleus-Encoded Protein BFA1 Promotes Efficient Assembly of the Chloroplast ATP Synthase Coupling Factor 1.

Zhang, L., Pu, H., Duan, Z., Li, Y., Liu, B., Zhang, Q., Li, W., Rochaix, J.D., Liu, L., Peng, L.

(2018) Plant Cell 30: 1770-1788

  • DOI: https://doi.org/10.1105/tpc.18.00075
  • Primary Citation Related Structures: 
    5YVF

  • PubMed Abstract: 

    F-type ATP synthases produce nearly all of the ATP found in cells. The catalytic module F 1 commonly comprises an α 3 β 3 hexamer surrounding a γ/ε stalk. However, it is unclear how these subunits assemble to form a catalytic motor. In this work, we identified and characterized a chloroplast protein that interacts with the CF 1 β, γ, and ε subunits of the chloroplast ATP synthase and is required for assembly of its F 1 module. We named this protein BIOGENESIS FACTOR REQUIRED FOR ATP SYNTHASE1 (BFA1) and determined its crystal structure at 2.8-Å resolution. BFA1 is comprised primarily of two interacting β-barrels that are oriented nearly perpendicularly to each other. The contact region between BFA1 and the CF 1 β and γ subunits was further mapped by yeast two-hybrid assays. An in silico molecular docking analysis was performed and revealed close fitting contact sites without steric conflicts between BFA1 and CF 1 β/γ. We propose that BFA1 acts mainly as a scaffold protein promoting the association of a CF 1 α/β heterodimer with CF 1 γ. The subsequent assembly of other CF 1 α/β heterodimers may shift the position of the CF 1 γ subunit to complete assembly of the CF 1 module. This CF 1 assembly process is likely to be valid for other F-type ATP synthases, as their structures are highly conserved.


  • Organizational Affiliation: 
    • College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China.

Macromolecule Content 

  • Total Structure Weight: 167.81 kDa 
  • Atom Count: 10,139 
  • Modeled Residue Count: 1,270 
  • Deposited Residue Count: 1,480 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BFA1
A, B, C, D
370Arabidopsis thalianaMutation(s): 0 
Gene Names: At3g29185, AXX17_At3g32040
UniProt
Find proteins for F4J1U2 (Arabidopsis thaliana)
Explore F4J1U2 
Go to UniProtKB:  F4J1U2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF4J1U2
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.261 (Depositor), 0.259 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 0.223 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.925α = 90
b = 134.628β = 90
c = 149.477γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
SHELXDphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2018-09-26
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references