3EIU | pdb_00003eiu

A second transient position of ATP on its trail to the nucleotide-binding site of subunit B of the motor protein A1Ao ATP synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.43 Å
  • R-Value Free: 
    0.315 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.246 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.249 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ATPClick on this verticalbar to view detailsBest fitted AESClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

A second transient position of ATP on its trail to the nucleotide-binding site of subunit B of the motor protein A(1)A(O) ATP synthase

Manimekalai, M.S.S.Kumar, A.Balakrishna, A.M.Gruber, G.

(2009) J Struct Biol 166: 38-45

  • DOI: https://doi.org/10.1016/j.jsb.2008.12.004
  • Primary Citation of Related Structures:  
    3EIU

  • PubMed Abstract: 

    The adenosine triphosphate (ATP) entrance into the nucleotide-binding subunits of ATP synthases is a puzzle. In the previously determined structure of subunit B mutant R416W of the Methanosarcina mazei Gö1 A-ATP synthase one ATP could be trapped at a transition position, close to the phosphate-binding loop. Using defined parameters for co-crystallization of an ATP-bound B-subunit, a unique transition position of ATP could be found in the crystallographic structure of this complex, solved at 3.4 A resolution. The nucleotide is found near the helix-turn-helix motif in the C-terminal domain of the protein; the location occupied by the gamma-subunit to interact with the empty beta-subunit in the thermoalkaliphilic Bacillus sp. TA2.A1 of the related F-ATP synthase. When compared with the determined structure of the ATP-transition position, close to the P-loop, and the nucleotide-free form of subunit B, the C-terminal domain of the B mutant is rotated by around 6 degrees, implicating an ATP moving pathway. We propose that, in the nucleotide empty state the central stalk subunit D is in close contact with subunit B and when the ATP molecule enters, D moves slightly, paving way for it to interact with the subunit B, which makes the C-terminal domain rotate by 6 degrees.


  • Organizational Affiliation

    Nanyang Technological University, Division of Structural & Computational Biology, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
V-type ATP synthase beta chain
A, B
469Methanosarcina mazeiMutation(s): 1 
Gene Names: ATP Synthase
EC: 3.6.3.14
UniProt
Find proteins for Q60187 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88))
Explore Q60187 
Go to UniProtKB:  Q60187
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ60187
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
C [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
AES
Query on AES

Download Ideal Coordinates CCD File 
D [auth B]4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE
C8 H10 F N O2 S
MGSKVZWGBWPBTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.43 Å
  • R-Value Free:  0.315 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.246 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.249 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.693α = 90
b = 96.867β = 90
c = 129.631γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ATPClick on this verticalbar to view detailsBest fitted AESClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-11-01
    Changes: Data collection, Refinement description