5KNB

Crystal structure of the 2 ADP-bound V1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

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Literature

Crystal structures of the ATP-binding and ADP-release dwells of the V1 rotary motor

Suzuki, K.Mizutani, K.Maruyama, S.Shimono, K.Imai, F.L.Muneyuki, E.Kakinuma, Y.Ishizuka-Katsura, Y.Shirouzu, M.Yokoyama, S.Yamato, I.Murata, T.

(2016) Nat Commun 7: 13235-13235

  • DOI: 10.1038/ncomms13235
  • Primary Citation of Related Structures:  
    5KNB, 5KNC, 5KND

  • PubMed Abstract: 
  • V 1 -ATPases are highly conserved ATP-driven rotary molecular motors found in various membrane systems. We recently reported the crystal structures for the Enterococcus hirae A 3 B 3 DF (V 1 ) complex, corresponding to the catalytic dwell state waiting for ATP hydrolysis ...

    V 1 -ATPases are highly conserved ATP-driven rotary molecular motors found in various membrane systems. We recently reported the crystal structures for the Enterococcus hirae A 3 B 3 DF (V 1 ) complex, corresponding to the catalytic dwell state waiting for ATP hydrolysis. Here we present the crystal structures for two other dwell states obtained by soaking nucleotide-free V 1 crystals in ADP. In the presence of 20 μM ADP, two ADP molecules bind to two of three binding sites and cooperatively induce conformational changes of the third site to an ATP-binding mode, corresponding to the ATP-binding dwell. In the presence of 2 mM ADP, all nucleotide-binding sites are occupied by ADP to induce conformational changes corresponding to the ADP-release dwell. Based on these and previous findings, we propose a V 1 -ATPase rotational mechanism model.


    Organizational Affiliation

    JST, PRESTO, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
V-type sodium ATPase catalytic subunit AA, B, C600Enterococcus hirae ATCC 9790Mutation(s): 0 
Gene Names: ntpAEHR_08260
EC: 3.6.3.15 (PDB Primary Data), 7.2.2.1 (UniProt)
UniProt
Find proteins for Q08636 (Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258 / NCTC 12367 / WDCM 00089 / R))
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UniProt GroupQ08636
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
V-type sodium ATPase subunit BD, E, F465Enterococcus hirae ATCC 9790Mutation(s): 0 
Gene Names: ntpBEHR_08265
UniProt
Find proteins for Q08637 (Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258 / NCTC 12367 / WDCM 00089 / R))
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UniProt GroupQ08637
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
V-type sodium ATPase subunit DG217Enterococcus hirae ATCC 9790Mutation(s): 0 
Gene Names: ntpDEHR_08270
UniProt
Find proteins for P43435 (Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258 / NCTC 12367 / WDCM 00089 / R))
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UniProt GroupP43435
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
V-type sodium ATPase subunit NtpG (F)H115Enterococcus hirae ATCC 9790Mutation(s): 0 
Gene Names: ntpGntpQEHR_08255
UniProt
Find proteins for P43455 (Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258 / NCTC 12367 / WDCM 00089 / R))
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
J [auth B],
M [auth C]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
K [auth B],
N [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth B],
L [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.35α = 90
b = 129.62β = 90
c = 237.21γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-02
    Type: Initial release
  • Version 1.1: 2016-11-16
    Changes: Database references
  • Version 1.2: 2020-02-19
    Changes: Data collection, Derived calculations