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PDBsum entry 6tk2
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Membrane protein
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PDB id
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6tk2
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PDB id:
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| Name: |
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Membrane protein
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Title:
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Femtosecond to millisecond structural changes in a light-driven sodium pump: 1ms structure of kr2 with extrapolated, light and dark datasets
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Structure:
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Sodium pumping rhodopsin. Chain: a. Engineered: yes
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Source:
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Dokdonia eikasta. Organism_taxid: 308116. Gene: nar. Expressed in: escherichia coli. Expression_system_taxid: 562
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Resolution:
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2.50Å
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R-factor:
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0.263
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R-free:
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0.324
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Authors:
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P.Skopintsev,D.Ehrenberg,T.Weinert,D.James,R.Kar,P.Johnson,D.Ozerov, A.Furrer,I.Martiel,F.Dworkowski,K.Nass,G.Knopp,C.Cirelli,D.Gashi, S.Mous,M.Wranik,T.Gruhl,D.Kekilli,S.Bruenle,X.Deupi,G.F.X.Schertler, R.Benoit,V.Panneels,P.Nogly,I.Schapiro,C.Milne,J.Heberle,J.Standfuss
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Key ref:
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P.Skopintsev
et al.
(2020).
Femtosecond-to-millisecond structural changes in a light-driven sodium pump.
Nature,
583,
314-318.
PubMed id:
DOI:
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Date:
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28-Nov-19
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Release date:
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27-May-20
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PROCHECK
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Headers
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References
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N0DKS8
(N0DKS8_9FLAO) -
Sodium pumping rhodopsin from Dokdonia eikasta
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Seq:
Struc:
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280 a.a.
265 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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DOI no:
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Nature
583:314-318
(2020)
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PubMed id:
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Femtosecond-to-millisecond structural changes in a light-driven sodium pump.
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P.Skopintsev,
D.Ehrenberg,
T.Weinert,
D.James,
R.K.Kar,
P.J.M.Johnson,
D.Ozerov,
A.Furrer,
I.Martiel,
F.Dworkowski,
K.Nass,
G.Knopp,
C.Cirelli,
C.Arrell,
D.Gashi,
S.Mous,
M.Wranik,
T.Gruhl,
D.Kekilli,
S.Brünle,
X.Deupi,
G.F.X.Schertler,
R.M.Benoit,
V.Panneels,
P.Nogly,
I.Schapiro,
C.Milne,
J.Heberle,
J.Standfuss.
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ABSTRACT
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Light-driven sodium pumps actively transport small cations across cellular
membranes1. These pumps are used by microorganisms to convert light
into membrane potential and have become useful optogenetic tools with
applications in neuroscience. Although the resting state structures of the
prototypical sodium pump Krokinobacter eikastus rhodopsin 2 (KR2) have been
solved2,3, it is unclear how structural alterations over time allow
sodium to be translocated against a concentration gradient. Here, using the
Swiss X-ray Free Electron Laser4, we have collected serial
crystallographic data at ten pump-probe delays from femtoseconds to
milliseconds. High-resolution structural snapshots throughout the KR2 photocycle
show how retinal isomerization is completed on the femtosecond timescale and
changes the local structure of the binding pocket in the early nanoseconds.
Subsequent rearrangements and deprotonation of the retinal Schiff base open an
electrostatic gate in microseconds. Structural and spectroscopic data, in
combination with quantum chemical calculations, indicate that a sodium ion binds
transiently close to the retinal within one millisecond. In the last structural
intermediate, at 20 milliseconds after activation, we identified a potential
second sodium-binding site close to the extracellular exit. These results
provide direct molecular insight into the dynamics of active cation transport
across biological membranes.
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