6ZI4

Ultrafast Structural Response to Charge Redistribution Within a Photosynthetic Reaction Centre - 5 ps (a) structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Ultrafast structural changes within a photosynthetic reaction centre.

Dods, R.Bath, P.Morozov, D.Gagner, V.A.Arnlund, D.Luk, H.L.Kubel, J.Maj, M.Vallejos, A.Wickstrand, C.Bosman, R.Beyerlein, K.R.Nelson, G.Liang, M.Milathianaki, D.Robinson, J.Harimoorthy, R.Berntsen, P.Malmerberg, E.Johansson, L.Andersson, R.Carbajo, S.Claesson, E.Conrad, C.E.Dahl, P.Hammarin, G.Hunter, M.S.Li, C.Lisova, S.Royant, A.Safari, C.Sharma, A.Williams, G.J.Yefanov, O.Westenhoff, S.Davidsson, J.DePonte, D.P.Boutet, S.Barty, A.Katona, G.Groenhof, G.Branden, G.Neutze, R.

(2021) Nature 589: 310-314

  • DOI: https://doi.org/10.1038/s41586-020-3000-7
  • Primary Citation of Related Structures:  
    6ZHW, 6ZI4, 6ZI5, 6ZI6, 6ZI9, 6ZIA, 6ZID

  • PubMed Abstract: 

    Photosynthetic reaction centres harvest the energy content of sunlight by transporting electrons across an energy-transducing biological membrane. Here we use time-resolved serial femtosecond crystallography 1 using an X-ray free-electron laser 2 to observe light-induced structural changes in the photosynthetic reaction centre of Blastochloris viridis on a timescale of picoseconds. Structural perturbations first occur at the special pair of chlorophyll molecules of the photosynthetic reaction centre that are photo-oxidized by light. Electron transfer to the menaquinone acceptor on the opposite side of the membrane induces a movement of this cofactor together with lower amplitude protein rearrangements. These observations reveal how proteins use conformational dynamics to stabilize the charge-separation steps of electron-transfer reactions.


  • Organizational Affiliation

    Centre for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center cytochrome c subunitA [auth C]336Blastochloris viridisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P07173 (Blastochloris viridis)
Explore P07173 
Go to UniProtKB:  P07173
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07173
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein H chainB [auth H]258Blastochloris viridisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P06008 (Blastochloris viridis)
Explore P06008 
Go to UniProtKB:  P06008
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06008
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein L chainC [auth L]273Blastochloris viridisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P06009 (Blastochloris viridis)
Explore P06009 
Go to UniProtKB:  P06009
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06009
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein M chainD [auth M]323Blastochloris viridisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P06010 (Blastochloris viridis)
Explore P06010 
Go to UniProtKB:  P06010
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06010
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BCB (Subject of Investigation/LOI)
Query on BCB

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AA [auth M],
S [auth L],
T [auth L],
V [auth L]
BACTERIOCHLOROPHYLL B
C55 H72 Mg N4 O6
QNWPCDKNPGOYNP-DSENBSCCSA-M
BPB (Subject of Investigation/LOI)
Query on BPB

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BA [auth M],
U [auth L]
BACTERIOPHEOPHYTIN B
C55 H74 N4 O6
SFKCKJXMIAKQMY-GTTFDWDMSA-N
MQ7 (Subject of Investigation/LOI)
Query on MQ7

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Z [auth M]MENAQUINONE-7
C46 H64 O2
RAKQPZMEYJZGPI-LJWNYQGCSA-N
DGA
Query on DGA

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I [auth C]DIACYL GLYCEROL
C39 H76 O5
UHUSDOQQWJGJQS-QNGWXLTQSA-N
HEC (Subject of Investigation/LOI)
Query on HEC

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E [auth C],
F [auth C],
G [auth C],
H [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
NS5
Query on NS5

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CA [auth M]15-cis-1,2-dihydroneurosporene
C40 H60
NHKJSVKSSGKUCH-DBWJSHEJSA-N
LDA
Query on LDA

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K [auth H],
P [auth H],
Q [auth H],
W [auth L]
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
HTO
Query on HTO

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R [auth H],
X [auth L]
HEPTANE-1,2,3-TRIOL
C7 H16 O3
HXYCHJFUBNTKQR-RNFRBKRXSA-N
SO4
Query on SO4

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DA [auth M]
EA [auth M]
FA [auth M]
GA [auth M]
HA [auth M]
DA [auth M],
EA [auth M],
FA [auth M],
GA [auth M],
HA [auth M],
IA [auth M],
J [auth C],
JA [auth M],
L [auth H],
M [auth H],
N [auth H],
O [auth H]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
FE
Query on FE

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Y [auth M]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
B [auth H]L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 226.4α = 90
b = 226.4β = 90
c = 113.7γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM103393
Swedish Research CouncilSweden2015-00560, 349-2011-6485, 2017-06734
The Swedish Foundation for Strategic ResearchSwedenSRL10-0036
Knut and Alice Wallenberg FoundationSwedenKAW 2012.0284, KAW 2014.0275
Academy of FinlandFinland290677, 304455

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-09
    Type: Initial release
  • Version 1.1: 2020-12-16
    Changes: Database references
  • Version 1.2: 2021-01-27
    Changes: Database references
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references
  • Version 1.4: 2024-01-31
    Changes: Refinement description