6ZI9

Ultrafast Structural Response to Charge Redistribution Within a Photosynthetic Reaction Centre - 300 ps (b) structure

  • Classification: ELECTRON TRANSPORT
  • Organism(s): Blastochloris viridis
  • Mutation(s): No 

  • Deposited: 2020-06-25 Released: 2020-12-09 
  • Deposition Author(s): Baath, P., Dods, R., Braenden, G., Neutze, R.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Swedish Research Council, The Swedish Foundation for Strategic Research, Knut and Alice Wallenberg Foundation, Academy of Finland

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

Starting Model: experimental
View more details

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

    Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center cytochrome c subunitA [auth C]336Blastochloris viridisMutation(s): 0 
UniProt
Find proteins for P07173 (Blastochloris viridis)
Go to UniProtKB:  P07173
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein H chainB [auth H]258Blastochloris viridisMutation(s): 0 
UniProt
Find proteins for P06008 (Blastochloris viridis)
Go to UniProtKB:  P06008
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein L chainC [auth L]273Blastochloris viridisMutation(s): 0 
UniProt
Find proteins for P06009 (Blastochloris viridis)
Go to UniProtKB:  P06009
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein M chainD [auth M]323Blastochloris viridisMutation(s): 0 
UniProt
Find proteins for P06010 (Blastochloris viridis)
Go to UniProtKB:  P06010
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BCB (Subject of Investigation/LOI)
Query on BCB

Download Ideal Coordinates CCD File 
FA [auth M],
W [auth L],
X [auth L],
Z [auth L]
BACTERIOCHLOROPHYLL B
C55 H72 Mg N4 O6
QNWPCDKNPGOYNP-DSENBSCCSA-M
BPB (Subject of Investigation/LOI)
Query on BPB

Download Ideal Coordinates CCD File 
GA [auth M],
Y [auth L]
BACTERIOPHEOPHYTIN B
C55 H74 N4 O6
SFKCKJXMIAKQMY-GTTFDWDMSA-N
MQ7 (Subject of Investigation/LOI)
Query on MQ7

Download Ideal Coordinates CCD File 
EA [auth M]MENAQUINONE-7
C46 H64 O2
RAKQPZMEYJZGPI-LJWNYQGCSA-N
DGA
Query on DGA

Download Ideal Coordinates CCD File 
I [auth C]DIACYL GLYCEROL
C39 H76 O5
UHUSDOQQWJGJQS-QNGWXLTQSA-N
HEC
Query on HEC

Download Ideal Coordinates CCD File 
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

Download Ideal Coordinates CCD File 
HA [auth M]15-cis-1,2-dihydroneurosporene
C40 H60
NHKJSVKSSGKUCH-DBWJSHEJSA-N
LDA
Query on LDA

Download Ideal Coordinates CCD File 
AA [auth L]
BA [auth L]
M [auth H]
PA [auth M]
QA [auth M]
AA [auth L],
BA [auth L],
M [auth H],
PA [auth M],
QA [auth M],
S [auth H],
T [auth H]
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
HTO
Query on HTO

Download Ideal Coordinates CCD File 
CA [auth L],
U [auth H],
V [auth H]
HEPTANE-1,2,3-TRIOL
C7 H16 O3
HXYCHJFUBNTKQR-RNFRBKRXSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
IA [auth M]
J [auth C]
JA [auth M]
K [auth C]
KA [auth M]
IA [auth M],
J [auth C],
JA [auth M],
K [auth C],
KA [auth M],
L [auth C],
LA [auth M],
MA [auth M],
N [auth H],
NA [auth M],
O [auth H],
OA [auth M],
P [auth H],
Q [auth H],
R [auth H]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
FE
Query on FE

Download Ideal Coordinates CCD File 
DA [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 = 226.5α = 90
b = 226.5β = 90
c = 113.9γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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