6ZID

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

PDB DOI: https://doi.org/10.2210/pdb6ZID/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Blastochloris viridis
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMDmpstruc

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: 0.183
R-Value Work: 0.159
R-Value Observed: 0.161

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 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

PubMed: 33268896 Search on PubMedSearch on PubMed Central
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.

Macromolecule Content

Total Structure Weight: 145.66 kDa
Atom Count: 11,472
Modelled Residue Count: 1,186
Deposited Residue Count: 1,190
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic reaction center cytochrome c subunit	A [auth C]	336	Blastochloris viridis	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P07173 (Blastochloris viridis) Explore P07173 Go to UniProtKB: P07173
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07173
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein H chain	B [auth H]	258	Blastochloris viridis	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P06008 (Blastochloris viridis) Explore P06008 Go to UniProtKB: P06008
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06008
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein L chain	C [auth L]	273	Blastochloris viridis	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P06009 (Blastochloris viridis) Explore P06009 Go to UniProtKB: P06009
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06009
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein M chain	D [auth M]	323	Blastochloris viridis	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P06010 (Blastochloris viridis) Explore P06010 Go to UniProtKB: P06010
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06010
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BCB (Subject of Investigation/LOI) Query on BCB Download Ideal Coordinates CCD File SDF format, chain FA [auth M] SDF format, chain W [auth L] SDF format, chain X [auth L] SDF format, chain Z [auth L] MOL2 format, chain FA [auth M] MOL2 format, chain W [auth L] MOL2 format, chain X [auth L] MOL2 format, chain Z [auth L] mmCIF format, chain FA [auth M] mmCIF format, chain W [auth L] mmCIF format, chain X [auth L] mmCIF format, chain Z [auth L]	FA [auth M], W [auth L], X [auth L], Z [auth L]	BACTERIOCHLOROPHYLL B C₅₅ H₇₂ Mg N₄ O₆ QNWPCDKNPGOYNP-DSENBSCCSA-M		Interactions Focus chain FA [auth M] Focus chain W [auth L] Focus chain X [auth L] Focus chain Z [auth L] Interactions & Density Focus chain FA [auth M] Focus chain W [auth L] Focus chain X [auth L] Focus chain Z [auth L]
BPB (Subject of Investigation/LOI) Query on BPB Download Ideal Coordinates CCD File SDF format, chain GA [auth M] SDF format, chain Y [auth L] MOL2 format, chain GA [auth M] MOL2 format, chain Y [auth L] mmCIF format, chain GA [auth M] mmCIF format, chain Y [auth L]	GA [auth M], Y [auth L]	BACTERIOPHEOPHYTIN B C₅₅ H₇₄ N₄ O₆ SFKCKJXMIAKQMY-GTTFDWDMSA-N		Interactions Focus chain GA [auth M] Focus chain Y [auth L] Interactions & Density Focus chain GA [auth M] Focus chain Y [auth L]
MQ7 (Subject of Investigation/LOI) Query on MQ7 Download Ideal Coordinates CCD File SDF format, chain EA [auth M] MOL2 format, chain EA [auth M] mmCIF format, chain EA [auth M]	EA [auth M]	MENAQUINONE-7 C₄₆ H₆₄ O₂ RAKQPZMEYJZGPI-LJWNYQGCSA-N		Interactions Focus chain EA [auth M] Interactions & Density Focus chain EA [auth M]
DGA Query on DGA Download Ideal Coordinates CCD File SDF format, chain I [auth C] MOL2 format, chain I [auth C] mmCIF format, chain I [auth C]	I [auth C]	DIACYL GLYCEROL C₃₉ H₇₆ O₅ UHUSDOQQWJGJQS-QNGWXLTQSA-N		Interactions Focus chain I [auth C] Interactions & Density Focus chain I [auth C]
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain E [auth C] SDF format, chain F [auth C] SDF format, chain G [auth C] SDF format, chain H [auth C] MOL2 format, chain E [auth C] MOL2 format, chain F [auth C] MOL2 format, chain G [auth C] MOL2 format, chain H [auth C] mmCIF format, chain E [auth C] mmCIF format, chain F [auth C] mmCIF format, chain G [auth C] mmCIF format, chain H [auth C]	E [auth C], F [auth C], G [auth C], H [auth C]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth C] Focus chain H [auth C] Interactions & Density Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth C] Focus chain H [auth C]
NS5 Query on NS5 Download Ideal Coordinates CCD File SDF format, chain HA [auth M] MOL2 format, chain HA [auth M] mmCIF format, chain HA [auth M]	HA [auth M]	15-cis-1,2-dihydroneurosporene C₄₀ H₆₀ NHKJSVKSSGKUCH-DBWJSHEJSA-N		Interactions Focus chain HA [auth M] Interactions & Density Focus chain HA [auth M]
LDA Query on LDA Download Ideal Coordinates CCD File SDF format, chain AA [auth L] SDF format, chain BA [auth L] SDF format, chain M [auth H] SDF format, chain PA [auth M] SDF format, chain QA [auth M] SDF format, chain S [auth H] SDF format, chain T [auth H] MOL2 format, chain AA [auth L] MOL2 format, chain BA [auth L] MOL2 format, chain M [auth H] MOL2 format, chain PA [auth M] MOL2 format, chain QA [auth M] MOL2 format, chain S [auth H] MOL2 format, chain T [auth H] mmCIF format, chain AA [auth L] mmCIF format, chain BA [auth L] mmCIF format, chain M [auth H] mmCIF format, chain PA [auth M] mmCIF format, chain QA [auth M] mmCIF format, chain S [auth H] mmCIF format, chain T [auth H]	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		Interactions Focus chain AA [auth L] Focus chain BA [auth L] Focus chain M [auth H] Focus chain PA [auth M] Focus chain QA [auth M] Focus chain S [auth H] Focus chain T [auth H] Interactions & Density Focus chain AA [auth L] Focus chain BA [auth L] Focus chain M [auth H] Focus chain PA [auth M] Focus chain QA [auth M] Focus chain S [auth H] Focus chain T [auth H]
HTO Query on HTO Download Ideal Coordinates CCD File SDF format, chain CA [auth L] SDF format, chain U [auth H] SDF format, chain V [auth H] MOL2 format, chain CA [auth L] MOL2 format, chain U [auth H] MOL2 format, chain V [auth H] mmCIF format, chain CA [auth L] mmCIF format, chain U [auth H] mmCIF format, chain V [auth H]	CA [auth L], U [auth H], V [auth H]	HEPTANE-1,2,3-TRIOL C₇ H₁₆ O₃ HXYCHJFUBNTKQR-RNFRBKRXSA-N		Interactions Focus chain CA [auth L] Focus chain U [auth H] Focus chain V [auth H] Interactions & Density Focus chain CA [auth L] Focus chain U [auth H] Focus chain V [auth H]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain IA [auth M] SDF format, chain J [auth C] SDF format, chain JA [auth M] SDF format, chain KA [auth M] SDF format, chain L [auth C] SDF format, chain LA [auth M] SDF format, chain MA [auth M] SDF format, chain N [auth H] SDF format, chain NA [auth M] SDF format, chain O [auth H] SDF format, chain OA [auth M] SDF format, chain P [auth H] SDF format, chain Q [auth H] SDF format, chain R [auth H] SDF format, chain K [auth C] MOL2 format, chain IA [auth M] MOL2 format, chain J [auth C] MOL2 format, chain JA [auth M] MOL2 format, chain KA [auth M] MOL2 format, chain L [auth C] MOL2 format, chain LA [auth M] MOL2 format, chain MA [auth M] MOL2 format, chain N [auth H] MOL2 format, chain NA [auth M] MOL2 format, chain O [auth H] MOL2 format, chain OA [auth M] MOL2 format, chain P [auth H] MOL2 format, chain Q [auth H] MOL2 format, chain R [auth H] MOL2 format, chain K [auth C] mmCIF format, chain IA [auth M] mmCIF format, chain J [auth C] mmCIF format, chain JA [auth M] mmCIF format, chain KA [auth M] mmCIF format, chain L [auth C] mmCIF format, chain LA [auth M] mmCIF format, chain MA [auth M] mmCIF format, chain N [auth H] mmCIF format, chain NA [auth M] mmCIF format, chain O [auth H] mmCIF format, chain OA [auth M] mmCIF format, chain P [auth H] mmCIF format, chain Q [auth H] mmCIF format, chain R [auth H] mmCIF format, chain K [auth C]	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		Interactions Focus chain IA [auth M] Focus chain J [auth C] Focus chain JA [auth M] Focus chain K [auth C] Focus chain KA [auth M] Focus chain L [auth C] Focus chain LA [auth M] Focus chain MA [auth M] Focus chain N [auth H] Focus chain NA [auth M] Focus chain O [auth H] Focus chain OA [auth M] Focus chain P [auth H] Focus chain Q [auth H] Focus chain R [auth H] Interactions & Density Focus chain IA [auth M] Focus chain J [auth C] Focus chain JA [auth M] Focus chain K [auth C] Focus chain KA [auth M] Focus chain L [auth C] Focus chain LA [auth M] Focus chain MA [auth M] Focus chain N [auth H] Focus chain NA [auth M] Focus chain O [auth H] Focus chain OA [auth M] Focus chain P [auth H] Focus chain Q [auth H] Focus chain R [auth H]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain DA [auth M] MOL2 format, chain DA [auth M] mmCIF format, chain DA [auth M]	DA [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain DA [auth M] Interactions & Density Focus chain DA [auth M]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME Query on FME	B [auth H]	L-PEPTIDE LINKING	C₆ H₁₁ N O₃ S		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.183
R-Value Work: 0.159
R-Value Observed: 0.161
Space Group: P 4₃ 2₁ 2
Diffraction Data: https://doi.org/10.11577/1726093

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 226.5	α = 90
b = 226.5	β = 90
c = 113.9	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-12-09

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P41GM103393
Swedish Research Council	Sweden	2015-00560, 349-2011-6485, 2017-06734
The Swedish Foundation for Strategic Research	Sweden	SRL10-0036
Knut and Alice Wallenberg Foundation	Sweden	KAW 2012.0284, KAW 2014.0275
Academy of Finland	Finland	290677, 304455