7O1V | pdb_00007o1v

Structure of a Minimal Photosystem I


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.31 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Two-Dimensional Electronic Spectroscopy of a Minimal Photosystem I Complex Reveals the Rate of Primary Charge Separation.

Akhtar, P.Caspy, I.Nowakowski, P.J.Malavath, T.Nelson, N.Tan, H.S.Lambrev, P.H.

(2021) J Am Chem Soc 143: 14601-14612

  • DOI: https://doi.org/10.1021/jacs.1c05010
  • Primary Citation Related Structures: 
    7O1V

  • PubMed Abstract: 

    Photosystem I (PSI), found in all oxygenic photosynthetic organisms, uses solar energy to drive electron transport with nearly 100% quantum efficiency, thanks to fast energy transfer among antenna chlorophylls and charge separation in the reaction center. There is no complete consensus regarding the kinetics of the elementary steps involved in the overall trapping, especially the rate of primary charge separation. In this work, we employed two-dimensional coherent electronic spectroscopy to follow the dynamics of energy and electron transfer in a monomeric PSI complex from Synechocystis PCC 6803, containing only subunits A-E, K, and M, at 77 K. We also determined the structure of the complex to 4.3 Å resolution by cryoelectron microscopy with refinements to 2.5 Å. We applied structure-based modeling using a combined Redfield-Förster theory to compute the excitation dynamics. The absorptive 2D electronic spectra revealed fast excitonic/vibronic relaxation on time scales of 50-100 fs from the high-energy side of the absorption spectrum. Antenna excitations were funneled within 1 ps to a small pool of chlorophylls absorbing around 687 nm, thereafter decaying with 4-20 ps lifetimes, independently of excitation wavelength. Redfield-Förster energy transfer computations showed that the kinetics is limited by transfer from these red-shifted pigments. The rate of primary charge separation, upon direct excitation of the reaction center, was determined to be 1.2-1.5 ps -1 . This result implies activationless electron transfer in PSI.


  • Organizational Affiliation
    • Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Nanyang Link 21, 637371 Singapore.

Macromolecule Content 

  • Total Structure Weight: 303.86 kDa 
  • Atom Count: 20,914 
  • Modeled Residue Count: 1,869 
  • Deposited Residue Count: 1,869 
  • Unique protein chains: 7

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1739Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P29254 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore P29254 
Go to UniProtKB:  P29254
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UniProt GroupP29254
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2729Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P29255 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore P29255 
Go to UniProtKB:  P29255
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UniProt GroupP29255
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center80Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P32422 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore P32422 
Go to UniProtKB:  P32422
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UniProt GroupP32422
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II141Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
UniProt
Find proteins for P19569 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Go to UniProtKB:  P19569
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UniProt GroupP19569
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV69Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12975 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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UniProt GroupP12975
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaK 2F [auth K]80Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P74564 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIG [auth M]31Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P72986 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore P72986 
Go to UniProtKB:  P72986
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UniProt GroupP72986
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Reference Sequence

Small Molecules

Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA

Query on CLA



Download:Ideal Coordinates CCD File
AA [auth A]
AC [auth B]
AD [auth B]
BA [auth A]
BC [auth B]
AA [auth A],
AC [auth B],
AD [auth B],
BA [auth A],
BC [auth B],
BD [auth B],
CA [auth A],
CC [auth B],
DA [auth A],
DC [auth B],
EA [auth A],
EC [auth B],
FA [auth A],
FC [auth B],
GA [auth A],
GC [auth B],
H [auth A],
HA [auth A],
HC [auth B],
I [auth A],
IA [auth A],
IC [auth B],
J [auth A],
JA [auth A],
JB [auth A],
JC [auth B],
K [auth A],
KA [auth A],
KC [auth B],
L [auth A],
LA [auth A],
LB [auth B],
LC [auth B],
M [auth A],
MA [auth A],
MB [auth B],
MC [auth B],
N [auth A],
NA [auth A],
NC [auth B],
O [auth A],
OA [auth A],
OB [auth B],
OC [auth B],
P [auth A],
PA [auth A],
PB [auth B],
PC [auth B],
Q [auth A],
QA [auth A],
QB [auth B],
QC [auth B],
R [auth A],
RA [auth A],
RB [auth B],
RC [auth B],
RD [auth K],
S [auth A],
SA [auth A],
SB [auth B],
SC [auth B],
SD [auth K],
T [auth A],
TA [auth A],
TB [auth B],
TC [auth B],
U [auth A],
UA [auth A],
UB [auth B],
UC [auth B],
V [auth A],
VA [auth A],
VB [auth B],
VC [auth B],
W [auth A],
WA [auth A],
WB [auth B],
WC [auth B],
X [auth A],
XA [auth A],
XB [auth B],
XC [auth B],
Y [auth A],
YB [auth B],
YC [auth B],
Z [auth A],
ZB [auth B],
ZC [auth B]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
SQD

Query on SQD



Download:Ideal Coordinates CCD File
OD [auth B]1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG

Query on LMG



Download:Ideal Coordinates CCD File
HB [auth A],
KD [auth B],
MD [auth B],
UD [auth K]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG

Query on LHG



Download:Ideal Coordinates CCD File
GB [auth A],
IB [auth A],
LD [auth B],
ND [auth B],
VD [auth M]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
ECH

Query on ECH



Download:Ideal Coordinates CCD File
FD [auth B],
WD [auth M]
beta,beta-caroten-4-one
C40 H54 O
QXNWZXMBUKUYMD-QQGJMDNJSA-N
BCR

Query on BCR



Download:Ideal Coordinates CCD File
AB [auth A]
BB [auth A]
CB [auth A]
DB [auth A]
DD [auth B]
AB [auth A],
BB [auth A],
CB [auth A],
DB [auth A],
DD [auth B],
EB [auth A],
ED [auth B],
FB [auth A],
GD [auth B],
HD [auth B],
ID [auth B],
JD [auth B],
NB [auth B],
TD [auth K],
ZA [auth A]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN

Query on PQN



Download:Ideal Coordinates CCD File
CD [auth B],
YA [auth A]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4

Query on SF4



Download:Ideal Coordinates CCD File
KB [auth A],
PD [auth C],
QD [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.31 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael569/17

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-01
    Type: Initial release
  • Version 1.1: 2021-09-15
    Changes: Advisory, Database references, Derived calculations
  • Version 1.2: 2021-09-22
    Changes: Data collection, Database references
  • Version 1.3: 2024-07-10
    Changes: Data collection