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 9QFP | pdb_00009qfp

Monomeric Photosystem I Cryo-EM structure at 1.8 A resolution

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.74 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history. 

Literature

High-resolution structure of monomeric photosystem I from Thermosynechococcus vestitus.

Boyka, J., Gaullier, G., Forsman, J., Graca, A.T., Golub, M., Croy, N., Wood, K., Duff, A.P., Moir, M., Pieper, J., Messinger, J., Muh, F., Zouni, A., Blikstad, C.

(2026) Photosynth Res 164

  • DOI: https://doi.org/10.1007/s11120-026-01237-x
  • Primary Citation Related Structures: 
    9QFP

  • PubMed Abstract: 

    Photosystem I (PSI) exists in trimeric (tPSI) and monomeric (mPSI) forms within the thylakoid membrane of cyanobacteria. PSI functions as a light-driven electron pump, enabling the transfer of electrons from cytochrome c 6 (Cyt c 6 ) or plastocyanin to ferredoxin. Here, we have developed a novel protocol to obtain large amounts of intact, active mPSI from Thermosynechococcus vestitus (Tv) by dissociating highly purified tPSI using the detergent octaethylene glycol monododecyl ether (C 12 E 8 ) at elevated temperatures. We analysed the stability of the protein-detergent complex employing a combination of spectroscopic methods, such as fluorescence at 77 K and circular dichroism (CD), and investigated the detergent's influence on delipidation and monomerisation. We determined the structure of mPSI to a resolution of 1.8 Å using cryogenic electron microscopy (cryo-EM). This structure retains all subunits except PsaL and we identified a sulfoquinovosyl diacylglycerol (SQD) molecule and 16 n-dodecyl ß-maltoside (βDM) molecules arranged in a ring around the complex. The mPSI structure was verified in solution at physiological temperature by applying small angle neutron scattering. Comparing the cofactor inventory of mPSI to that of tPSI, we suggest the assignment of a red-shifted chlorophyll pigment and discuss the influence of detergents and lipids on stability and oligomeric state of PSI. Finally, when adding native Tv Cyt c 6 under reducing conditions, additional density was observed in close proximity of the P 700 pigments, which indicates the presence of a transiently bound Cyt c 6 .

    • Organizational Affiliation: 
    • Department of Biology, Humboldt-Universität zu Berlin, 10099, Berlin, Germany.

Macromolecule Content 

  • Total Structure Weight: 348.96 kDa 
  • Atom Count: 25,572 
  • Modeled Residue Count: 2,134 
  • Deposited Residue Count: 2,188 
  • Unique protein chains: 11

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1755Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for P0A405 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore P0A405 
Go to UniProtKB:  P0A405
Entity Groups
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UniProt GroupP0A405
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2741Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for P0A407 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore P0A407 
Go to UniProtKB:  P0A407
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UniProt GroupP0A407
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center81Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for P0A415 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II139Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for P0A420 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV76Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for P0A423 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III164Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for P0A401 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIG [auth I]38Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for P0A427 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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UniProt GroupP0A427
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXH [auth J]41Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for P0A429 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaKI [auth K]83Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for P0A425 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIJ [auth M]31Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for P0A403 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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UniProt GroupP0A403
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I 4.8K proteinK [auth X]39Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DKP6 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence

Small Molecules

Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL0

Query on CL0


Download:Ideal Coordinates CCD File
FB [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
CLA
(Subject of Investigation/LOI)

Query on CLA


Download:Ideal Coordinates CCD File
AA [auth A]
AD [auth B]
BA [auth A]
BC [auth B]
BD [auth B]
AA [auth A],
AD [auth B],
BA [auth A],
BC [auth B],
BD [auth B],
CA [auth A],
CB [auth A],
CC [auth B],
CD [auth B],
CE [auth F],
DA [auth A],
DC [auth B],
DD [auth B],
EA [auth A],
EC [auth B],
ED [auth B],
FA [auth A],
FC [auth B],
FD [auth B],
GA [auth A],
GB [auth A],
GC [auth B],
GD [auth B],
GE [auth J],
HA [auth A],
HB [auth A],
HC [auth B],
HD [auth B],
HE [auth J],
IA [auth A],
IB [auth A],
ID [auth B],
JA [auth A],
JB [auth A],
JC [auth B],
JD [auth B],
KA [auth A],
KC [auth B],
KD [auth B],
KE [auth K],
LA [auth A],
LB [auth A],
LC [auth B],
LD [auth B],
MA [auth A],
MB [auth A],
MC [auth B],
MD [auth B],
NA [auth A],
NB [auth A],
NC [auth B],
ND [auth B],
NE [auth K],
OA [auth A],
OB [auth A],
OC [auth B],
OD [auth B],
P [auth A],
PA [auth A],
PB [auth A],
PC [auth B],
PD [auth B],
Q [auth A],
QA [auth A],
QB [auth A],
QC [auth B],
QD [auth B],
R [auth A],
RA [auth A],
RB [auth A],
RC [auth B],
RD [auth B],
RE [auth X],
S [auth A],
SB [auth A],
SD [auth B],
T [auth A],
TB [auth A],
TD [auth B],
U [auth A],
UD [auth B],
V [auth A],
VB [auth A],
W [auth A],
X [auth A],
Y [auth A],
YC [auth B],
Z [auth A],
ZC [auth B],
ZD [auth F]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
SQD
(Subject of Investigation/LOI)

Query on SQD


Download:Ideal Coordinates CCD File
QE [auth X]1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG
(Subject of Investigation/LOI)

Query on LMG


Download:Ideal Coordinates CCD File
AC [auth B]1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
(Subject of Investigation/LOI)

Query on LHG


Download:Ideal Coordinates CCD File
BB [auth A],
FE [auth I],
KB [auth A],
TE [auth X],
WB [auth A]		1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR
(Subject of Investigation/LOI)

Query on BCR


Download:Ideal Coordinates CCD File
AB [auth A]
AE [auth F]
BE [auth F]
EE [auth F]
IE [auth J]
AB [auth A],
AE [auth F],
BE [auth F],
EE [auth F],
IE [auth J],
JE [auth J],
ME [auth K],
PE [auth M],
SC [auth B],
UB [auth A],
UC [auth B],
VC [auth B],
WA [auth A],
WC [auth B],
XA [auth A],
YA [auth A],
YB [auth B],
ZA [auth A],
ZB [auth B]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
(Subject of Investigation/LOI)

Query on LMT


Download:Ideal Coordinates CCD File
DB [auth A]
DE [auth F]
L [auth A]
LE [auth K]
M [auth A]
DB [auth A],
DE [auth F],
L [auth A],
LE [auth K],
M [auth A],
N [auth A],
O [auth A],
OE [auth K],
SA [auth A],
SE [auth X],
TA [auth A],
UA [auth A],
VD [auth B],
WD [auth B],
XB [auth B],
XC [auth B]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN
(Subject of Investigation/LOI)

Query on PQN


Download:Ideal Coordinates CCD File
TC [auth B],
VA [auth A]		PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
(Subject of Investigation/LOI)

Query on SF4


Download:Ideal Coordinates CCD File
EB [auth A],
XD [auth C],
YD [auth C]		IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
MG
(Subject of Investigation/LOI)

Query on MG


Download:Ideal Coordinates CCD File
IC [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.74 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.5
MODEL REFINEMENTISOLDE1.8
MODEL REFINEMENTServalcat0.4.88

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Germanys Excellence StrategyGermanyEXC 2008/1-390540038
German Research Foundation (DFG)GermanySFB1078 - TP A5
Swedish Research CouncilSweden2019-03700_VR
FormasSweden2019-01171_Formas

Revision History  (Full details and data files)

  • Version 1.0: 2026-09-30
    Type: Initial release
  • Version 1.1: 2026-10-28
    Changes: Data collection, Database references