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 7QCO | pdb_00007qco

The structure of Photosystem I tetramer from Chroococcidiopsis TS-821, a thermophilic, unicellular, non-heterocyst-forming cyanobacterium

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history. 

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 6QWJ

Literature

Cryo-EM structure of a tetrameric photosystem I from Chroococcidiopsis TS-821, a thermophilic, unicellular, non-heterocyst-forming cyanobacterium.

Semchonok, D.A., Mondal, J., Cooper, C.J., Schlum, K., Li, M., Amin, M., Sorzano, C.O.S., Ramirez-Aportela, E., Kastritis, P.L., Boekema, E.J., Guskov, A., Bruce, B.D.

(2022) Plant Commun 3: 100248-100248

  • DOI: https://doi.org/10.1016/j.xplc.2021.100248
  • Primary Citation Related Structures: 
    7QCO

  • PubMed Abstract: 

    Photosystem I (PSI) is one of two photosystems involved in oxygenic photosynthesis. PSI of cyanobacteria exists in monomeric, trimeric, and tetrameric forms, in contrast to the strictly monomeric form of PSI in plants and algae. The tetrameric organization raises questions about its structural, physiological, and evolutionary significance. Here we report the ∼3.72 Å resolution cryo-electron microscopy structure of tetrameric PSI from the thermophilic, unicellular cyanobacterium Chroococcidiopsis sp. TS-821. The structure resolves 44 subunits and 448 cofactor molecules. We conclude that the tetramer is arranged via two different interfaces resulting from a dimer-of-dimers organization. The localization of chlorophyll molecules permits an excitation energy pathway within and between adjacent monomers. Bioinformatics analysis reveals conserved regions in the PsaL subunit that correlate with the oligomeric state. Tetrameric PSI may function as a key evolutionary step between the trimeric and monomeric forms of PSI organization in photosynthetic organisms.

    • Organizational Affiliation: 
    • Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Groningen, the Netherlands.

Macromolecule Content 

  • Total Structure Weight: 1,441.06 kDa 
  • Atom Count: 90,396 
  • Modeled Residue Count: 8,812 
  • Deposited Residue Count: 9,652 
  • Unique protein chains: 11

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1A,
HA [auth a],
L [auth E],
W [auth e]		752Chroococcidiopsis sp. TS-821Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A1U7HUQ7 (Chroogloeocystis siderophila 5.2 s.c.1)
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Find proteins for A0ABR9UP93 (Gloeocapsopsis crepidinum LEGE 06123)
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Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsA0A1U7HUQ7A0ABR9UP93
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2B,
IA [auth b],
M [auth G],
X [auth g]		737Chroococcidiopsis sp. TS-821Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A1U7HUT8 (Chroogloeocystis siderophila 5.2 s.c.1)
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UniProt GroupA0A1U7HUT8
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerC,
JA [auth c],
N [auth H],
Y [auth h]		82Chroococcidiopsis sp. TS-821Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P31085 (Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1))
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UniProt GroupP31085
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IID,
KA [auth d],
O [auth N],
Z [auth n]		168Chroococcidiopsis sp. TS-821Mutation(s): 0 
UniProt
Find proteins for A0A1U7HY62 (Chroogloeocystis siderophila 5.2 s.c.1)
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UniProt GroupA0A1U7HY62
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVAA [auth v],
E [auth V],
LA [auth w],
P [auth W]		126Chroococcidiopsis sp. TS-821Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1U7HXX7 (Chroogloeocystis siderophila 5.2 s.c.1)
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UniProt GroupA0A1U7HXX7
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIBA [auth o],
F,
MA [auth f],
Q [auth O]		164Chroococcidiopsis sp. TS-821Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1U7HW25 (Chroogloeocystis siderophila 5.2 s.c.1)
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIICA [auth p],
G [auth I],
NA [auth i],
R [auth P]		39Chroococcidiopsis sp. TS-821Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1U7HVS4 (Chroogloeocystis siderophila 5.2 s.c.1)
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXDA [auth q],
H [auth J],
OA [auth j],
S [auth Q]		49Chroococcidiopsis sp. TS-821Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for V5JYA2 (Chroococcidiopsis sp. TS-821)
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UniProt GroupV5JYA2
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaKEA [auth r],
I [auth K],
PA [auth k],
T [auth R]		93Chroococcidiopsis sp. TS-821Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1U7HFX2 (Chroogloeocystis siderophila 5.2 s.c.1)
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Entity Groups
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UniProt GroupA0A1U7HFX2
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIFA [auth s],
J [auth L],
QA [auth l],
U [auth S]		172Chroococcidiopsis sp. TS-821Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for V5JYE0 (Chroococcidiopsis sp. TS-821)
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIGA [auth t],
K [auth M],
RA [auth m],
V [auth T]		31Chroococcidiopsis sp. TS-821Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1U7HWJ3 (Chroogloeocystis siderophila 5.2 s.c.1)
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA

Query on CLA


Download:Ideal Coordinates CCD File
AB [auth A]
AC [auth A]
AD [auth B]
AE [auth B]
AF [auth L]
AB [auth A],
AC [auth A],
AD [auth B],
AE [auth B],
AF [auth L],
AG [auth E],
AI [auth G],
AK [auth e],
AL [auth e],
AM [auth g],
AN [auth g],
AP [auth a],
AR [auth b],
AS [auth f],
BB [auth A],
BC [auth A],
BD [auth B],
BE [auth B],
BF [auth L],
BG [auth E],
BI [auth G],
BK [auth e],
BL [auth e],
BM [auth g],
BN [auth g],
BP [auth a],
BQ [auth b],
BR [auth b],
CB [auth A],
CC [auth A],
CD [auth B],
CE [auth B],
CG [auth E],
CI [auth G],
CK [auth e],
CL [auth e],
CM [auth g],
CN [auth g],
CP [auth a],
CQ [auth b],
CR [auth b],
DB [auth A],
DC [auth A],
DD [auth B],
DE [auth B],
DG [auth E],
DH [auth G],
DI [auth G],
DJ [auth O],
DK [auth e],
DL [auth e],
DM [auth g],
DN [auth g],
DO [auth a],
DP [auth a],
DQ [auth b],
DR [auth b],
EB [auth A],
EC [auth A],
ED [auth B],
EE [auth B],
EG [auth E],
EH [auth G],
EI [auth G],
EK [auth e],
EL [auth e],
EM [auth g],
EN [auth g],
EO [auth a],
EP [auth a],
EQ [auth b],
ER [auth b],
ES [auth k],
FB [auth A],
FC [auth A],
FD [auth B],
FE [auth B],
FF [auth E],
FG [auth E],
FH [auth G],
FI [auth G],
FK [auth e],
FL [auth e],
FM [auth g],
FO [auth a],
FP [auth a],
FQ [auth b],
FR [auth b],
FS [auth l],
GB [auth A],
GC [auth A],
GD [auth B],
GE [auth B],
GF [auth E],
GG [auth E],
GH [auth G],
GI [auth G],
GK [auth e],
GL [auth e],
GM [auth g],
GO [auth a],
GP [auth a],
GQ [auth b],
GR [auth b],
HB [auth A],
HC [auth A],
HD [auth B],
HE [auth B],
HF [auth E],
HG [auth E],
HH [auth G],
HI [auth G],
HJ [auth R],
HK [auth e],
HM [auth g],
HO [auth a],
HP [auth a],
HQ [auth b],
HR [auth b],
HS [auth l],
IB [auth A],
IC [auth A],
ID [auth B],
IF [auth E],
IG [auth E],
IH [auth G],
II [auth G],
IK [auth e],
IM [auth g],
IO [auth a],
IP [auth a],
IQ [auth b],
IR [auth b],
IS [auth l],
JB [auth A],
JC [auth A],
JD [auth B],
JF [auth E],
JG [auth E],
JH [auth G],
JI [auth G],
JK [auth e],
JM [auth g],
JO [auth a],
JP [auth a],
JQ [auth b],
JR [auth b],
JS [auth l],
KB [auth A],
KC [auth A],
KD [auth B],
KF [auth E],
KG [auth E],
KH [auth G],
KI [auth G],
KJ [auth S],
KK [auth e],
KM [auth g],
KO [auth a],
KP [auth a],
KQ [auth b],
KR [auth b],
LB [auth A],
LD [auth B],
LF [auth E],
LG [auth E],
LH [auth G],
LI [auth G],
LJ [auth S],
LK [auth e],
LM [auth g],
LO [auth a],
LP [auth a],
LQ [auth b],
LR [auth b],
MB [auth A],
MD [auth B],
MF [auth E],
MG [auth E],
MH [auth G],
MI [auth G],
MK [auth e],
MM [auth g],
MO [auth a],
MP [auth a],
MQ [auth b],
MR [auth b],
NB [auth A],
ND [auth B],
NF [auth E],
NG [auth E],
NH [auth G],
NI [auth G],
NJ [auth S],
NK [auth e],
NM [auth g],
NO [auth a],
NP [auth a],
NQ [auth b],
NR [auth b],
OB [auth A],
OD [auth B],
OF [auth E],
OG [auth E],
OH [auth G],
OI [auth G],
OK [auth e],
OL [auth e],
OM [auth g],
OO [auth a],
OP [auth a],
OQ [auth b],
OR [auth b],
PB [auth A],
PD [auth B],
PF [auth E],
PG [auth E],
PH [auth G],
PI [auth G],
PK [auth e],
PL [auth g],
PM [auth g],
PN [auth o],
PO [auth a],
PP [auth a],
PQ [auth b],
QB [auth A],
QD [auth B],
QF [auth E],
QG [auth E],
QH [auth G],
QI [auth G],
QK [auth e],
QL [auth g],
QM [auth g],
QO [auth a],
QP [auth a],
QQ [auth b],
RB [auth A],
RD [auth B],
RF [auth E],
RG [auth E],
RH [auth G],
RI [auth G],
RJ [auth e],
RK [auth e],
RL [auth g],
RM [auth g],
RO [auth a],
RP [auth a],
RQ [auth b],
SB [auth A],
SC [auth A],
SD [auth B],
SE [auth F],
SF [auth E],
SG [auth E],
SH [auth G],
SJ [auth e],
SK [auth e],
SM [auth g],
SO [auth a],
SP [auth a],
SQ [auth b],
TB [auth A],
TC [auth B],
TD [auth B],
TF [auth E],
TG [auth E],
TH [auth G],
TJ [auth e],
TK [auth e],
TL [auth g],
TM [auth g],
TN [auth r],
TO [auth a],
TQ [auth b],
UA [auth A],
UB [auth A],
UC [auth B],
UD [auth B],
UF [auth E],
UG [auth E],
UH [auth G],
UJ [auth e],
UK [auth e],
UL [auth g],
UM [auth g],
UN [auth r],
UO [auth a],
UQ [auth b],
VA [auth A],
VB [auth A],
VD [auth B],
VF [auth E],
VG [auth E],
VH [auth G],
VJ [auth e],
VK [auth e],
VL [auth g],
VM [auth g],
VO [auth a],
VQ [auth b],
WA [auth A],
WB [auth A],
WC [auth B],
WD [auth B],
WE [auth K],
WF [auth E],
WG [auth E],
WH [auth G],
WJ [auth e],
WK [auth e],
WL [auth g],
WM [auth g],
WN [auth s],
WO [auth a],
WQ [auth b],
XA [auth A],
XB [auth A],
XC [auth B],
XD [auth B],
XE [auth K],
XF [auth E],
XH [auth G],
XJ [auth e],
XK [auth e],
XL [auth g],
XM [auth g],
XN [auth s],
XO [auth a],
XQ [auth b],
YA [auth A],
YB [auth A],
YC [auth B],
YD [auth B],
YF [auth E],
YH [auth G],
YJ [auth e],
YK [auth e],
YL [auth g],
YM [auth g],
YO [auth a],
YQ [auth b],
ZA [auth A],
ZB [auth A],
ZC [auth B],
ZD [auth B],
ZE [auth L],
ZF [auth E],
ZH [auth G],
ZJ [auth e],
ZK [auth e],
ZL [auth g],
ZM [auth g],
ZN [auth s],
ZO [auth a],
ZP [auth a],
ZQ [auth b]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LHG

Query on LHG


Download:Ideal Coordinates CCD File
AO [auth a],
PJ [auth e],
QJ [auth e],
SA [auth A],
TA [auth A]		1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR

Query on BCR


Download:Ideal Coordinates CCD File
AH [auth E]
AQ [auth a]
BH [auth E]
BJ [auth O]
BO [auth a]
AH [auth E],
AQ [auth a],
BH [auth E],
BJ [auth O],
BO [auth a],
BS [auth i],
CF [auth L],
CH [auth E],
CJ [auth O],
CO [auth a],
CS [auth j],
DF [auth E],
DS [auth k],
EF [auth E],
EJ [auth P],
FJ [auth Q],
GJ [auth R],
GN [auth g],
GS [auth l],
HN [auth g],
IJ [auth S],
IL [auth e],
IN [auth g],
JE [auth B],
JJ [auth S],
JL [auth e],
JN [auth g],
KE [auth B],
KL [auth e],
KN [auth g],
KS [auth l],
LE [auth B],
LL [auth e],
LN [auth g],
LS [auth m],
MC [auth A],
ME [auth B],
MJ [auth S],
ML [auth e],
NC [auth A],
NE [auth B],
NL [auth e],
OC [auth A],
OE [auth B],
OJ [auth T],
ON [auth o],
PC [auth A],
QC [auth A],
QN [auth p],
QR [auth b],
RC [auth A],
RE [auth F],
RN [auth q],
RR [auth b],
SN [auth q],
SR [auth b],
TE [auth I],
TI [auth G],
TR [auth b],
UE [auth J],
UI [auth G],
UR [auth b],
VE [auth J],
VI [auth G],
VN [auth s],
VP [auth a],
VR [auth b],
WI [auth G],
WP [auth a],
XI [auth G],
XP [auth a],
YE [auth L],
YI [auth G],
YN [auth s],
YP [auth a],
YR [auth f],
ZG [auth E],
ZR [auth f]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN

Query on PQN


Download:Ideal Coordinates CCD File
FN [auth g]
HL [auth e]
IE [auth B]
LC [auth A]
PR [auth b]
FN [auth g],
HL [auth e],
IE [auth B],
LC [auth A],
PR [auth b],
SI [auth G],
UP [auth a],
YG [auth E]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4

Query on SF4


Download:Ideal Coordinates CCD File
AJ [auth H]
MN [auth h]
NN [auth h]
PE [auth C]
QE [auth C]
AJ [auth H],
MN [auth h],
NN [auth h],
PE [auth C],
QE [auth C],
SL [auth g],
TP [auth a],
VC [auth B],
WR [auth c],
XG [auth E],
XR [auth c],
ZI [auth H]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.14
RECONSTRUCTIONRELION3.0

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesDGE-0801470
National Science Foundation (NSF, United States)United StatesEPS-1004083
National Science Foundation (NSF, United States)United States2017219379

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-06
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Refinement description, Structure summary
  • Version 1.2: 2026-09-16
    Type: Remediation
    Reason: Metalloprotein remediation
    Changes: Data collection, Derived calculations, Structure summary