9E0J | pdb_00009e0j

Structure and evolution of Photosystem I in the early-branching cyanobacterium Anthocerotibacter panamensis

  • Classification: PHOTOSYNTHESIS
  • Organism(s): Anthocerotibacter panamensis
  • Mutation(s): No 

  • Deposited: 2024-10-18 Released: 2025-05-07 
  • Deposition Author(s): Gisriel, C.J., Ho, M.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structure and evolution of photosystem I in the early-branching cyanobacterium Anthocerotibacter panamensis.

Jiang, H.W.Gisriel, C.J.Cardona, T.Flesher, D.A.Brudvig, G.W.Ho, M.Y.

(2025) Proc Natl Acad Sci U S A 122: e2427090122-e2427090122

  • DOI: https://doi.org/10.1073/pnas.2427090122
  • Primary Citation of Related Structures:  
    9E0J

  • PubMed Abstract: 

    Thylakoid-free cyanobacteria are thought to preserve ancestral traits of early-evolving organisms capable of oxygenic photosynthesis. However, and until recently, photosynthesis studies in thylakoid-free cyanobacteria were only possible in the model strain Gloeobacter violaceus , limiting our understanding of photosynthesis evolution. Here, we report the isolation, biochemical characterization, cryo-EM structure, and phylogenetic analysis of photosystem I (PSI) from a recently discovered thylakoid-free cyanobacterium, Anthocerotibacter panamensis , a distant relative of the genus Gloeobacter . We find that A. panamensis PSI exhibits a distinct carotenoid composition and has one conserved low-energy chlorophyll site, which was lost in G. violaceus . Furthermore, PSI in thylakoid-free cyanobacteria has changed at the sequence level to a degree comparable to that of other strains, yet its subunit composition and oligomeric form might be identical to that of the most recent common ancestor of cyanobacteria. This study therefore provides a glimpse into the ancient evolution of photosynthesis.


  • Organizational Affiliation
    • Department of Life Science, National Taiwan University, Taipei 10617, Taiwan (Republic of China).

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1A [auth G],
K [auth a],
U [auth A]
785Anthocerotibacter panamensisMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIB [auth T],
L [auth m],
V [auth M]
32Anthocerotibacter panamensisMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2C [auth H],
M [auth b],
W [auth B]
749Anthocerotibacter panamensisMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerD [auth K],
N [auth c],
X [auth C]
81Anthocerotibacter panamensisMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIE [auth N],
O [auth d],
Y [auth D]
143Anthocerotibacter panamensisMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVF [auth O],
P [auth e],
Z [auth E]
64Anthocerotibacter panamensisMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIAA [auth F],
G [auth P],
Q [auth f]
177Anthocerotibacter panamensisMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIBA [auth I],
H [auth Q],
R [auth i]
32Anthocerotibacter panamensisMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXCA [auth J],
I [auth R],
S [auth j]
41Anthocerotibacter panamensisMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIDA [auth L],
J [auth S],
T [auth l]
160Anthocerotibacter panamensisMutation(s): 0 
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Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL0
Query on CL0

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EA [auth G],
PJ [auth A],
XE [auth a]
CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
CLA
Query on CLA

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AB [auth G]
AD [auth H]
AF [auth a]
AG [auth a]
AI [auth b]
AB [auth G],
AD [auth H],
AF [auth a],
AG [auth a],
AI [auth b],
AK [auth A],
AL [auth A],
AM [auth B],
AN [auth B],
AO [auth L],
BB [auth G],
BD [auth H],
BF [auth a],
BG [auth a],
BH [auth b],
BI [auth b],
BJ [auth f],
BK [auth A],
BL [auth A],
BM [auth B],
BN [auth B],
CB [auth G],
CD [auth H],
CF [auth a],
CG [auth a],
CH [auth b],
CI [auth b],
CK [auth A],
CL [auth A],
CM [auth B],
CN [auth B],
CO [auth L],
DB [auth G],
DD [auth H],
DF [auth a],
DG [auth a],
DH [auth b],
DI [auth b],
DK [auth A],
DL [auth A],
DM [auth B],
DN [auth B],
DO [auth L],
EB [auth G],
ED [auth H],
EF [auth a],
EG [auth a],
EH [auth b],
EI [auth b],
EK [auth A],
EM [auth B],
EN [auth B],
EO [auth L],
FA [auth G],
FB [auth G],
FD [auth H],
FF [auth a],
FG [auth a],
FH [auth b],
FI [auth b],
FK [auth A],
FM [auth B],
GA [auth G],
GB [auth G],
GC [auth G],
GD [auth H],
GE [auth H],
GF [auth a],
GG [auth a],
GH [auth b],
GI [auth b],
GJ [auth j],
GK [auth A],
GM [auth B],
HA [auth G],
HB [auth G],
HC [auth G],
HD [auth H],
HF [auth a],
HG [auth a],
HH [auth b],
HI [auth b],
HK [auth A],
HM [auth B],
IA [auth G],
IB [auth G],
ID [auth H],
IF [auth a],
IG [auth a],
IH [auth b],
II [auth b],
IJ [auth j],
IK [auth A],
IM [auth B],
JA [auth G],
JB [auth G],
JC [auth H],
JD [auth H],
JE [auth P],
JF [auth a],
JG [auth a],
JH [auth b],
JI [auth b],
JK [auth A],
JM [auth B],
KA [auth G],
KB [auth G],
KC [auth H],
KD [auth H],
KF [auth a],
KG [auth a],
KH [auth b],
KI [auth b],
KJ [auth l],
KK [auth A],
KM [auth B],
LA [auth G],
LB [auth G],
LC [auth H],
LD [auth H],
LE [auth P],
LF [auth a],
LG [auth a],
LH [auth b],
LI [auth b],
LK [auth A],
LM [auth B],
MA [auth G],
MB [auth G],
MC [auth H],
MD [auth H],
MF [auth a],
MH [auth b],
MJ [auth l],
MK [auth A],
MM [auth B],
NA [auth G],
NB [auth G],
NC [auth H],
ND [auth H],
NF [auth a],
NH [auth b],
NJ [auth l],
NK [auth A],
NM [auth B],
OA [auth G],
OB [auth G],
OC [auth H],
OD [auth H],
OF [auth a],
OH [auth b],
OJ [auth l],
OK [auth A],
OM [auth B],
PA [auth G],
PB [auth G],
PC [auth H],
PD [auth H],
PF [auth a],
PH [auth b],
PK [auth A],
PM [auth B],
QA [auth G],
QB [auth G],
QC [auth H],
QD [auth H],
QF [auth a],
QH [auth b],
QJ [auth A],
QK [auth A],
QL [auth A],
QM [auth B],
QN [auth F],
RA [auth G],
RB [auth G],
RC [auth H],
RD [auth H],
RE [auth R],
RF [auth a],
RH [auth b],
RJ [auth A],
RK [auth A],
RL [auth A],
RM [auth B],
SA [auth G],
SB [auth G],
SC [auth H],
SD [auth H],
SF [auth a],
SH [auth b],
SJ [auth A],
SK [auth A],
SM [auth B],
SN [auth F],
TA [auth G],
TB [auth G],
TC [auth H],
TD [auth H],
TE [auth S],
TF [auth a],
TH [auth b],
TJ [auth A],
TK [auth A],
TL [auth B],
TM [auth B],
UA [auth G],
UC [auth H],
UD [auth H],
UE [auth S],
UF [auth a],
UH [auth b],
UJ [auth A],
UK [auth A],
UL [auth B],
UM [auth B],
VA [auth G],
VC [auth H],
VD [auth H],
VE [auth S],
VF [auth a],
VH [auth b],
VJ [auth A],
VK [auth A],
VL [auth B],
VM [auth B],
WA [auth G],
WC [auth H],
WF [auth a],
WH [auth b],
WI [auth b],
WJ [auth A],
WK [auth A],
WL [auth B],
WM [auth B],
XA [auth G],
XC [auth H],
XF [auth a],
XH [auth b],
XJ [auth A],
XK [auth A],
XL [auth B],
XM [auth B],
XN [auth J],
YA [auth G],
YC [auth H],
YE [auth a],
YF [auth a],
YG [auth a],
YH [auth b],
YJ [auth A],
YK [auth A],
YL [auth B],
YM [auth B],
ZA [auth G],
ZC [auth H],
ZE [auth a],
ZF [auth a],
ZG [auth a],
ZH [auth b],
ZI [auth f],
ZJ [auth A],
ZK [auth A],
ZL [auth B],
ZM [auth B]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG
Query on LMG

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DE [auth H],
MN [auth B],
TI [auth b]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

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CC [auth G]
DC [auth G]
FC [auth G]
ML [auth A]
NL [auth A]
CC [auth G],
DC [auth G],
FC [auth G],
ML [auth A],
NL [auth A],
PL [auth A],
UG [auth a],
VG [auth a],
XG [auth a]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
45D (Subject of Investigation/LOI)
Query on 45D

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AH [auth m],
IC [auth T],
SL [auth M]
beta,beta-carotene-4,4'-dione
C40 H52 O2
FDSDTBUPSURDBL-DKLMTRRASA-N
BCR
Query on BCR

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AC [auth G]
AE [auth H]
AJ [auth f]
BC [auth G]
BE [auth H]
AC [auth G],
AE [auth H],
AJ [auth f],
BC [auth G],
BE [auth H],
BO [auth L],
CE [auth H],
CJ [auth f],
DJ [auth i],
EC [auth G],
EJ [auth i],
FE [auth H],
FJ [auth j],
FO [auth L],
GL [auth A],
GN [auth B],
HJ [auth j],
HL [auth A],
HN [auth B],
IL [auth A],
IN [auth B],
JJ [auth l],
JL [auth A],
JN [auth B],
KE [auth P],
KL [auth A],
KN [auth B],
LJ [auth l],
LL [auth A],
LN [auth B],
ME [auth P],
NE [auth Q],
NI [auth b],
OE [auth Q],
OG [auth a],
OI [auth b],
OL [auth A],
PE [auth R],
PG [auth a],
PI [auth b],
QE [auth R],
QG [auth a],
QI [auth b],
RG [auth a],
RI [auth b],
RN [auth F],
SE [auth S],
SG [auth a],
SI [auth b],
TG [auth a],
TN [auth F],
UN [auth I],
VI [auth b],
VN [auth J],
WB [auth G],
WE [auth S],
WG [auth a],
WN [auth J],
XB [auth G],
XD [auth H],
YB [auth G],
YD [auth H],
YN [auth J],
ZB [auth G],
ZD [auth H],
ZN [auth L]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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EE [auth H],
NN [auth B],
UI [auth b]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
1L3
Query on 1L3

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EL [auth A]
FN [auth B]
MG [auth a]
MI [auth b]
UB [auth G]
EL [auth A],
FN [auth B],
MG [auth a],
MI [auth b],
UB [auth G],
WD [auth H]
Menaquinone-4
C31 H40 O2
DKHGMERMDICWDU-GHDNBGIDSA-N
SF4
Query on SF4

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FL [auth A]
HE [auth K]
IE [auth K]
NG [auth a]
ON [auth C]
FL [auth A],
HE [auth K],
IE [auth K],
NG [auth a],
ON [auth C],
PN [auth C],
VB [auth G],
XI [auth c],
YI [auth c]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR00GM140174
Department of Energy (DOE, United States)United StatesDE-FG02-05ER15646

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-07
    Type: Initial release
  • Version 1.1: 2025-05-28
    Changes: Data collection, Database references