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

Validation slider image for 9E0J

This is version 1.1 of the entry. See complete history

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 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).

Macromolecule Content 

  • Total Structure Weight: 1,039.56 kDa 
  • Atom Count: 69,921 
  • Modeled Residue Count: 6,498 
  • Deposited Residue Count: 6,792 
  • Unique protein chains: 10

Macromolecules

Find similar proteins by:|  3D Structure
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 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIB [auth T],
L [auth m],
V [auth M]
32Anthocerotibacter panamensisMutation(s): 0 
Find similar proteins by:|  3D Structure
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 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerD [auth K],
N [auth c],
X [auth C]
81Anthocerotibacter panamensisMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIE [auth N],
O [auth d],
Y [auth D]
143Anthocerotibacter panamensisMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVF [auth O],
P [auth e],
Z [auth E]
64Anthocerotibacter panamensisMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIAA [auth F],
G [auth P],
Q [auth f]
177Anthocerotibacter panamensisMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIBA [auth I],
H [auth Q],
R [auth i]
32Anthocerotibacter panamensisMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXCA [auth J],
I [auth R],
S [auth j]
41Anthocerotibacter panamensisMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIDA [auth L],
J [auth S],
T [auth l]
160Anthocerotibacter panamensisMutation(s): 0 

Small Molecules

Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA

Query on CLA



Download:Ideal Coordinates CCD File
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
CL0

Query on CL0



Download:Ideal Coordinates CCD File
EA [auth G],
PJ [auth A],
XE [auth a]
CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
LMG

Query on LMG



Download:Ideal Coordinates CCD File
DE [auth H],
MN [auth B],
TI [auth b]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG

Query on LHG



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
EE [auth H],
NN [auth B],
UI [auth b]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
1L3

Query on 1L3



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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