6VPV | pdb_00006vpv

Trimeric Photosystem I from the High-Light Tolerant Cyanobacteria Cyanobacterium Aponinum


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

The structure of photosystem I from a high-light tolerant Cyanobacteria.

Dobson, Z.Ahad, S.Vanlandingham, J.Toporik, H.Vaughn, N.Vaughn, M.Williams, D.Reppert, M.Fromme, P.Mazor, Y.

(2021) Elife 10

  • DOI: https://doi.org/10.7554/eLife.67518
  • Primary Citation Related Structures: 
    6VPV

  • PubMed Abstract: 

    Photosynthetic organisms have adapted to survive a myriad of extreme environments from the earth's deserts to its poles, yet the proteins that carry out the light reactions of photosynthesis are highly conserved from the cyanobacteria to modern day crops. To investigate adaptations of the photosynthetic machinery in cyanobacteria to excessive light stress, we isolated a new strain of cyanobacteria, Cyanobacterium aponinum 0216, from the extreme light environment of the Sonoran Desert. Here we report the biochemical characterization and the 2.7 Å resolution structure of trimeric photosystem I from this high-light-tolerant cyanobacterium. The structure shows a new conformation of the PsaL C-terminus that supports trimer formation of cyanobacterial photosystem I. The spectroscopic analysis of this photosystem I revealed a decrease in far-red absorption, which is attributed to a decrease in the number of long- wavelength chlorophylls. Using these findings, we constructed two chimeric PSIs in Synechocystis sp. PCC 6803 demonstrating how unique structural features in photosynthetic complexes can change spectroscopic properties, allowing organisms to thrive under different environmental stresses.


  • Organizational Affiliation
    • School of Molecular Sciences, Arizona State University, Tempe, United States.

Macromolecule Content 

  • Total Structure Weight: 1,051.66 kDa 
  • Atom Count: 72,192 
  • Modeled Residue Count: 6,753 
  • Deposited Residue Count: 6,753 
  • Unique protein chains: 11

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1A,
L [auth a],
W [auth 1]
741Cyanobacterium aponinum 0216Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for K9Z0B2 (Cyanobacterium aponinum (strain PCC 10605))
Explore K9Z0B2 
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Entity Groups
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UniProt GroupK9Z0B2
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2B,
M [auth b],
X [auth 2]
737Cyanobacterium aponinum 0216Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for K9Z2J7 (Cyanobacterium aponinum (strain PCC 10605))
Explore K9Z2J7 
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerC,
N [auth c],
Y [auth 3]
80Cyanobacterium aponinum 0216Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for K9Z1N0 (Cyanobacterium aponinum (strain PCC 10605))
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IID,
O [auth d],
Z [auth 4]
139Cyanobacterium aponinum 0216Mutation(s): 0 
UniProt
Find proteins for K9ZAD9 (Cyanobacterium aponinum (strain PCC 10605))
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVAA [auth 5],
E,
P [auth e]
68Cyanobacterium aponinum 0216Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for K9Z0X2 (Cyanobacterium aponinum (strain PCC 10605))
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
PSI-FBA [auth 6],
F,
Q [auth f]
141Cyanobacterium aponinum 0216Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for K9YZN5 (Cyanobacterium aponinum (strain PCC 10605))
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIICA [auth 7],
G [auth I],
R [auth i]
38Cyanobacterium aponinum 0216Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for K9Z9J3 (Cyanobacterium aponinum (strain PCC 10605))
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXDA [auth 8],
H [auth J],
S [auth j]
39Cyanobacterium aponinum 0216Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for K9Z1F7 (Cyanobacterium aponinum (strain PCC 10605))
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaKEA [auth 9],
I [auth K],
T [auth k]
78Cyanobacterium aponinum 0216Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for K9Z7M2 (Cyanobacterium aponinum (strain PCC 10605))
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIFA [auth 0],
J [auth L],
U [auth l]
160Cyanobacterium aponinum 0216Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for K9Z7Y0 (Cyanobacterium aponinum (strain PCC 10605))
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIGA [auth z],
K [auth M],
V [auth m]
30Cyanobacterium aponinum 0216Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for K9Z6P4 (Cyanobacterium aponinum (strain PCC 10605))
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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
AB [auth A]
AD [auth B]
AF [auth L]
AG [auth a]
AI [auth b]
AB [auth A],
AD [auth B],
AF [auth L],
AG [auth a],
AI [auth b],
AL [auth 1],
AN [auth 2],
AO [auth 6],
BB [auth A],
BD [auth B],
BE [auth B],
BG [auth a],
BI [auth b],
BK [auth l],
BL [auth 1],
BN [auth 2],
CB [auth A],
CD [auth B],
CF [auth L],
CG [auth a],
CI [auth b],
CL [auth 1],
CM [auth 1],
CN [auth 2],
CO [auth 6],
DB [auth A],
DD [auth B],
DG [auth a],
DI [auth b],
DJ [auth f],
DL [auth 1],
DM [auth 2],
DN [auth 2],
DO [auth 6],
EB [auth A],
ED [auth B],
EG [auth a],
EH [auth a],
EI [auth b],
EK [auth 1],
EL [auth 1],
EM [auth 2],
EN [auth 2],
FB [auth A],
FD [auth B],
FE [auth F],
FG [auth a],
FH [auth b],
FI [auth b],
FJ [auth f],
FK [auth 1],
FL [auth 1],
FM [auth 2],
FN [auth 2],
GB [auth A],
GC [auth A],
GD [auth B],
GF [auth a],
GG [auth a],
GH [auth b],
GI [auth b],
GJ [auth f],
GK [auth 1],
GL [auth 1],
GM [auth 2],
GN [auth 2],
GO [auth 7],
HB [auth A],
HC [auth B],
HD [auth B],
HE [auth F],
HF [auth a],
HG [auth a],
HH [auth b],
HI [auth b],
HK [auth 1],
HL [auth 1],
HM [auth 2],
HN [auth 2],
IA [auth A],
IB [auth A],
IC [auth B],
ID [auth B],
IE [auth F],
IF [auth a],
IG [auth a],
IH [auth b],
II [auth b],
IK [auth 1],
IL [auth 1],
IM [auth 2],
IN [auth 2],
IO [auth 8],
JA [auth A],
JB [auth A],
JC [auth B],
JD [auth B],
JF [auth a],
JG [auth a],
JH [auth b],
JI [auth b],
JJ [auth i],
JK [auth 1],
JL [auth 1],
JM [auth 2],
JN [auth 2],
JO [auth 8],
KA [auth A],
KB [auth A],
KC [auth B],
KD [auth B],
KE [auth I],
KF [auth a],
KG [auth a],
KH [auth b],
KI [auth b],
KK [auth 1],
KL [auth 1],
KM [auth 2],
KN [auth 2],
KO [auth 8],
LA [auth A],
LB [auth A],
LC [auth B],
LD [auth B],
LF [auth a],
LG [auth a],
LH [auth b],
LI [auth b],
LJ [auth j],
LK [auth 1],
LL [auth 1],
LM [auth 2],
LN [auth 2],
MA [auth A],
MB [auth A],
MC [auth B],
MD [auth B],
MF [auth a],
MG [auth a],
MH [auth b],
MI [auth b],
MJ [auth j],
MK [auth 1],
ML [auth 1],
MM [auth 2],
MN [auth 2],
NA [auth A],
NB [auth A],
NC [auth B],
ND [auth B],
NE [auth J],
NF [auth a],
NG [auth a],
NH [auth b],
NI [auth b],
NJ [auth j],
NK [auth 1],
NL [auth 1],
NM [auth 2],
NN [auth 2],
OA [auth A],
OB [auth A],
OC [auth B],
OD [auth B],
OE [auth J],
OF [auth a],
OG [auth a],
OH [auth b],
OI [auth b],
OK [auth 1],
OL [auth 1],
OM [auth 2],
OO [auth 9],
PA [auth A],
PB [auth A],
PC [auth B],
PD [auth B],
PE [auth J],
PF [auth a],
PG [auth a],
PH [auth b],
PI [auth b],
PK [auth 1],
PL [auth 1],
PM [auth 2],
PO [auth 9],
QA [auth A],
QB [auth A],
QC [auth B],
QD [auth B],
QF [auth a],
QG [auth a],
QH [auth b],
QI [auth b],
QK [auth 1],
QL [auth 1],
QM [auth 2],
RA [auth A],
RB [auth A],
RC [auth B],
RD [auth B],
RF [auth a],
RG [auth a],
RH [auth b],
RJ [auth k],
RK [auth 1],
RL [auth 1],
RM [auth 2],
RO [auth 9],
SA [auth A],
SB [auth A],
SC [auth B],
SD [auth B],
SF [auth a],
SG [auth a],
SH [auth b],
SJ [auth k],
SK [auth 1],
SL [auth 1],
SM [auth 2],
TA [auth A],
TB [auth A],
TC [auth B],
TE [auth K],
TF [auth a],
TG [auth a],
TH [auth b],
TK [auth 1],
TM [auth 2],
TO [auth 0],
UA [auth A],
UB [auth A],
UC [auth B],
UE [auth K],
UF [auth a],
UG [auth a],
UH [auth b],
UJ [auth k],
UK [auth 1],
UM [auth 2],
UO [auth 0],
VA [auth A],
VB [auth A],
VC [auth B],
VF [auth a],
VH [auth b],
VK [auth 1],
VM [auth 2],
WA [auth A],
WB [auth A],
WC [auth B],
WE [auth K],
WF [auth a],
WH [auth b],
WJ [auth l],
WK [auth 1],
WM [auth 2],
WN [auth 2],
WO [auth 0],
XA [auth A],
XC [auth B],
XE [auth L],
XF [auth a],
XH [auth b],
XK [auth 1],
XM [auth 2],
XO [auth 0],
YA [auth A],
YC [auth B],
YF [auth a],
YH [auth b],
YJ [auth l],
YK [auth 1],
YM [auth 2],
ZA [auth A],
ZC [auth B],
ZE [auth L],
ZF [auth a],
ZH [auth b],
ZI [auth b],
ZJ [auth l],
ZK [auth 1],
ZM [auth 2],
ZO [auth 0]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0

Query on CL0



Download:Ideal Coordinates CCD File
DK [auth 1],
FF [auth a],
HA [auth A]
CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
SQD

Query on SQD



Download:Ideal Coordinates CCD File
FO [auth 7],
IJ [auth i],
ME [auth I]
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
AE [auth B],
VN [auth 2],
YI [auth b]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG

Query on LHG



Download:Ideal Coordinates CCD File
AM [auth 1]
BH [auth a]
CH [auth a]
DC [auth A]
EC [auth A]
AM [auth 1],
BH [auth a],
CH [auth a],
DC [auth A],
EC [auth A],
ZL [auth 1]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR

Query on BCR



Download:Ideal Coordinates CCD File
AC [auth A]
AH [auth a]
AJ [auth b]
AK [auth l]
AP [auth z]
AC [auth A],
AH [auth a],
AJ [auth b],
AK [auth l],
AP [auth z],
BC [auth A],
BF [auth L],
BM [auth 1],
BO [auth 6],
CC [auth A],
CE [auth B],
CK [auth m],
DF [auth L],
DH [auth a],
EF [auth M],
EJ [auth f],
EO [auth 6],
FC [auth A],
GE [auth F],
HJ [auth f],
HO [auth 7],
JE [auth F],
KJ [auth i],
LE [auth I],
LO [auth 8],
MO [auth 8],
NO [auth 9],
OJ [auth j],
PJ [auth j],
PN [auth 2],
QE [auth J],
QJ [auth k],
QN [auth 2],
QO [auth 9],
RE [auth J],
RN [auth 2],
SE [auth K],
SI [auth b],
SN [auth 2],
SO [auth 0],
TI [auth b],
TJ [auth k],
TN [auth 2],
UD [auth B],
UI [auth b],
UN [auth 2],
VD [auth B],
VE [auth K],
VI [auth b],
VJ [auth l],
VL [auth 1],
VO [auth 0],
WD [auth B],
WI [auth b],
WL [auth 1],
XD [auth B],
XG [auth a],
XI [auth b],
XJ [auth l],
XL [auth 1],
XN [auth 2],
YD [auth B],
YE [auth L],
YG [auth a],
YL [auth 1],
YO [auth 0],
ZB [auth A],
ZD [auth B],
ZG [auth a]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN

Query on PQN



Download:Ideal Coordinates CCD File
ON [auth 2]
RI [auth b]
TD [auth B]
TL [auth 1]
VG [auth a]
ON [auth 2],
RI [auth b],
TD [auth B],
TL [auth 1],
VG [auth a],
XB [auth A]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4

Query on SF4



Download:Ideal Coordinates CCD File
BJ [auth c]
CJ [auth c]
DE [auth C]
EE [auth C]
UL [auth 1]
BJ [auth c],
CJ [auth c],
DE [auth C],
EE [auth C],
UL [auth 1],
WG [auth a],
YB [auth A],
YN [auth 3],
ZN [auth 3]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-04
    Type: Initial release
  • Version 1.1: 2021-09-08
    Changes: Database references
  • Version 1.2: 2024-11-20
    Changes: Data collection, Structure summary