7S3D

Structure of photosystem I with bound ferredoxin from Synechococcus sp. PCC 7335 acclimated to far-red light


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.91 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of a photosystem I-ferredoxin complex from a marine cyanobacterium provides insights into far-red light photoacclimation.

Gisriel, C.J.Flesher, D.A.Shen, G.Wang, J.Ho, M.Y.Brudvig, G.W.Bryant, D.A.

(2021) J Biol Chem 298: 101408-101408

  • DOI: https://doi.org/10.1016/j.jbc.2021.101408
  • Primary Citation of Related Structures:  
    7S3D

  • PubMed Abstract: 

    Far-red light photoacclimation exhibited by some cyanobacteria allows these organisms to use the far-red region of the solar spectrum (700-800 nm) for photosynthesis. Part of this process includes the replacement of six photosystem I (PSI) subunits with isoforms that confer the binding of chlorophyll (Chl) f molecules that absorb far-red light (FRL). However, the exact sites at which Chl f molecules are bound are still challenging to determine. To aid in the identification of Chl f-binding sites, we solved the cryo-EM structure of PSI from far-red light-acclimated cells of the cyanobacterium Synechococcus sp. PCC 7335. We identified six sites that bind Chl f with high specificity and three additional sites that are likely to bind Chl f at lower specificity. All of these binding sites are in the core-antenna regions of PSI, and Chl f was not observed among the electron transfer cofactors. This structural analysis also reveals both conserved and nonconserved Chl f-binding sites, the latter of which exemplify the diversity in FRL-PSI among species. We found that the FRL-PSI structure also contains a bound soluble ferredoxin, PetF1, at low occupancy, which suggests that ferredoxin binds less transiently than expected according to the canonical view of ferredoxin-binding to facilitate electron transfer. We suggest that this may result from structural changes in FRL-PSI that occur specifically during FRL photoacclimation.


  • Organizational Affiliation

    Department of Chemistry, Yale University, New Haven, Connecticut, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1A,
M [auth G],
Y [auth a]
782Synechococcus sp. PCC 7335Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for B4WP20 (Synechococcus sp. (strain ATCC 29403 / PCC 7335))
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UniProt GroupB4WP20
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2B,
N [auth H],
Z [auth b]
743Synechococcus sp. PCC 7335Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for B4WP21 (Synechococcus sp. (strain ATCC 29403 / PCC 7335))
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UniProt GroupB4WP21
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PsaCAA [auth c],
C,
O [auth N]
81Synechococcus sp. PCC 7335Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I 16 kDa polypeptideBA [auth d],
D,
P [auth O]
155Synechococcus sp. PCC 7335Mutation(s): 0 
UniProt
Find proteins for B4WFP8 (Synechococcus sp. (strain ATCC 29403 / PCC 7335))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVCA [auth e],
E,
Q [auth P]
71Synechococcus sp. PCC 7335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B4WSJ5 (Synechococcus sp. (strain ATCC 29403 / PCC 7335))
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UniProt GroupB4WSJ5
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
PSI-FDA [auth f],
F,
R [auth Q]
168Synechococcus sp. PCC 7335Mutation(s): 0 
UniProt
Find proteins for B4WP24 (Synechococcus sp. (strain ATCC 29403 / PCC 7335))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
PsaI2EA [auth i],
G [auth I],
S [auth R]
70Synechococcus sp. PCC 7335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXFA [auth j],
H [auth J],
T [auth S]
46Synechococcus sp. PCC 7335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaKGA [auth k],
I [auth K],
U [auth T]
84Synechococcus sp. PCC 7335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B4WL17 (Synechococcus sp. (strain ATCC 29403 / PCC 7335))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
PSI subunit VHA [auth l],
J [auth L],
V [auth U]
174Synechococcus sp. PCC 7335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B4WP22 (Synechococcus sp. (strain ATCC 29403 / PCC 7335))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
PsaMIA [auth m],
K [auth M],
W [auth V]
31Synechococcus sp. PCC 7335Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
2Fe-2S ferredoxin-type domain-containing proteinJA [auth x],
L [auth X],
X [auth W]
99Synechococcus sp. PCC 7335Mutation(s): 0 
UniProt
Find proteins for B4WFX2 (Synechococcus sp. (strain ATCC 29403 / PCC 7335))
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Small Molecules
Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
F6C (Subject of Investigation/LOI)
Query on F6C

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BD [auth B]
FE [auth B]
FO [auth b]
GE [auth B]
HB [auth A]
BD [auth B],
FE [auth B],
FO [auth b],
GE [auth B],
HB [auth A],
HJ [auth H],
KI [auth H],
ND [auth B],
OJ [auth H],
PJ [auth H],
QG [auth G],
QO [auth b],
TN [auth b],
WI [auth H],
XO [auth b],
YD [auth B],
YO [auth b],
ZL [auth a]
Chlorophyll F
C55 H68 Mg N4 O6
YUTLCKLMRUVWDE-FOFJUSMOSA-M
CLA
Query on CLA

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AB [auth A]
AC [auth A]
AD [auth B]
AE [auth B]
AG [auth G]
AB [auth A],
AC [auth A],
AD [auth B],
AE [auth B],
AG [auth G],
AH [auth G],
AJ [auth H],
AM [auth a],
AO [auth b],
AP [auth b],
BB [auth A],
BC [auth A],
BE [auth B],
BG [auth G],
BH [auth G],
BI [auth H],
BJ [auth H],
BM [auth a],
BO [auth b],
CB [auth A],
CD [auth B],
CE [auth B],
CF [auth K],
CG [auth G],
CH [auth G],
CI [auth H],
CJ [auth H],
CM [auth a],
CO [auth b],
DB [auth A],
DD [auth B],
DE [auth B],
DG [auth G],
DH [auth G],
DI [auth H],
DJ [auth H],
DL [auth a],
DM [auth a],
DO [auth b],
EB [auth A],
ED [auth B],
EE [auth B],
EG [auth G],
EH [auth G],
EI [auth H],
EJ [auth H],
EL [auth a],
EM [auth a],
EO [auth b],
FB [auth A],
FD [auth B],
FF [auth L],
FG [auth G],
FH [auth G],
FI [auth H],
FJ [auth H],
FL [auth a],
FM [auth a],
GB [auth A],
GD [auth B],
GF [auth L],
GG [auth G],
GH [auth G],
GI [auth H],
GJ [auth H],
GL [auth a],
GM [auth a],
GO [auth b],
HD [auth B],
HE [auth B],
HF [auth L],
HG [auth G],
HH [auth G],
HI [auth H],
HL [auth a],
HM [auth a],
HO [auth b],
HQ [auth m],
IB [auth A],
ID [auth B],
IE [auth B],
IG [auth G],
IH [auth G],
II [auth H],
IJ [auth H],
IL [auth a],
IM [auth a],
IO [auth b],
JB [auth A],
JD [auth B],
JG [auth G],
JH [auth G],
JI [auth H],
JJ [auth H],
JL [auth a],
JM [auth a],
JO [auth b],
KB [auth A],
KD [auth B],
KG [auth G],
KH [auth G],
KJ [auth H],
KL [auth a],
KM [auth a],
KN [auth b],
KO [auth b],
LA [auth A],
LB [auth A],
LD [auth B],
LG [auth G],
LI [auth H],
LJ [auth H],
LK [auth T],
LL [auth a],
LM [auth a],
LN [auth b],
LO [auth b],
MA [auth A],
MB [auth A],
MD [auth B],
MG [auth G],
MI [auth H],
MJ [auth H],
ML [auth a],
MM [auth a],
MN [auth b],
MO [auth b],
NA [auth A],
NB [auth A],
NG [auth G],
NI [auth H],
NJ [auth H],
NL [auth a],
NM [auth a],
NN [auth b],
NO [auth b],
OA [auth A],
OB [auth A],
OD [auth B],
OG [auth G],
OI [auth H],
OK [auth U],
OL [auth a],
OM [auth a],
ON [auth b],
OO [auth b],
PA [auth A],
PB [auth A],
PD [auth B],
PF [auth M],
PG [auth G],
PI [auth H],
PK [auth U],
PL [auth a],
PM [auth a],
PN [auth b],
PO [auth b],
QA [auth A],
QB [auth A],
QD [auth B],
QI [auth H],
QJ [auth H],
QK [auth U],
QL [auth a],
QM [auth a],
QN [auth b],
RA [auth A],
RB [auth A],
RD [auth B],
RG [auth G],
RI [auth H],
RJ [auth H],
RL [auth a],
RM [auth a],
RN [auth b],
RO [auth b],
SA [auth A],
SB [auth A],
SC [auth B],
SD [auth B],
SG [auth G],
SI [auth H],
SL [auth a],
SM [auth a],
SN [auth b],
SO [auth b],
TA [auth A],
TB [auth A],
TC [auth B],
TD [auth B],
TG [auth G],
TI [auth H],
TL [auth a],
TM [auth a],
TO [auth b],
UA [auth A],
UB [auth A],
UC [auth B],
UD [auth B],
UF [auth G],
UG [auth G],
UI [auth H],
UL [auth a],
UN [auth b],
UO [auth b],
UP [auth k],
VA [auth A],
VB [auth A],
VC [auth B],
VD [auth B],
VF [auth G],
VG [auth G],
VI [auth H],
VL [auth a],
VN [auth b],
VO [auth b],
WA [auth A],
WB [auth A],
WC [auth B],
WD [auth B],
WF [auth G],
WG [auth G],
WL [auth a],
WN [auth b],
WO [auth b],
XA [auth A],
XB [auth A],
XC [auth B],
XD [auth B],
XF [auth G],
XG [auth G],
XI [auth H],
XL [auth a],
XN [auth b],
XP [auth l],
YA [auth A],
YB [auth A],
YC [auth B],
YF [auth G],
YG [auth G],
YI [auth H],
YK [auth V],
YL [auth a],
YN [auth b],
YP [auth l],
ZA [auth A],
ZB [auth A],
ZC [auth B],
ZD [auth B],
ZF [auth G],
ZG [auth G],
ZI [auth H],
ZN [auth b],
ZO [auth b],
ZP [auth l]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0
Query on CL0

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CL [auth a],
KA [auth A],
TF [auth G]
CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
LMG
Query on LMG

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AF [auth I]
AK [auth H]
EN [auth a]
JK [auth R]
JP [auth b]
AF [auth I],
AK [auth H],
EN [auth a],
JK [auth R],
JP [auth b],
MC [auth A],
RE [auth B],
SP [auth i],
VH [auth G]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

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CN [auth a]
CQ [auth l]
DN [auth a]
DQ [auth l]
KC [auth A]
CN [auth a],
CQ [auth l],
DN [auth a],
DQ [auth l],
KC [auth A],
KF [auth L],
LC [auth A],
LF [auth L],
TH [auth G],
TK [auth U],
UH [auth G],
UK [auth U]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR
Query on BCR

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AN [auth a]
AQ [auth l]
BN [auth a]
BQ [auth l]
CP [auth b]
AN [auth a],
AQ [auth l],
BN [auth a],
BQ [auth l],
CP [auth b],
DF [auth K],
DP [auth b],
EC [auth A],
EP [auth b],
FC [auth A],
FP [auth b],
GC [auth A],
GP [auth b],
HC [auth A],
HK [auth R],
HP [auth b],
IC [auth A],
IF [auth L],
IK [auth R],
IP [auth b],
IQ [auth m],
JC [auth A],
JF [auth L],
KE [auth B],
LE [auth B],
ME [auth B],
MK [auth T],
NE [auth B],
NH [auth G],
OE [auth B],
OH [auth G],
PE [auth B],
PH [auth G],
QE [auth B],
QF [auth M],
QH [auth G],
QP [auth i],
RH [auth G],
RK [auth U],
RP [auth i],
SH [auth G],
SK [auth U],
TJ [auth H],
UJ [auth H],
VJ [auth H],
VP [auth k],
WJ [auth H],
WM [auth a],
XJ [auth H],
XM [auth a],
YE [auth I],
YJ [auth H],
YM [auth a],
ZE [auth I],
ZJ [auth H],
ZK [auth V],
ZM [auth a]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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AL [auth V]
BF [auth I]
BK [auth H]
CK [auth H]
DK [auth H]
AL [auth V],
BF [auth I],
BK [auth H],
CK [auth H],
DK [auth H],
EK [auth H],
EQ [auth l],
FN [auth a],
FQ [auth l],
GN [auth a],
GQ [auth l],
HN [auth a],
IN [auth a],
JQ [auth m],
KK [auth R],
KP [auth b],
LP [auth b],
MF [auth L],
MP [auth b],
NC [auth A],
NF [auth L],
NP [auth b],
OC [auth A],
OF [auth L],
PC [auth A],
QC [auth A],
RF [auth M],
SE [auth B],
TE [auth B],
TP [auth i],
UE [auth B],
VE [auth B],
VK [auth U],
WH [auth G],
WK [auth U],
XH [auth G],
XK [auth U],
YH [auth G],
ZH [auth G]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN
Query on PQN

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BP [auth b]
CC [auth A]
JE [auth B]
LH [auth G]
SJ [auth H]
BP [auth b],
CC [auth A],
JE [auth B],
LH [auth G],
SJ [auth H],
UM [auth a]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4

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DC [auth A]
FK [auth N]
GK [auth N]
MH [auth G]
OP [auth c]
DC [auth A],
FK [auth N],
GK [auth N],
MH [auth G],
OP [auth c],
PP [auth c],
VM [auth a],
WE [auth C],
XE [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES

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BL [auth W],
KQ [auth x],
SF [auth X]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
CA
Query on CA

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EF [auth L],
NK [auth U],
WP [auth l]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

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AI [auth G],
JN [auth a],
RC [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.91 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-FG02-05ER15646
National Science Foundation (NSF, United States)United StatesMCB-1613022

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-24
    Type: Initial release
  • Version 1.1: 2021-12-01
    Changes: Database references
  • Version 1.2: 2021-12-29
    Changes: Database references