6UZV

The structure of a red shifted photosystem I complex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

The structure of a red-shifted photosystem I reveals a red site in the core antenna.

Toporik, H., Khmelnitskiy, A., Dobson, Z., Riddle, R., Williams, D., Lin, S., Jankowiak, R., Mazor, Y.

(2020) Nat Commun 11: 5279-5279

  • DOI: https://doi.org/10.1038/s41467-020-18884-w
  • Primary Citation of Related Structures:  
    6UZV

  • PubMed Abstract: 

    Photosystem I coordinates more than 90 chlorophylls in its core antenna while achieving near perfect quantum efficiency. Low energy chlorophylls (also known as red chlorophylls) residing in the antenna are important for energy transfer dynamics and yield, however, their precise location remained elusive. Here, we construct a chimeric Photosystem I complex in Synechocystis PCC 6803 that shows enhanced absorption in the red spectral region. We combine Cryo-EM and spectroscopy to determine the structure - function relationship in this red-shifted Photosystem I complex. Determining the structure of this complex reveals the precise architecture of the low energy site as well as large scale structural heterogeneity which is probably universal to all trimeric Photosystem I complexes. Identifying the structural elements that constitute red sites can expand the absorption spectrum of oxygenic photosynthetic and potentially modulate light harvesting efficiency.

    • Organizational Affiliation: 

    School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1A,
L [auth a],
M [auth 1]		751Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P29254 (Synechocystis sp. (strain PCC 6803 / Kazusa))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2B,
P [auth b],
Q [auth 2]		735Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerC,
N [auth c],
O [auth 3]		81Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P32422 (Synechocystis sp. (strain PCC 6803 / Kazusa))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IID,
R [auth d],
S [auth 4]		141Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVE,
T [auth e],
U [auth 5]		74Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIF,
V [auth f],
W [auth 6]		165Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIG [auth I],
X [auth i],
Y [auth h]		40Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXAA [auth 7],
H [auth J],
Z [auth j]		40Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIDA [auth l],
EA [auth 0],
I [auth L]		157Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIFA [auth m],
GA [auth 9],
J [auth M]		31Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaK 2BA [auth k],
CA [auth 8],
K		90Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA (Subject of Investigation/LOI)
Query on CLA
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AB [auth A]
AD [auth B]
AE [auth B]
AF [auth L]
AG [auth a]
AB [auth A],
AD [auth B],
AE [auth B],
AF [auth L],
AG [auth a],
AH [auth a],
AI [auth 1],
AJ [auth 1],
AK [auth b],
AL [auth b],
AM [auth 2],
AN [auth 2],
BB [auth A],
BD [auth B],
BF [auth L],
BG [auth a],
BH [auth a],
BI [auth 1],
BJ [auth 1],
BK [auth b],
BL [auth b],
BM [auth 2],
BN [auth 2],
BP [auth 8],
CB [auth A],
CD [auth B],
CG [auth a],
CH [auth a],
CI [auth 1],
CJ [auth 1],
CK [auth b],
CL [auth b],
CM [auth 2],
CN [auth 2],
CP [auth 8],
DB [auth A],
DD [auth B],
DG [auth a],
DH [auth a],
DI [auth 1],
DJ [auth 1],
DK [auth b],
DL [auth b],
DM [auth 2],
DN [auth 2],
DO [auth 6],
DP [auth 8],
EB [auth A],
ED [auth B],
EG [auth a],
EH [auth a],
EI [auth 1],
EJ [auth 1],
EK [auth b],
EL [auth b],
EM [auth 2],
EN [auth 2],
EO [auth 6],
FB [auth A],
FD [auth B],
FG [auth a],
FI [auth 1],
FJ [auth 1],
FK [auth b],
FL [auth b],
FM [auth 2],
FN [auth 2],
GB [auth A],
GD [auth B],
GG [auth a],
GI [auth 1],
GJ [auth 1],
GK [auth b],
GL [auth b],
GM [auth 2],
GN [auth 2],
HB [auth A],
HD [auth B],
HG [auth a],
HI [auth 1],
HK [auth b],
HL [auth b],
HM [auth 2],
HN [auth 2],
HP [auth l],
IB [auth A],
IC [auth B],
ID [auth B],
IG [auth a],
II [auth 1],
IK [auth b],
IL [auth b],
IM [auth 2],
IN [auth 2],
IP [auth l],
JB [auth A],
JC [auth B],
JD [auth B],
JF [auth K],
JG [auth a],
JI [auth 1],
JK [auth b],
JL [auth b],
JM [auth 2],
JN [auth 2],
JP [auth l],
KA [auth A],
KB [auth A],
KD [auth B],
KF [auth K],
KG [auth a],
KI [auth 1],
KK [auth b],
KL [auth b],
KM [auth 2],
KN [auth 2],
KP [auth l],
LA [auth A],
LB [auth A],
LC [auth B],
LD [auth B],
LF [auth K],
LG [auth a],
LI [auth 1],
LK [auth b],
LM [auth 2],
LN [auth 2],
MA [auth A],
MB [auth A],
MC [auth B],
MD [auth B],
ME [auth F],
MG [auth a],
MI [auth 1],
MK [auth b],
MM [auth 2],
MN [auth 2],
NA [auth A],
NB [auth A],
NC [auth B],
ND [auth B],
NG [auth a],
NI [auth 1],
NK [auth b],
NM [auth 2],
NO [auth j],
NP [auth 0],
OA [auth A],
OB [auth A],
OC [auth B],
OD [auth B],
OG [auth a],
OH [auth a],
OI [auth 1],
OK [auth b],
OM [auth 2],
OO [auth j],
PA [auth A],
PB [auth A],
PC [auth B],
PD [auth B],
PE [auth F],
PG [auth a],
PI [auth 1],
PK [auth b],
PM [auth 2],
QA [auth A],
QB [auth A],
QC [auth B],
QD [auth B],
QE [auth F],
QF [auth a],
QG [auth a],
QI [auth 1],
QK [auth b],
QM [auth 2],
RA [auth A],
RB [auth A],
RC [auth B],
RD [auth B],
RF [auth a],
RG [auth a],
RI [auth 1],
RK [auth b],
RM [auth 2],
RO [auth 7],
RP [auth 0],
SA [auth A],
SB [auth A],
SC [auth B],
SD [auth B],
SF [auth a],
SG [auth a],
SH [auth 1],
SI [auth 1],
SK [auth b],
SM [auth 2],
SO [auth 7],
SP [auth 0],
TA [auth A],
TB [auth A],
TC [auth B],
TD [auth B],
TF [auth a],
TG [auth a],
TH [auth 1],
TI [auth 1],
TJ [auth b],
TK [auth b],
TM [auth 2],
TO [auth 7],
TP [auth 0],
UA [auth A],
UB [auth A],
UC [auth B],
UD [auth B],
UF [auth a],
UG [auth a],
UH [auth 1],
UI [auth 1],
UJ [auth b],
UK [auth b],
UM [auth 2],
VA [auth A],
VB [auth A],
VC [auth B],
VD [auth B],
VE [auth J],
VF [auth a],
VG [auth a],
VH [auth 1],
VI [auth 1],
VK [auth b],
VL [auth 2],
VM [auth 2],
VN [auth f],
WA [auth A],
WB [auth A],
WC [auth B],
WD [auth B],
WE [auth J],
WF [auth a],
WG [auth a],
WH [auth 1],
WI [auth 1],
WJ [auth b],
WK [auth b],
WM [auth 2],
XA [auth A],
XB [auth A],
XC [auth B],
XD [auth B],
XF [auth a],
XG [auth a],
XH [auth 1],
XI [auth 1],
XJ [auth b],
XK [auth b],
XL [auth 2],
XM [auth 2],
XO [auth k],
YA [auth A],
YB [auth A],
YC [auth B],
YD [auth B],
YF [auth a],
YG [auth a],
YH [auth 1],
YI [auth 1],
YJ [auth b],
YK [auth b],
YL [auth 2],
YM [auth 2],
YN [auth f],
YO [auth k],
ZA [auth A],
ZC [auth B],
ZD [auth B],
ZE [auth L],
ZF [auth a],
ZG [auth a],
ZH [auth 1],
ZI [auth 1],
ZJ [auth b],
ZK [auth b],
ZL [auth 2],
ZM [auth 2],
ZN [auth f]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0
Query on CL0
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JA [auth A],
PF [auth a],
RH [auth 1]		CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
LMG
Query on LMG
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EF [auth L]
GC [auth A]
GP [auth l]
HC [auth A]
KC [auth B]
EF [auth L],
GC [auth A],
GP [auth l],
HC [auth A],
KC [auth B],
MH [auth a],
MP [auth 0],
NH [auth a],
OJ [auth 1],
OP [auth 0],
VJ [auth b],
WL [auth 2]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG
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GF [auth M]
HA [auth A]
IA [auth A]
IE [auth B]
NF [auth a]
GF [auth M],
HA [auth A],
IA [auth A],
IE [auth B],
NF [auth a],
OF [auth a],
PH [auth 1],
QH [auth 1],
SL [auth b],
UN [auth 2],
WP [auth m],
XP [auth 9]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR
Query on BCR
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AO [auth f]
AP [auth 8]
BC [auth A]
CC [auth A]
CE [auth B]
AO [auth f],
AP [auth 8],
BC [auth A],
CC [auth A],
CE [auth B],
CF [auth L],
CO [auth 6],
DC [auth A],
DE [auth B],
DF [auth L],
EC [auth A],
EE [auth B],
EP [auth 8],
FC [auth A],
FE [auth B],
FO [auth 6],
GE [auth B],
GO [auth 6],
HE [auth B],
HF [auth M],
HH [auth a],
IF [auth K],
IH [auth a],
IO [auth i],
JE [auth B],
JH [auth a],
JJ [auth 1],
JO [auth i],
KH [auth a],
KJ [auth 1],
KO [auth h],
LH [auth a],
LJ [auth 1],
LO [auth h],
LP [auth l],
MF [auth K],
MJ [auth 1],
ML [auth b],
NJ [auth 1],
NL [auth b],
OE [auth F],
OL [auth b],
ON [auth 2],
PL [auth b],
PN [auth 2],
PO [auth j],
PP [auth 0],
QL [auth b],
QN [auth 2],
QO [auth j],
RE [auth F],
RL [auth b],
RN [auth 2],
SE [auth I],
SN [auth 2],
TE [auth I],
TL [auth b],
TN [auth 2],
UL [auth b],
UO [auth 7],
UP [auth 0],
VO [auth 7],
VP [auth 0],
WO [auth k],
XE [auth J],
XN [auth f],
YE [auth J],
YP [auth 9],
ZO [auth k]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT
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BO [auth 6]
HO [auth i]
MO [auth h]
NE [auth F]
UE [auth I]
BO [auth 6],
HO [auth i],
MO [auth h],
NE [auth F],
UE [auth I],
WN [auth f]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN
Query on PQN
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BE [auth B]
FH [auth a]
HJ [auth 1]
LL [auth b]
NN [auth 2]
BE [auth B],
FH [auth a],
HJ [auth 1],
LL [auth b],
NN [auth 2],
ZB [auth A]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4
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AC [auth A]
GH [auth a]
IJ [auth 1]
KE [auth C]
LE [auth C]
AC [auth A],
GH [auth a],
IJ [auth 1],
KE [auth C],
LE [auth C],
PJ [auth c],
QJ [auth c],
RJ [auth 3],
SJ [auth 3]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
CA
Query on CA
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FF [auth L],
FP [auth l],
QP [auth 0]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX1.16-3549

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-16
    Type: Initial release
  • Version 1.1: 2020-11-04
    Changes: Database references