6JEO

Structure of PSI tetramer from Anabaena

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

Structure of a cyanobacterial photosystem I tetramer revealed by cryo-electron microscopy.

Kato, K., Nagao, R., Jiang, T.Y., Ueno, Y., Yokono, M., Chan, S.K., Watanabe, M., Ikeuchi, M., Shen, J.R., Akimoto, S., Miyazaki, N., Akita, F.

(2019) Nat Commun 10: 4929-4929

  • DOI: https://doi.org/10.1038/s41467-019-12942-8
  • Primary Citation of Related Structures:  
    6JEO

  • PubMed Abstract: 

    Photosystem I (PSI) functions to harvest light energy for conversion into chemical energy. The organisation of PSI is variable depending on the species of organism. Here we report the structure of a tetrameric PSI core isolated from a cyanobacterium, Anabaena sp. PCC 7120, analysed by single-particle cryo-electron microscopy (cryo-EM) at 3.3 Å resolution. The PSI tetramer has a C2 symmetry and is organised in a dimer of dimers form. The structure reveals interactions at the dimer-dimer interface and the existence of characteristic pigment orientations and inter-pigment distances within the dimer units that are important for unique excitation energy transfer. In particular, characteristic residues of PsaL are identified to be responsible for the formation of the tetramer. Time-resolved fluorescence analyses showed that the PSI tetramer has an enhanced excitation-energy quenching. These structural and spectroscopic findings provide insights into the physiological significance of the PSI tetramer and evolutionary changes of the PSI organisations.

    • Organizational Affiliation: 

    Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1A [auth aA],
KA [auth dA],
M [auth bA],
Y [auth cA]		752Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P58576 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2 1B [auth aB],
LA [auth dB],
N [auth bB],
Z [auth cB]		741Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P58565 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerAA [auth cC],
C [auth aC],
MA [auth dC],
O [auth bC]		81Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P0A410 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIBA [auth cD],
D [auth aD],
NA [auth dD],
P [auth bD]		139Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P58573 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVCA [auth cE],
E [auth aE],
OA [auth dE],
Q [auth bE]		70Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P58575 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIDA [auth cF],
F [auth aF],
PA [auth dF],
R [auth bF]		164Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P58564 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIEA [auth cI],
G [auth aI],
QA [auth dI],
S [auth bI]		46Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P58560 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXFA [auth cJ],
H [auth aJ],
RA [auth dJ],
T [auth bJ]		49Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P58568 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaK 1GA [auth cK],
I [auth aK],
SA [auth dK],
U [auth bK]		86Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P58583 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIHA [auth cL],
J [auth aL],
TA [auth dL],
V [auth bL]		172Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P58577 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIIA [auth cM],
K [auth aM],
UA [auth dM],
W [auth bM]		40Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8YNB0 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I 4.8 kDa proteinJA [auth cX],
L [auth aX],
VA [auth dX],
X [auth bX]		44Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P58566 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA
Download Ideal Coordinates CCD File 
AB [auth aA]
AC [auth aA]
AD [auth aB]
AE [auth aB]
AF [auth aF]
AB [auth aA],
AC [auth aA],
AD [auth aB],
AE [auth aB],
AF [auth aF],
AG [auth bA],
AH [auth bA],
AI [auth bB],
AJ [auth bB],
AL [auth cA],
AM [auth cA],
AN [auth cB],
AO [auth cB],
AP [auth cK],
AQ [auth dA],
AS [auth dB],
AU [auth dL],
BB [auth aA],
BC [auth aA],
BD [auth aB],
BE [auth aB],
BG [auth bA],
BH [auth bA],
BI [auth bB],
BJ [auth bB],
BK [auth bK],
BL [auth cA],
BM [auth cA],
BN [auth cB],
BO [auth cB],
BQ [auth dA],
BS [auth dB],
BU [auth dL],
CB [auth aA],
CC [auth aA],
CD [auth aB],
CE [auth aB],
CG [auth bA],
CH [auth bA],
CI [auth bB],
CJ [auth bB],
CL [auth cA],
CM [auth cA],
CN [auth cB],
CO [auth cB],
CP [auth cL],
CQ [auth dA],
CS [auth dB],
DB [auth aA],
DC [auth aA],
DD [auth aB],
DE [auth aB],
DF [auth aJ],
DG [auth bA],
DH [auth bA],
DI [auth bB],
DJ [auth bB],
DK [auth bK],
DL [auth cA],
DM [auth cA],
DN [auth cB],
DO [auth cB],
DP [auth cL],
DQ [auth dA],
DS [auth dB],
EB [auth aA],
EC [auth aA],
ED [auth aB],
EE [auth aB],
EF [auth aJ],
EG [auth bA],
EH [auth bA],
EI [auth bB],
EJ [auth bB],
EK [auth bL],
EL [auth cA],
EM [auth cA],
EN [auth cB],
EP [auth cL],
EQ [auth dA],
ES [auth dB],
FB [auth aA],
FC [auth aA],
FD [auth aB],
FE [auth aB],
FG [auth bA],
FH [auth bA],
FI [auth bB],
FJ [auth bB],
FK [auth bL],
FL [auth cA],
FN [auth cB],
FQ [auth dA],
FS [auth dB],
FU [auth dX],
GB [auth aA],
GC [auth aA],
GD [auth aB],
GE [auth aB],
GG [auth bA],
GH [auth bA],
GI [auth bB],
GL [auth cA],
GN [auth cB],
GQ [auth dA],
GS [auth dB],
HB [auth aA],
HC [auth aA],
HD [auth aB],
HE [auth aB],
HF [auth aK],
HG [auth bA],
HI [auth bB],
HK [auth bL],
HL [auth cA],
HN [auth cB],
HQ [auth dA],
HS [auth dB],
IB [auth aA],
IC [auth aA],
ID [auth aB],
IE [auth aB],
IF [auth aK],
IG [auth bA],
II [auth bB],
IK [auth bL],
IL [auth cA],
IN [auth cB],
IP [auth cX],
IQ [auth dA],
IR [auth dB],
IS [auth dB],
JB [auth aA],
JC [auth aA],
JD [auth aB],
JE [auth aB],
JG [auth bA],
JI [auth bB],
JK [auth bL],
JL [auth cA],
JN [auth cB],
JQ [auth dA],
JR [auth dB],
JS [auth dB],
KB [auth aA],
KC [auth aA],
KD [auth aB],
KE [auth aB],
KF [auth aL],
KG [auth bA],
KI [auth bB],
KL [auth cA],
KN [auth cB],
KP [auth dA],
KQ [auth dA],
KR [auth dB],
KS [auth dB],
KT [auth dF],
LB [auth aA],
LC [auth aA],
LD [auth aB],
LE [auth aB],
LF [auth aL],
LG [auth bA],
LI [auth bB],
LL [auth cA],
LN [auth cB],
LP [auth dA],
LQ [auth dA],
LR [auth dB],
LS [auth dB],
MB [auth aA],
MC [auth aA],
MD [auth aB],
MF [auth aL],
MG [auth bA],
MI [auth bB],
ML [auth cA],
MN [auth cB],
MP [auth dA],
MQ [auth dA],
MR [auth dB],
MS [auth dB],
MT [auth dF],
NB [auth aA],
ND [auth aB],
NG [auth bA],
NI [auth bB],
NK [auth bX],
NL [auth cA],
NN [auth cB],
NP [auth dA],
NQ [auth dA],
NR [auth dB],
NS [auth dB],
OB [auth aA],
OD [auth aB],
OG [auth bA],
OI [auth bB],
OL [auth cA],
ON [auth cB],
OP [auth dA],
OQ [auth dA],
OR [auth dB],
OS [auth dB],
PB [auth aA],
PD [auth aB],
PG [auth bA],
PI [auth bB],
PK [auth cA],
PL [auth cA],
PM [auth cB],
PN [auth cB],
PP [auth dA],
PQ [auth dA],
PR [auth dB],
PS [auth dB],
PT [auth dJ],
QB [auth aA],
QD [auth aB],
QF [auth aX],
QG [auth bA],
QH [auth bB],
QI [auth bB],
QK [auth cA],
QL [auth cA],
QM [auth cB],
QN [auth cB],
QO [auth cF],
QP [auth dA],
QQ [auth dA],
QR [auth dB],
QS [auth dB],
QT [auth dJ],
RB [auth aA],
RD [auth aB],
RG [auth bA],
RH [auth bB],
RI [auth bB],
RK [auth cA],
RL [auth cA],
RM [auth cB],
RN [auth cB],
RP [auth dA],
RQ [auth dA],
RR [auth dB],
RS [auth dB],
SB [auth aA],
SD [auth aB],
SF [auth bA],
SG [auth bA],
SH [auth bB],
SI [auth bB],
SJ [auth bF],
SK [auth cA],
SL [auth cA],
SM [auth cB],
SN [auth cB],
SO [auth cF],
SP [auth dA],
SQ [auth dA],
SR [auth dB],
SS [auth dB],
TB [auth aA],
TD [auth aB],
TF [auth bA],
TG [auth bA],
TH [auth bB],
TI [auth bB],
TK [auth cA],
TL [auth cA],
TM [auth cB],
TN [auth cB],
TP [auth dA],
TQ [auth dA],
TR [auth dB],
TS [auth dB],
TT [auth dK],
UB [auth aA],
UD [auth aB],
UF [auth bA],
UG [auth bA],
UH [auth bB],
UI [auth bB],
UJ [auth bF],
UK [auth cA],
UL [auth cA],
UM [auth cB],
UN [auth cB],
UP [auth dA],
UQ [auth dA],
UR [auth dB],
US [auth dB],
VB [auth aA],
VD [auth aB],
VF [auth bA],
VG [auth bA],
VH [auth bB],
VI [auth bB],
VK [auth cA],
VL [auth cA],
VM [auth cB],
VN [auth cB],
VO [auth cJ],
VP [auth dA],
VQ [auth dA],
VR [auth dB],
VS [auth dB],
VT [auth dK],
WB [auth aA],
WD [auth aB],
WF [auth bA],
WG [auth bA],
WH [auth bB],
WI [auth bB],
WK [auth cA],
WL [auth cA],
WM [auth cB],
WN [auth cB],
WO [auth cJ],
WP [auth dA],
WQ [auth dA],
WR [auth dB],
WS [auth dB],
WT [auth dL],
XA [auth aA],
XB [auth aA],
XC [auth aB],
XD [auth aB],
XF [auth bA],
XG [auth bA],
XH [auth bB],
XI [auth bB],
XJ [auth bJ],
XK [auth cA],
XL [auth cA],
XM [auth cB],
XN [auth cB],
XP [auth dA],
XQ [auth dA],
XR [auth dB],
XS [auth dB],
XT [auth dL],
YA [auth aA],
YB [auth aA],
YC [auth aB],
YD [auth aB],
YE [auth aF],
YF [auth bA],
YG [auth bA],
YH [auth bB],
YI [auth bB],
YJ [auth bJ],
YK [auth cA],
YL [auth cA],
YM [auth cB],
YN [auth cB],
YP [auth dA],
YQ [auth dA],
YR [auth dB],
ZA [auth aA],
ZB [auth aA],
ZC [auth aB],
ZD [auth aB],
ZF [auth bA],
ZG [auth bA],
ZH [auth bB],
ZI [auth bB],
ZK [auth cA],
ZL [auth cA],
ZM [auth cB],
ZN [auth cB],
ZO [auth cK],
ZP [auth dA],
ZR [auth dB],
ZT [auth dL]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0
Query on CL0
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JP [auth dA],
OK [auth cA],
RF [auth bA],
WA [auth aA]		CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
LMG
Query on LMG
Download Ideal Coordinates CCD File 
FT [auth dB],
LO [auth cB],
NJ [auth bB],
TE [auth aB]		1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG
Download Ideal Coordinates CCD File 
GR [auth dA]
GT [auth dB]
HR [auth dA]
MO [auth cB]
NM [auth cA]
GR [auth dA],
GT [auth dB],
HR [auth dA],
MO [auth cB],
NM [auth cA],
OH [auth bA],
OJ [auth bB],
OM [auth cA],
PH [auth bA],
UE [auth aB],
VC [auth aA],
WC [auth aA]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR
Query on BCR
Download Ideal Coordinates CCD File 
AK [auth bJ]
AT [auth dB]
BF [auth aF]
BP [auth cL]
BR [auth dA]
AK [auth bJ],
AT [auth dB],
BF [auth aF],
BP [auth cL],
BR [auth dA],
BT [auth dB],
CF [auth aI],
CK [auth bK],
CR [auth dA],
CT [auth dB],
CU [auth dL],
DR [auth dA],
DT [auth dB],
DU [auth dL],
ER [auth dA],
ET [auth dB],
EU [auth dM],
FF [auth aJ],
FO [auth cB],
FP [auth cL],
FR [auth dA],
GF [auth aJ],
GK [auth bL],
GO [auth cB],
GP [auth cL],
HJ [auth bB],
HM [auth cA],
HO [auth cB],
HP [auth cM],
HT [auth dB],
IJ [auth bB],
IM [auth cA],
IO [auth cB],
JF [auth aL],
JH [auth bA],
JJ [auth bB],
JM [auth cA],
JO [auth cB],
KH [auth bA],
KJ [auth bB],
KK [auth bL],
KM [auth cA],
KO [auth cB],
LH [auth bA],
LJ [auth bB],
LK [auth bL],
LM [auth cA],
LT [auth dF],
MH [auth bA],
MJ [auth bB],
MK [auth bM],
MM [auth cA],
NE [auth aB],
NF [auth aL],
NH [auth bA],
NO [auth cB],
NT [auth dF],
OE [auth aB],
OF [auth aL],
OT [auth dI],
PC [auth aA],
PE [auth aB],
PF [auth aM],
PJ [auth bB],
QC [auth aA],
QE [auth aB],
RC [auth aA],
RE [auth aB],
RO [auth cF],
RT [auth dJ],
SC [auth aA],
SE [auth aB],
ST [auth dJ],
TC [auth aA],
TJ [auth bF],
TO [auth cF],
UC [auth aA],
UO [auth cI],
UT [auth dK],
VE [auth aB],
VJ [auth bF],
WJ [auth bI],
XO [auth cJ],
YO [auth cJ],
YT [auth dL],
ZE [auth aF],
ZJ [auth bJ],
ZS [auth dB]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN
Query on PQN
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EO [auth cB]
FM [auth cA]
GJ [auth bB]
HH [auth bA]
ME [auth aB]
EO [auth cB],
FM [auth cA],
GJ [auth bB],
HH [auth bA],
ME [auth aB],
NC [auth aA],
YS [auth dB],
ZQ [auth dA]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4
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AR [auth dA]
GM [auth cA]
IH [auth bA]
IT [auth dC]
JT [auth dC]
AR [auth dA],
GM [auth cA],
IH [auth bA],
IT [auth dC],
JT [auth dC],
OC [auth aA],
OO [auth cC],
PO [auth cC],
QJ [auth bC],
RJ [auth bC],
WE [auth aC],
XE [auth aC]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3
MODEL REFINEMENTPHENIX1.13_2998

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-13
    Type: Initial release