6TCL | pdb_00006tcl

Photosystem I tetramer

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history. 


Literature

Distinct structural modulation of photosystem I and lipid environment stabilizes its tetrameric assembly.

Chen, M., Perez-Boerema, A., Zhang, L., Li, Y., Yang, M., Li, S., Amunts, A.

(2020) Nat Plants 6: 314-320

  • DOI: https://doi.org/10.1038/s41477-020-0610-x
  • Primary Citation of Related Structures:  
    6TCL

  • PubMed Abstract: 

    Photosystem I (PSI) is able to form different oligomeric states across various species. To reveal the structural basis for PSI dimerization and tetramerization, we structurally investigated PSI from the cyanobacterium Anabaena. This revealed a disrupted trimerization domain due to lack of the terminal residues of PsaL in the lumen, which resulted in PSI dimers with loose connections between monomers and weaker energy-coupled chlorophylls than in the trimer. At the dimer surface, specific phospholipids, cofactors and interactions in combination facilitated recruitment of another dimer to form a tetramer. Taken together, the relaxed luminal connections and lipid specificity at the dimer interface account for membrane curvature. PSI tetramer assembly appears to increase the surface area of the thylakoid membrane, which would contribute to PSI crowding.

    • Organizational Affiliation: 
    • Beijing Engineering Research Center for Biofuels, Institute of Nuclear and New, Energy Technology, Tsinghua University, Beijing, P. R. China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1A [auth A1],
KA [auth AA],
M [auth A2],
Y [auth A]		740Nostoc 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 B1],
LA [auth BB],
N [auth B2],
Z [auth B]		739Nostoc 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 C],
C [auth C1],
MA [auth CC],
O [auth C2]		80Nostoc 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 D],
D [auth D1],
NA [auth DD],
P [auth D2]		134Nostoc 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 IVE [auth E1],
Q [auth E2]		60Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIDA [auth F],
F [auth F1],
PA [auth FF]		139Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIEA [auth I],
G [auth I1],
QA [auth II]		31Nostoc sp. PCC 7120 = FACHB-418Mutation(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 J1],
RA [auth JJ],
T [auth J2]		48Nostoc 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 K],
I [auth K1],
SA [auth KK]		74Nostoc 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 XIJ [auth L1]166Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIIA [auth M],
K [auth M1],
UA [auth MM],
W [auth M2]		31Nostoc 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 X],
L [auth X1],
VA [auth XX],
X [auth X2]		39Nostoc 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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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIR [auth F2]137Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIS [auth I2]33Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaK 1U [auth K2]73Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIV [auth L2]167Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVCA [auth E],
OA [auth EE]		63Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIHA [auth L],
TA [auth LL]		154Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AJP
Query on AJP
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AQ [auth B]
BL [auth I2]
BM [auth A]
CO [auth A]
CR [auth K]
AQ [auth B],
BL [auth I2],
BM [auth A],
CO [auth A],
CR [auth K],
HQ [auth B],
KR [auth L],
LR [auth L],
MI [auth A2],
OL [auth L2],
PL [auth L2],
PV [auth BB],
QV [auth BB],
RR [auth AA],
TT [auth AA],
TW [auth KK],
VL [auth M2],
XC [auth A1],
YC [auth A1],
YF [auth L1],
ZF [auth L1],
ZP [auth B]
Digitonin
C56 H92 O29
UVYVLBIGDKGWPX-KUAJCENISA-N
DGD (Subject of Investigation/LOI)
Query on DGD
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GQ [auth B],
VV [auth BB]		DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CL0
Query on CL0
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CM [auth A],
NG [auth A2],
SR [auth AA],
XA [auth A1]		CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
CLA
Query on CLA
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AB [auth A1]
AC [auth A1]
AE [auth B1]
AG [auth L1]
AH [auth A2]
AB [auth A1],
AC [auth A1],
AE [auth B1],
AG [auth L1],
AH [auth A2],
AI [auth A2],
AJ [auth B2],
AM [auth A],
AN [auth A],
AP [auth B],
AR [auth K],
AS [auth AA],
AT [auth AA],
AU [auth BB],
AV [auth BB],
AX [auth XX],
BB [auth A1],
BC [auth A1],
BD [auth B1],
BE [auth B1],
BG [auth L1],
BH [auth A2],
BJ [auth B2],
BN [auth A],
BP [auth B],
BS [auth AA],
BT [auth AA],
BU [auth BB],
BV [auth BB],
BW [auth FF],
CB [auth A1],
CC [auth A1],
CD [auth B1],
CE [auth B1],
CG [auth L1],
CH [auth A2],
CI [auth A2],
CJ [auth B2],
CN [auth A],
CP [auth B],
CS [auth AA],
CT [auth AA],
CU [auth BB],
CV [auth BB],
CW [auth FF],
DB [auth A1],
DC [auth A1],
DD [auth B1],
DE [auth B1],
DF [auth F1],
DH [auth A2],
DJ [auth B2],
DL [auth J2],
DM [auth A],
DN [auth A],
DO [auth B],
DP [auth B],
DS [auth AA],
DT [auth AA],
DU [auth BB],
DV [auth BB],
EB [auth A1],
EC [auth A1],
ED [auth B1],
EE [auth B1],
EF [auth F1],
EH [auth A2],
EJ [auth B2],
EM [auth A],
EN [auth A],
EO [auth B],
EP [auth B],
EQ [auth B],
ER [auth L],
ES [auth AA],
ET [auth AA],
EU [auth BB],
FB [auth A1],
FC [auth A1],
FD [auth B1],
FE [auth B1],
FH [auth A2],
FJ [auth B2],
FL [auth J2],
FM [auth A],
FN [auth A],
FO [auth B],
FP [auth B],
FR [auth L],
FS [auth AA],
FT [auth AA],
FU [auth BB],
FW [auth FF],
GB [auth A1],
GC [auth A1],
GD [auth B1],
GE [auth B1],
GH [auth A2],
GJ [auth B2],
GM [auth A],
GN [auth A],
GO [auth B],
GP [auth B],
GR [auth L],
GS [auth AA],
GT [auth AA],
GU [auth BB],
HB [auth A1],
HC [auth A1],
HD [auth B1],
HE [auth B1],
HF [auth F1],
HH [auth A2],
HJ [auth B2],
HM [auth A],
HN [auth A],
HO [auth B],
HP [auth B],
HS [auth AA],
HU [auth BB],
IB [auth A1],
IC [auth A1],
ID [auth B1],
IE [auth B1],
IG [auth X1],
IH [auth A2],
IJ [auth B2],
IK [auth B2],
IL [auth K2],
IM [auth A],
IN [auth A],
IO [auth B],
IP [auth B],
IQ [auth B],
IS [auth AA],
IT [auth AA],
IU [auth BB],
JB [auth A1],
JC [auth A1],
JD [auth B1],
JE [auth B1],
JH [auth A2],
JJ [auth B2],
JM [auth A],
JN [auth A],
JO [auth B],
JP [auth B],
JQ [auth B],
JS [auth AA],
JU [auth BB],
KB [auth A1],
KC [auth A1],
KD [auth B1],
KE [auth B1],
KH [auth A2],
KI [auth A2],
KJ [auth B2],
KL [auth K2],
KM [auth A],
KN [auth A],
KO [auth B],
KP [auth B],
KQ [auth B],
KS [auth AA],
KU [auth BB],
LB [auth A1],
LC [auth A1],
LD [auth B1],
LF [auth J1],
LG [auth A2],
LH [auth A2],
LJ [auth B2],
LK [auth B2],
LM [auth A],
LN [auth A],
LO [auth B],
LP [auth B],
LS [auth AA],
LU [auth BB],
MB [auth A1],
MD [auth B1],
MG [auth A2],
MH [auth A2],
MJ [auth B2],
MK [auth B2],
MM [auth A],
MN [auth A],
MO [auth B],
MP [auth B],
MS [auth AA],
MU [auth BB],
MV [auth BB],
MW [auth JJ],
NB [auth A1],
NC [auth A1],
ND [auth B1],
NF [auth J1],
NH [auth A2],
NJ [auth B2],
NK [auth B2],
NM [auth A],
NN [auth A],
NO [auth B],
NP [auth B],
NS [auth AA],
NU [auth BB],
OB [auth A1],
OD [auth B1],
OG [auth A2],
OH [auth A2],
OJ [auth B2],
OK [auth B2],
OM [auth A],
ON [auth A],
OO [auth B],
OQ [auth F],
OR [auth X],
OS [auth AA],
OU [auth BB],
OW [auth JJ],
PB [auth A1],
PD [auth B1],
PG [auth A2],
PH [auth A2],
PI [auth B2],
PJ [auth B2],
PM [auth A],
PN [auth A],
PO [auth B],
PQ [auth F],
PS [auth AA],
PU [auth BB],
QB [auth A1],
QD [auth B1],
QF [auth K1],
QG [auth A2],
QH [auth A2],
QI [auth B2],
QJ [auth B2],
QL [auth L2],
QM [auth A],
QO [auth B],
QR [auth AA],
QS [auth AA],
QT [auth AA],
QU [auth BB],
QW [auth KK],
RB [auth A1],
RD [auth B1],
RF [auth K1],
RG [auth A2],
RH [auth A2],
RI [auth B2],
RJ [auth B2],
RL [auth L2],
RM [auth A],
RN [auth A],
RO [auth B],
RS [auth AA],
RU [auth BB],
RW [auth KK],
SB [auth A1],
SD [auth B1],
SG [auth A2],
SH [auth A2],
SI [auth B2],
SJ [auth B2],
SL [auth L2],
SM [auth A],
SO [auth B],
SS [auth AA],
SU [auth BB],
TB [auth A1],
TD [auth B1],
TE [auth B1],
TF [auth K1],
TG [auth A2],
TH [auth A2],
TI [auth B2],
TJ [auth B2],
TK [auth F2],
TM [auth A],
TO [auth B],
TR [auth AA],
TS [auth AA],
TU [auth BB],
TV [auth BB],
UB [auth A1],
UD [auth B1],
UG [auth A2],
UH [auth A2],
UI [auth B2],
UJ [auth B2],
UK [auth F2],
UM [auth A],
UO [auth B],
UR [auth AA],
US [auth AA],
UT [auth BB],
UU [auth BB],
UW [auth LL],
VB [auth A1],
VC [auth A1],
VD [auth B1],
VG [auth A2],
VH [auth A2],
VI [auth B2],
VJ [auth B2],
VM [auth A],
VO [auth B],
VQ [auth J],
VR [auth AA],
VS [auth AA],
VT [auth BB],
VU [auth BB],
VW [auth LL],
WA [auth A1],
WB [auth A1],
WD [auth B1],
WE [auth B1],
WG [auth A2],
WH [auth A2],
WI [auth B2],
WJ [auth B2],
WM [auth A],
WO [auth B],
WP [auth B],
WR [auth AA],
WS [auth AA],
WT [auth BB],
WU [auth BB],
WV [auth BB],
WW [auth LL],
XB [auth A1],
XD [auth B1],
XE [auth B1],
XG [auth A2],
XH [auth A2],
XI [auth B2],
XJ [auth B2],
XL [auth X2],
XM [auth A],
XO [auth B],
XQ [auth J],
XR [auth AA],
XS [auth AA],
XT [auth BB],
XU [auth BB],
XV [auth BB],
YA [auth A1],
YB [auth A1],
YD [auth B1],
YE [auth B1],
YG [auth A2],
YH [auth A2],
YI [auth B2],
YJ [auth B2],
YM [auth A],
YO [auth B],
YR [auth AA],
YS [auth AA],
YT [auth BB],
YU [auth BB],
ZA [auth A1],
ZB [auth A1],
ZD [auth B1],
ZG [auth A2],
ZH [auth A2],
ZI [auth B2],
ZJ [auth B2],
ZM [auth A],
ZN [auth A],
ZO [auth B],
ZQ [auth K],
ZR [auth AA],
ZS [auth AA],
ZT [auth BB],
ZU [auth BB]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG (Subject of Investigation/LOI)
Query on LMG
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AD [auth A1]
AF [auth B1]
BQ [auth B]
CL [auth I2]
DR [auth L]
AD [auth A1],
AF [auth B1],
BQ [auth B],
CL [auth I2],
DR [auth L],
FG [auth L1],
FQ [auth B],
HK [auth B2],
HL [auth K2],
JK [auth B2],
JW [auth II],
KF [auth I1],
LV [auth BB],
LW [auth II],
ML [auth K2],
NI [auth A2],
NL [auth L2],
NR [auth M],
NV [auth BB],
OI [auth A2],
PF [auth K1],
QK [auth B2],
SE [auth B1],
UE [auth B1],
UV [auth BB],
VF [auth K1],
VP [auth B],
XF [auth L1],
XP [auth B],
ZC [auth A1]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG (Subject of Investigation/LOI)
Query on LHG
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BX [auth XX]
CQ [auth B]
DI [auth A2]
DQ [auth B]
EI [auth A2]
BX [auth XX],
CQ [auth B],
DI [auth A2],
DQ [auth B],
EI [auth A2],
GG [auth L1],
JG [auth X1],
JR [auth L],
JT [auth AA],
KG [auth X1],
KK [auth B2],
KT [auth AA],
OC [auth A1],
PC [auth A1],
PR [auth X],
RV [auth BB],
SN [auth A],
SV [auth BB],
TN [auth A],
UL [auth L2],
VE [auth B1],
YL [auth X2],
YW [auth LL],
ZL [auth X2]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
ECH
Query on ECH
Download Ideal Coordinates CCD File 
DK [auth B2],
HV [auth BB],
OE [auth B1],
RP [auth B]		beta,beta-caroten-4-one
C40 H54 O
QXNWZXMBUKUYMD-QQGJMDNJSA-N
BCR
Query on BCR
Download Ideal Coordinates CCD File 
AL [auth I2]
AO [auth A]
BK [auth B2]
BO [auth A]
BR [auth K]
AL [auth I2],
AO [auth A],
BK [auth B2],
BO [auth A],
BR [auth K],
CK [auth B2],
DG [auth L1],
DW [auth FF],
EG [auth L1],
EK [auth B2],
EL [auth J2],
EW [auth FF],
FF [auth F1],
FI [auth A2],
FK [auth B2],
FV [auth BB],
GF [auth F1],
GI [auth A2],
GK [auth B2],
GL [auth J2],
GV [auth BB],
GW [auth FF],
HG [auth M1],
HI [auth A2],
HR [auth L],
HW [auth II],
IF [auth F1],
II [auth A2],
IR [auth L],
IV [auth BB],
IW [auth II],
JF [auth I1],
JI [auth A2],
JL [auth K2],
JV [auth BB],
KV [auth BB],
KW [auth II],
LI [auth A2],
LL [auth K2],
LT [auth AA],
ME [auth B1],
MF [auth J1],
MR [auth M],
MT [auth AA],
NE [auth B1],
NT [auth AA],
NW [auth JJ],
OF [auth J1],
OT [auth AA],
OV [auth BB],
PE [auth B1],
PP [auth B],
PT [auth AA],
PW [auth JJ],
QC [auth A1],
QE [auth B1],
QP [auth B],
QQ [auth F],
RC [auth A1],
RE [auth B1],
RQ [auth F],
RT [auth AA],
SC [auth A1],
SF [auth K1],
SP [auth B],
SQ [auth F],
ST [auth AA],
SW [auth KK],
TC [auth A1],
TL [auth L2],
TP [auth B],
TQ [auth I],
UC [auth A1],
UF [auth K1],
UN [auth A],
UP [auth B],
UQ [auth I],
VK [auth F2],
VN [auth A],
WC [auth A1],
WF [auth L1],
WK [auth F2],
WL [auth M2],
WN [auth A],
WQ [auth J],
XK [auth F2],
XN [auth A],
XW [auth LL],
YK [auth I2],
YN [auth A],
YP [auth B],
YQ [auth J],
ZK [auth I2],
ZW [auth MM]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN
Query on PQN
Download Ideal Coordinates CCD File 
AK [auth B2]
BI [auth A2]
EV [auth BB]
HT [auth AA]
LE [auth B1]
AK [auth B2],
BI [auth A2],
EV [auth BB],
HT [auth AA],
LE [auth B1],
MC [auth A1],
OP [auth B],
QN [auth A]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4
Download Ideal Coordinates CCD File 
AW [auth CC]
BF [auth C1]
CF [auth C1]
LQ [auth B]
MQ [auth C]
AW [auth CC],
BF [auth C1],
CF [auth C1],
LQ [auth B],
MQ [auth C],
NQ [auth C],
PK [auth B2],
RK [auth C2],
SK [auth C2],
YV [auth BB],
ZE [auth B1],
ZV [auth CC]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swedish Research CouncilSwedenNT_2015-04107
European Research Council (ERC)SwedenERC-2018-StG-805230
Knut and Alice Wallenberg FoundationSweden2018.0080
National Natural Science Foundation of China (NSFC)China21506113
National Natural Science Foundation of China (NSFC)China31470229

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-19
    Type: Initial release
  • Version 1.1: 2020-03-25
    Changes: Database references
  • Version 2.0: 2024-05-22
    Changes: Advisory, Atomic model, Data collection, Database references, Non-polymer description, Other