6YAC | pdb_00006yac

Plant PSI-ferredoxin supercomplex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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This is version 2.1 of the entry. See complete history. 

Literature

The structure of a triple complex of plant photosystem I with ferredoxin and plastocyanin.

Caspy, I., Borovikova-Sheinker, A., Klaiman, D., Shkolnisky, Y., Nelson, N.

(2020) Nat Plants 6: 1300-1305

  • DOI: https://doi.org/10.1038/s41477-020-00779-9
  • Primary Citation Related Structures: 
    6YAC, 6YEZ

  • PubMed Abstract: 

    The ability of photosynthetic organisms to use sunlight as a sole source of energy is endowed by two large membrane complexes-photosystem I (PSI) and photosystem II (PSII). PSI and PSII are the fundamental components of oxygenic photosynthesis, providing oxygen, food and an energy source for most living organisms on Earth. Currently, high-resolution crystal structures of these complexes from various organisms are available. The crystal structures of megadalton complexes have revealed excitation transfer and electron-transport pathways within the various complexes. PSI is defined as plastocyanin-ferredoxin oxidoreductase but a high-resolution structure of the entire triple supercomplex is not available. Here, using a new cryo-electron microscopy technique, we solve the structure of native plant PSI in complex with its electron donor plastocyanin and the electron acceptor ferredoxin. We reveal all of the contact sites and the modes of interaction between the interacting electron carriers and PSI.

    • Organizational Affiliation: 
    • Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.

Macromolecule Content 

  • Total Structure Weight: 562.54 kDa 
  • Atom Count: 38,469 
  • Modeled Residue Count: 3,332 
  • Deposited Residue Count: 3,332 
  • Unique protein chains: 17

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1743Lathyrus oleraceusMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A0F6NFW5 (Pisum sativum)
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2733Lathyrus oleraceusMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A0F6NGI2 (Pisum sativum)
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center80Lathyrus oleraceusMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P10793 (Pisum sativum)
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaD143Lathyrus oleraceusMutation(s): 0 
UniProt
Find proteins for E1C9K8 (Pisum sativum)
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaE66Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaF154Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A0M3KL12 (Pisum sativum)
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaG97Lathyrus oleraceusMutation(s): 0 
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaH88Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A0M3KL10 (Pisum sativum)
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIII31Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P17227 (Pisum sativum)
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IX42Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit X psaK81Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaL157Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for E1C9L1 (Pisum sativum)
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Lhca1M [auth 1]193Lathyrus oleraceusMutation(s): 0 
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticN [auth 2]208Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q41038 (Pisum sativum)
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 3, chloroplasticO [auth 3]221Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q32904 (Pisum sativum)
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein P4, chloroplasticP [auth 4]198Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9SQL2 (Pisum sativum)
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Ferredoxin-1, chloroplasticQ [auth N]97Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P09911 (Pisum sativum)
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Reference Sequence

Small Molecules

Ligands 15 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD


Download:Ideal Coordinates CCD File
EF [auth J]
EI [auth 3]
LE [auth F]
LG [auth 1]
TE [auth G]
EF [auth J],
EI [auth 3],
LE [auth F],
LG [auth 1],
TE [auth G],
WD [auth B],
XI [auth 4],
YI [auth 4]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL

Query on CHL


Download:Ideal Coordinates CCD File
BH [auth 2]
CH [auth 2]
DG [auth 1]
EG [auth 1]
GG [auth 1]
BH [auth 2],
CH [auth 2],
DG [auth 1],
EG [auth 1],
GG [auth 1],
RH [auth 3],
RI [auth 4],
SI [auth 4],
UH [auth 3],
UI [auth 4],
VI [auth 4],
XG [auth 2],
XH [auth 3],
YG [auth 2],
ZG [auth 2]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA

Query on CLA


Download:Ideal Coordinates CCD File
AA [auth A]
AB [auth A]
AC [auth B]
AD [auth B]
AG [auth 1]
AA [auth A],
AB [auth A],
AC [auth B],
AD [auth B],
AG [auth 1],
AH [auth 2],
AI [auth 3],
BA [auth A],
BB [auth A],
BC [auth B],
BD [auth B],
BF [auth J],
BG [auth 1],
BI [auth 3],
CA [auth A],
CB [auth A],
CC [auth B],
CD [auth B],
CG [auth 1],
DA [auth A],
DB [auth A],
DC [auth B],
DD [auth B],
DE [auth F],
EA [auth A],
EB [auth A],
EC [auth B],
ED [auth B],
EE [auth F],
FA [auth A],
FB [auth A],
FC [auth B],
FD [auth B],
FG [auth 1],
GA [auth A],
GB [auth A],
GC [auth B],
GD [auth B],
GF [auth K],
HA [auth A],
HB [auth A],
HC [auth B],
HD [auth B],
HF [auth K],
HG [auth 1],
IA [auth A],
IB [auth A],
IC [auth B],
ID [auth B],
IF [auth K],
IG [auth 1],
II [auth 4],
JA [auth A],
JC [auth B],
JD [auth B],
JF [auth K],
JI [auth 4],
KA [auth A],
KC [auth B],
KD [auth B],
KI [auth 4],
LA [auth A],
LC [auth B],
LD [auth B],
LI [auth 4],
MA [auth A],
MC [auth B],
MF [auth L],
MI [auth 4],
NA [auth A],
NC [auth B],
NE [auth G],
NF [auth L],
NI [auth 4],
OA [auth A],
OC [auth B],
OE [auth G],
OF [auth L],
OH [auth 3],
OI [auth 4],
PA [auth A],
PC [auth B],
PE [auth G],
PG [auth 2],
PH [auth 3],
PI [auth 4],
QA [auth A],
QC [auth B],
QG [auth 2],
QH [auth 3],
QI [auth 4],
RA [auth A],
RC [auth B],
RG [auth 2],
S [auth A],
SA [auth A],
SC [auth B],
SG [auth 2],
SH [auth 3],
T [auth A],
TA [auth A],
TC [auth B],
TG [auth 2],
TH [auth 3],
TI [auth 4],
U [auth A],
UA [auth A],
UC [auth B],
UG [auth 2],
V [auth A],
VA [auth A],
VC [auth B],
VF [auth 1],
VG [auth 2],
VH [auth 3],
W [auth A],
WA [auth A],
WB [auth B],
WC [auth B],
WF [auth 1],
WG [auth 2],
WH [auth 3],
WI [auth 4],
X [auth A],
XA [auth A],
XB [auth B],
XC [auth B],
XE [auth G],
XF [auth 1],
Y [auth A],
YA [auth A],
YB [auth B],
YC [auth B],
YF [auth 1],
YH [auth 3],
Z [auth A],
ZA [auth A],
ZB [auth B],
ZC [auth B],
ZF [auth 1],
ZH [auth 3]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0

Query on CL0


Download:Ideal Coordinates CCD File
R [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
LMG

Query on LMG


Download:Ideal Coordinates CCD File
DI [auth 3]
EH [auth 2]
FH [auth 2]
GH [auth 2]
HE [auth F]
DI [auth 3],
EH [auth 2],
FH [auth 2],
GH [auth 2],
HE [auth F],
HH [auth 2],
IE [auth F],
IH [auth 2],
JE [auth F],
KE [auth F],
KG [auth 1],
ME [auth F],
RE [auth G],
SE [auth G],
UB [auth A],
UD [auth B],
VD [auth B],
WE [auth G],
YD [auth B]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG

Query on LHG


Download:Ideal Coordinates CCD File
CI [auth 3]
DH [auth 2]
JG [auth 1]
JH [auth 2]
RB [auth A]
CI [auth 3],
DH [auth 2],
JG [auth 1],
JH [auth 2],
RB [auth A],
SB [auth A],
SD [auth B],
TD [auth B]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
XAT

Query on XAT


Download:Ideal Coordinates CCD File
GI [auth 4],
NG [auth 2]		(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O4
SZCBXWMUOPQSOX-WVJDLNGLSA-N
LUT

Query on LUT


Download:Ideal Coordinates CCD File
DF [auth J]
FI [auth 4]
KH [auth 3]
LH [auth 3]
MG [auth 2]
DF [auth J],
FI [auth 4],
KH [auth 3],
LH [auth 3],
MG [auth 2],
RF [auth 1],
SF [auth 1]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
C7Z

Query on C7Z


Download:Ideal Coordinates CCD File
HI [auth 4](1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol
C40 H56 O2
JKQXZKUSFCKOGQ-ANDPMPNWSA-N
BCR

Query on BCR


Download:Ideal Coordinates CCD File
AF [auth I]
CF [auth J]
FE [auth F]
GE [auth F]
KF [auth K]
AF [auth I],
CF [auth J],
FE [auth F],
GE [auth F],
KF [auth K],
LB [auth A],
LF [auth K],
MB [auth A],
MH [auth 3],
NB [auth A],
ND [auth B],
NH [auth 3],
OB [auth A],
OD [auth B],
OG [auth 2],
PB [auth A],
PD [auth B],
PF [auth L],
QB [auth A],
QD [auth B],
QE [auth G],
QF [auth L],
RD [auth B],
TF [auth 1],
UF [auth 1],
YE [auth G],
ZE [auth I]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT

Query on LMT


Download:Ideal Coordinates CCD File
FF [auth J]
TB [auth A]
UE [auth G]
VE [auth G]
XD [auth B]
FF [auth J],
TB [auth A],
UE [auth G],
VE [auth G],
XD [auth B],
ZD [auth B]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN

Query on PQN


Download:Ideal Coordinates CCD File
JB [auth A],
MD [auth B]		PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4

Query on SF4


Download:Ideal Coordinates CCD File
BE [auth C],
CE [auth C],
KB [auth A]		IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES

Query on FES


Download:Ideal Coordinates CCD File
ZI [auth N]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
CA

Query on CA


Download:Ideal Coordinates CCD File
AE [auth B],
VB [auth A]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael569/17
German-Israeli Foundation for Research and DevelopmentIsrael1483

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2020-10-21
    Changes: Database references
  • Version 2.0: 2025-04-09
    Changes: Data collection, Database references, Non-polymer description, Refinement description, Structure summary
  • Version 2.1: 2025-10-01
    Changes: Advisory, Data collection, Derived calculations, Structure summary