6YEZ

Plant PSI-ferredoxin-plastocyanin supercomplex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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 of 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1743Pisum sativumMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A0F6NFW5 (Pisum sativum)
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UniProt GroupA0A0F6NFW5
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2733Pisum sativumMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A0F6NGI2 (Pisum sativum)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center80Pisum sativumMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P10793 (Pisum sativum)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
PsaD143Pisum sativumMutation(s): 0 
UniProt
Find proteins for E1C9K8 (Pisum sativum)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
PsaE66Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for E1C9K6 (Pisum sativum)
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UniProt GroupE1C9K6
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
PsaF154Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A0M3KL12 (Pisum sativum)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
PsaG97Pisum sativumMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
PsaH93Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A0M3KL10 (Pisum sativum)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIII31Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P17227 (Pisum sativum)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
PsaJ42Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D5MAL3 (Pisum sativum)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit X psaK81Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for E1C9L3 (Pisum sativum)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
PsaL159Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for E1C9L1 (Pisum sativum)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Lhca1M [auth 1]193Pisum sativumMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticN [auth 2]208Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q41038 (Pisum sativum)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 3, chloroplasticO [auth 3]221Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q32904 (Pisum sativum)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein P4, chloroplasticP [auth 4]198Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9SQL2 (Pisum sativum)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Ferredoxin-1, chloroplasticQ [auth N]97Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P09911 (Pisum sativum)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Plastocyanin, chloroplasticR [auth P]99Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P16002 (Pisum sativum)
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Small Molecules
Ligands 17 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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FF [auth J]
FI [auth 3]
KE [auth F]
RF [auth 1]
TD [auth B]
FF [auth J],
FI [auth 3],
KE [auth F],
RF [auth 1],
TD [auth B],
XE [auth G],
ZI [auth 4]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL
Query on CHL

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AH [auth 2]
BH [auth 2]
DG [auth 1]
FG [auth 1]
HH [auth 2]
AH [auth 2],
BH [auth 2],
DG [auth 1],
FG [auth 1],
HH [auth 2],
KG [auth 1],
SH [auth 3],
SI [auth 4],
TI [auth 4],
VH [auth 3],
VI [auth 4],
WI [auth 4],
XG [auth 2],
YG [auth 2],
YH [auth 3]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA
Query on CLA

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AA [auth A]
AB [auth A]
AC [auth B]
AD [auth B]
AE [auth B]
AA [auth A],
AB [auth A],
AC [auth B],
AD [auth B],
AE [auth B],
AG [auth 1],
AI [auth 3],
BA [auth A],
BB [auth A],
BC [auth B],
BD [auth B],
BE [auth B],
BG [auth 1],
BI [auth 3],
CA [auth A],
CB [auth A],
CC [auth B],
CD [auth B],
CG [auth 1],
CI [auth 3],
DA [auth A],
DB [auth A],
DC [auth B],
DD [auth B],
DF [auth J],
EA [auth A],
EB [auth A],
EC [auth B],
ED [auth B],
EE [auth F],
EG [auth 1],
FA [auth A],
FB [auth A],
FC [auth B],
FD [auth B],
GA [auth A],
GC [auth B],
GD [auth B],
GG [auth 1],
HA [auth A],
HC [auth B],
HD [auth B],
HF [auth K],
HG [auth 1],
HI [auth 4],
IA [auth A],
IC [auth B],
ID [auth B],
IF [auth K],
JA [auth A],
JC [auth B],
JD [auth B],
JF [auth K],
KA [auth A],
KC [auth B],
KF [auth K],
KI [auth 4],
LA [auth A],
LC [auth B],
LI [auth 4],
MA [auth A],
MC [auth B],
ME [auth F],
MI [auth 4],
NA [auth A],
NC [auth B],
NF [auth L],
NI [auth 4],
OA [auth A],
OC [auth B],
OF [auth L],
OI [auth 4],
PA [auth A],
PB [auth A],
PC [auth B],
PE [auth G],
PF [auth L],
PG [auth 2],
PH [auth 3],
PI [auth 4],
QA [auth A],
QB [auth A],
QC [auth B],
QE [auth G],
QG [auth 2],
QH [auth 3],
QI [auth 4],
RA [auth A],
RB [auth A],
RC [auth B],
RE [auth G],
RG [auth 2],
RH [auth 3],
RI [auth 4],
SA [auth A],
SC [auth B],
SG [auth 2],
T [auth A],
TA [auth A],
TC [auth B],
TG [auth 2],
TH [auth 3],
U [auth A],
UA [auth A],
UB [auth A],
UC [auth B],
UG [auth 2],
UH [auth 3],
UI [auth 4],
V [auth A],
VA [auth A],
VC [auth B],
VF [auth 1],
VG [auth 2],
W [auth A],
WA [auth A],
WC [auth B],
WF [auth 1],
WG [auth 2],
WH [auth 3],
X [auth A],
XA [auth A],
XB [auth B],
XC [auth B],
XF [auth 1],
XH [auth 3],
XI [auth 4],
Y [auth A],
YA [auth A],
YB [auth B],
YC [auth B],
YE [auth H],
YF [auth 1],
Z [auth A],
ZA [auth A],
ZB [auth B],
ZC [auth B],
ZD [auth B],
ZF [auth 1],
ZG [auth 2],
ZH [auth 3]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0
Query on CL0

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S [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
LMG
Query on LMG

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DH [auth 2]
EH [auth 2]
EI [auth 3]
FH [auth 2]
GH [auth 2]
DH [auth 2],
EH [auth 2],
EI [auth 3],
FH [auth 2],
GH [auth 2],
HE [auth F],
IE [auth F],
IG [auth 1],
JE [auth F],
JH [auth 2],
LE [auth F],
NE [auth F],
RD [auth B],
SD [auth B],
UE [auth G],
VB [auth A],
VD [auth B],
VE [auth G],
WE [auth G]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

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CH [auth 2]
DI [auth 3]
LG [auth 1]
MB [auth A]
NB [auth A]
CH [auth 2],
DI [auth 3],
LG [auth 1],
MB [auth A],
NB [auth A],
PD [auth B],
QD [auth B],
YI [auth 4]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
3PH
Query on 3PH

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KH [auth 2]1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
XAT
Query on XAT

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JI [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
C7Z
Query on C7Z

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GI [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
LUT
Query on LUT

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CF [auth J]
II [auth 4]
LH [auth 3]
MG [auth 2]
MH [auth 3]
CF [auth J],
II [auth 4],
LH [auth 3],
MG [auth 2],
MH [auth 3],
SF [auth 1],
TF [auth 1]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
BCR
Query on BCR

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AF [auth I]
BF [auth I]
EF [auth J]
FE [auth F]
GE [auth F]
AF [auth I],
BF [auth I],
EF [auth J],
FE [auth F],
GE [auth F],
GF [auth K],
HB [auth A],
IB [auth A],
JB [auth A],
JG [auth 1],
KB [auth A],
LB [auth A],
LD [auth B],
LF [auth K],
MD [auth B],
MF [auth L],
ND [auth B],
NH [auth 3],
OD [auth B],
OG [auth 2],
OH [auth 3],
QF [auth L],
SE [auth G],
TB [auth A],
UF [auth 1],
YD [auth B],
ZE [auth H]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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IH [auth 2]
OB [auth A]
OE [auth G]
TE [auth G]
UD [auth B]
IH [auth 2],
OB [auth A],
OE [auth G],
TE [auth G],
UD [auth B],
WD [auth B]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN
Query on PQN

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GB [auth A],
KD [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4

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CE [auth C],
DE [auth C],
SB [auth A]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES

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AJ [auth N]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
CU
Query on CU

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BJ [auth P]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
CA
Query on CA

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WB [auth A],
XD [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0.7
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: 2021-07-07
    Type: Coordinate replacement
    Reason: Sequence discrepancy
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2024-10-09
    Changes: Data collection, Database references, Refinement description, Structure summary