6YAC

Plant PSI-ferredoxin supercomplex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 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 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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)
Explore A0A0F6NFW5 
Go to UniProtKB:  A0A0F6NFW5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0F6NFW5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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)
Explore A0A0F6NGI2 
Go to UniProtKB:  A0A0F6NGI2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0F6NGI2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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)
Explore P10793 
Go to UniProtKB:  P10793
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10793
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
PsaD143Pisum sativumMutation(s): 0 
UniProt
Find proteins for E1C9K8 (Pisum sativum)
Explore E1C9K8 
Go to UniProtKB:  E1C9K8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE1C9K8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
PsaE66Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for E1C9K6 (Pisum sativum)
Explore E1C9K6 
Go to UniProtKB:  E1C9K6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE1C9K6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
PsaF154Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A0M3KL12 (Pisum sativum)
Explore A0A0M3KL12 
Go to UniProtKB:  A0A0M3KL12
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M3KL12
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
PsaG97Pisum sativumMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
PsaH88Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A0M3KL10 (Pisum sativum)
Explore A0A0M3KL10 
Go to UniProtKB:  A0A0M3KL10
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M3KL10
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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)
Explore P17227 
Go to UniProtKB:  P17227
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17227
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IX42Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D5MAL3 (Pisum sativum)
Explore D5MAL3 
Go to UniProtKB:  D5MAL3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD5MAL3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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)
Explore E1C9L3 
Go to UniProtKB:  E1C9L3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE1C9L3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
PsaL157Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for E1C9L1 (Pisum sativum)
Explore E1C9L1 
Go to UniProtKB:  E1C9L1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE1C9L1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Lhca1M [auth 1]193Pisum sativumMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticN [auth 2]208Pisum sativumMutation(s): 0 
UniProt
Find proteins for Q41038 (Pisum sativum)
Explore Q41038 
Go to UniProtKB:  Q41038
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ41038
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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)
Explore Q32904 
Go to UniProtKB:  Q32904
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ32904
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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)
Explore Q9SQL2 
Go to UniProtKB:  Q9SQL2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SQL2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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)
Explore P09911 
Go to UniProtKB:  P09911
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09911
Sequence Annotations
Expand
  • 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
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
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
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

View Full Validation Report



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