6ZOO | pdb_00006zoo

Photosystem I reduced Plastocyanin Complex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.74 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

Structure of plant photosystem I-plastocyanin complex reveals strong hydrophobic interactions.

Caspy, I., Fadeeva, M., Kuhlgert, S., Borovikova-Sheinker, A., Klaiman, D., Masrati, G., Drepper, F., Ben-Tal, N., Hippler, M., Nelson, N.

(2021) Biochem J 478: 2371-2384

  • DOI: https://doi.org/10.1042/BCJ20210267
  • Primary Citation of Related Structures:  
    6ZOO

  • PubMed Abstract: 

    Photosystem I is defined as plastocyanin-ferredoxin oxidoreductase. Taking advantage of genetic engineering, kinetic analyses and cryo-EM, our data provide novel mechanistic insights into binding and electron transfer between PSI and Pc. Structural data at 2.74 Å resolution reveals strong hydrophobic interactions in the plant PSI-Pc ternary complex, leading to exclusion of water molecules from PsaA-PsaB/Pc interface once the PSI-Pc complex forms. Upon oxidation of Pc, a slight tilt of bound oxidized Pc allows water molecules to accommodate the space between Pc and PSI to drive Pc dissociation. Such a scenario is consistent with the six times larger dissociation constant of oxidized as compared with reduced Pc and mechanistically explains how this molecular machine optimized electron transfer for fast turnover.

    • Organizational Affiliation: 
    • Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1743Lathyrus oleraceusMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
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UniProt GroupA0A0F6NFW5
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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
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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
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
PsaD143Lathyrus oleraceusMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Putative uncharacterized protein66Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III154Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
photosystem I reaction center97Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupA0A0M3KL13
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VI,Photosystem I reaction center subunit VI93Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIII31Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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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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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit X psaK81Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
PsaL domain-containing protein159Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 6, chloroplasticM [auth 1]193Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
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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 
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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
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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 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Plastocyanin, chloroplasticQ [auth P]99Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Small Molecules
Ligands 15 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD
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EF [auth J]
EI [auth 3]
ME [auth F]
QF [auth 1]
TD [auth B]
EF [auth J],
EI [auth 3],
ME [auth F],
QF [auth 1],
TD [auth B],
WE [auth G],
YI [auth 4]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL
Query on CHL
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CG [auth 1]
DG [auth 1]
FG [auth 1]
IH [auth 2]
RH [auth 3]
CG [auth 1],
DG [auth 1],
FG [auth 1],
IH [auth 2],
RH [auth 3],
RI [auth 4],
SI [auth 4],
UI [auth 4],
VG [auth 2],
VI [auth 4],
WG [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
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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],
BF [auth J],
BG [auth 1],
BI [auth 3],
CA [auth A],
CB [auth A],
CC [auth B],
CD [auth B],
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],
EG [auth 1],
FA [auth A],
FB [auth A],
FC [auth B],
FD [auth B],
GA [auth A],
GC [auth B],
GD [auth B],
GF [auth K],
GG [auth 1],
GI [auth 4],
HA [auth A],
HC [auth B],
HD [auth B],
HF [auth K],
HG [auth 1],
HH [auth 2],
HI [auth 4],
IA [auth A],
IC [auth B],
ID [auth B],
IF [auth K],
JA [auth A],
JC [auth B],
JF [auth K],
KA [auth A],
KC [auth B],
KI [auth 4],
LA [auth A],
LC [auth B],
LF [auth L],
LI [auth 4],
MA [auth A],
MC [auth B],
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],
OG [auth 2],
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],
RB [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],
TB [auth A],
TC [auth B],
TG [auth 2],
TH [auth 3],
TI [auth 4],
U [auth A],
UA [auth A],
UB [auth A],
UC [auth B],
UF [auth 1],
UG [auth 2],
UH [auth 3],
V [auth A],
VA [auth A],
VC [auth B],
VF [auth 1],
VH [auth 3],
W [auth A],
WA [auth A],
WB [auth B],
WC [auth B],
WF [auth 1],
WH [auth 3],
WI [auth 4],
X [auth A],
XA [auth A],
XB [auth B],
XC [auth B],
XD [auth B],
XE [auth H],
XF [auth 1],
XG [auth 2],
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],
ZD [auth B],
ZF [auth 1],
ZH [auth 3]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0
Query on CL0
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R [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
LMG
Query on LMG
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BH [auth 2]
CH [auth 2]
DH [auth 2]
DI [auth 3]
EH [auth 2]
BH [auth 2],
CH [auth 2],
DH [auth 2],
DI [auth 3],
EH [auth 2],
FH [auth 2],
HE [auth F],
IE [auth F],
JE [auth F],
JG [auth 1],
KE [auth F],
LE [auth F],
RD [auth B],
SB [auth A],
SD [auth B],
TE [auth G],
UD [auth B],
UE [auth G],
VE [auth G]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG
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AH [auth 2]
CI [auth 3]
IG [auth 1]
OB [auth A]
PB [auth A]
AH [auth 2],
CI [auth 3],
IG [auth 1],
OB [auth A],
PB [auth A],
PD [auth B],
QD [auth B],
XI [auth 4]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
3PH
Query on 3PH
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GH [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],
MG [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
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DF [auth J]
FI [auth 4]
II [auth 4]
KH [auth 3]
LG [auth 2]
DF [auth J],
FI [auth 4],
II [auth 4],
KH [auth 3],
LG [auth 2],
LH [auth 3],
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
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AF [auth I]
CF [auth J]
FE [auth F]
FF [auth K]
GE [auth F]
AF [auth I],
CF [auth J],
FE [auth F],
FF [auth K],
GE [auth F],
IB [auth A],
JB [auth A],
KB [auth A],
KD [auth B],
KF [auth K],
KG [auth 1],
LB [auth A],
LD [auth B],
MB [auth A],
MD [auth B],
MF [auth L],
MH [auth 3],
NB [auth A],
ND [auth B],
NG [auth 2],
NH [auth 3],
OD [auth B],
PF [auth L],
QE [auth G],
TF [auth 1],
YE [auth H],
ZE [auth I]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT
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JH [auth 2]
QB [auth A]
RE [auth G]
SE [auth G]
VD [auth B]
JH [auth 2],
QB [auth A],
RE [auth G],
SE [auth G],
VD [auth B],
YD [auth B]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN
Query on PQN
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GB [auth A],
JD [auth B]		PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4
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BE [auth C],
CE [auth C],
HB [auth A]		IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
CU
Query on CU
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ZI [auth P]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
CA
Query on CA
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VB [auth A],
WD [auth B]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SNK
Query on SNK
A
L-PEPTIDE LINKINGC8 H11 N3 O3 SHIS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.74 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0.7
MODEL REFINEMENTPHENIX1.18.2

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael569/17
Israel Science FoundationIsrael2716/17
German-Israeli Foundation for Research and DevelopmentIsraelG-1483-207/2018
European Research Council (ERC)Belgium723991

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-16
    Type: Initial release
  • 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: 2025-04-09
    Changes: Data collection, Database references, Refinement description, Structure summary