8VU3 | pdb_00008vu3

Cryo-EM structure of cyanobacterial PSI with bound platinum nanoparticles

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structure of a biohybrid photosystem I-platinum nanoparticle solar fuel catalyst.

Gisriel, C.J., Malavath, T., Qiu, T., Menzel, J.P., Batista, V.S., Brudvig, G.W., Utschig, L.M.

(2024) Nat Commun 15: 9519-9519

  • DOI: https://doi.org/10.1038/s41467-024-53476-y
  • Primary Citation of Related Structures:  
    8VU3

  • PubMed Abstract: 

    Biohybrid solar fuel catalysts leverage natural light-driven enzymes to produce valuable fuel products. One useful biological platform for such a system is photosystem I, a pigment-protein complex that captures sunlight and converts it into chemical energy with near unity quantum efficiency, which generates low potential reducing equivalents for metabolism. Realizing and understanding the molecular basis for an approach that utilizes those electrons and stores solar energy as a fuel is therefore appealing. Here, we report the 2.27-Å global resolution cryo-EM structure of a photosystem I complex with bound platinum nanoparticles that catalyzes light-driven H 2 production. The platinum nanoparticle binding sites and possible stabilizing interactions are described. Overall, the investigation reveals a direct structural look at a photon-to-fuels photosynthetic biohybrid system.

    • Organizational Affiliation: 
    • Department of Chemistry, Yale University, New Haven, CT, 06520, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1A,
G,
Y [auth a]		755Parathermosynechococcus lividusMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A2D2Q201 (Parathermosynechococcus lividus PCC 6715)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2B,
H,
Z [auth b]		741Parathermosynechococcus lividusMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A2D2Q1Z9 (Parathermosynechococcus lividus PCC 6715)
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UniProt GroupA0A2D2Q1Z9
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerAA [auth c],
C,
N		81Parathermosynechococcus lividusMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A2D2Q1F9 (Parathermosynechococcus lividus PCC 6715)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIBA [auth d],
D,
O		139Parathermosynechococcus lividusMutation(s): 0 
UniProt
Find proteins for A0A2D2Q2Y6 (Parathermosynechococcus lividus PCC 6715)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVCA [auth e],
E,
P		75Parathermosynechococcus lividusMutation(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,
Q		164Parathermosynechococcus lividusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIEA [auth i],
I,
R		40Parathermosynechococcus lividusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXFA [auth j],
J,
S		43Parathermosynechococcus lividusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaKGA [auth k],
K,
T		83Parathermosynechococcus lividusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIHA [auth l],
L,
U		155Parathermosynechococcus lividusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIIA [auth m],
M,
V		31Parathermosynechococcus lividusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
PhosphorylaseJA [auth x],
W,
X		36Parathermosynechococcus lividusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL0
Query on CL0
Download Ideal Coordinates CCD File 
EK [auth a],
KA [auth A],
QE [auth G]		CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
CLA
Query on CLA
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AB [auth A]
AC [auth A]
AD [auth B]
AE [auth B]
AF [auth G]
AB [auth A],
AC [auth A],
AD [auth B],
AE [auth B],
AF [auth G],
AG [auth G],
AH [auth H],
AI [auth H],
AJ [auth L],
AK [auth V],
AL [auth a],
AN [auth b],
AP [auth x],
BB [auth A],
BC [auth A],
BD [auth B],
BF [auth G],
BG [auth G],
BH [auth H],
BI [auth H],
BJ [auth L],
BL [auth a],
BN [auth b],
CB [auth A],
CC [auth A],
CD [auth B],
CF [auth G],
CG [auth G],
CH [auth H],
CI [auth H],
CJ [auth L],
CK [auth W],
CL [auth a],
CN [auth b],
DB [auth A],
DD [auth B],
DF [auth G],
DG [auth G],
DH [auth H],
DI [auth H],
DK [auth X],
DL [auth a],
DN [auth b],
EB [auth A],
ED [auth B],
EF [auth G],
EG [auth G],
EH [auth H],
EI [auth H],
EJ [auth M],
EL [auth a],
EN [auth b],
FB [auth A],
FD [auth B],
FF [auth G],
FG [auth G],
FH [auth H],
FI [auth H],
FK [auth a],
FL [auth a],
FN [auth b],
GB [auth A],
GD [auth B],
GF [auth G],
GG [auth G],
GH [auth H],
GI [auth H],
GK [auth a],
GL [auth a],
GM [auth a],
GN [auth b],
HB [auth A],
HD [auth B],
HF [auth G],
HG [auth G],
HH [auth H],
HK [auth a],
HL [auth a],
HM [auth b],
HN [auth b],
HO [auth f],
IB [auth A],
ID [auth B],
IF [auth G],
IG [auth G],
IH [auth H],
IJ [auth Q],
IK [auth a],
IL [auth a],
IM [auth b],
IN [auth b],
JB [auth A],
JD [auth B],
JF [auth G],
JH [auth H],
JK [auth a],
JL [auth a],
JM [auth b],
JN [auth b],
JO [auth i],
KB [auth A],
KD [auth B],
KF [auth G],
KH [auth H],
KJ [auth Q],
KK [auth a],
KL [auth a],
KM [auth b],
KN [auth b],
LA [auth A],
LB [auth A],
LD [auth B],
LF [auth G],
LH [auth H],
LK [auth a],
LL [auth a],
LM [auth b],
LN [auth b],
LO [auth j],
MA [auth A],
MB [auth A],
MD [auth B],
MF [auth G],
MH [auth H],
MK [auth a],
ML [auth a],
MM [auth b],
MN [auth b],
MO [auth j],
NA [auth A],
NB [auth A],
NC [auth B],
ND [auth B],
NE [auth F],
NF [auth G],
NH [auth H],
NK [auth a],
NL [auth a],
NM [auth b],
NN [auth b],
OA [auth A],
OB [auth A],
OC [auth B],
OD [auth B],
OF [auth G],
OH [auth H],
OK [auth a],
OL [auth a],
OM [auth b],
ON [auth b],
PA [auth A],
PB [auth A],
PC [auth B],
PD [auth B],
PE [auth F],
PF [auth G],
PH [auth H],
PJ [auth S],
PK [auth a],
PL [auth a],
PM [auth b],
PN [auth b],
PO [auth k],
QA [auth A],
QB [auth A],
QC [auth B],
QD [auth B],
QF [auth G],
QH [auth H],
QJ [auth S],
QK [auth a],
QL [auth a],
QM [auth b],
QN [auth b],
RA [auth A],
RB [auth A],
RC [auth B],
RD [auth B],
RE [auth G],
RF [auth G],
RH [auth H],
RK [auth a],
RL [auth a],
RM [auth b],
RN [auth b],
RO [auth l],
SA [auth A],
SB [auth A],
SC [auth B],
SD [auth B],
SE [auth G],
SF [auth G],
SH [auth H],
SI [auth J],
SK [auth a],
SL [auth a],
SM [auth b],
SN [auth b],
TA [auth A],
TB [auth A],
TC [auth B],
TD [auth B],
TE [auth G],
TF [auth G],
TG [auth H],
TH [auth H],
TJ [auth T],
TK [auth a],
TL [auth a],
TM [auth b],
TN [auth b],
UA [auth A],
UB [auth A],
UC [auth B],
UD [auth B],
UE [auth G],
UF [auth G],
UG [auth H],
UH [auth H],
UJ [auth U],
UK [auth a],
UL [auth a],
UM [auth b],
UN [auth b],
UO [auth l],
VA [auth A],
VB [auth A],
VC [auth B],
VD [auth B],
VE [auth G],
VF [auth G],
VG [auth H],
VH [auth H],
VI [auth K],
VK [auth a],
VL [auth a],
VM [auth b],
VO [auth l],
WA [auth A],
WB [auth A],
WC [auth B],
WD [auth B],
WE [auth G],
WF [auth G],
WG [auth H],
WH [auth H],
WI [auth K],
WK [auth a],
WM [auth b],
WO [auth l],
XA [auth A],
XB [auth A],
XC [auth B],
XD [auth B],
XE [auth G],
XF [auth G],
XG [auth H],
XH [auth H],
XI [auth L],
XJ [auth U],
XK [auth a],
XM [auth b],
YA [auth A],
YB [auth A],
YC [auth B],
YD [auth B],
YE [auth G],
YF [auth G],
YG [auth H],
YH [auth H],
YJ [auth U],
YK [auth a],
YM [auth b],
YO [auth m],
ZA [auth A],
ZB [auth A],
ZC [auth B],
ZD [auth B],
ZE [auth G],
ZF [auth G],
ZG [auth H],
ZH [auth H],
ZJ [auth U],
ZK [auth a],
ZM [auth b]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG
Query on LMG
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CO [auth b],
JE [auth B],
OI [auth H]		1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG
Download Ideal Coordinates CCD File 
EM [auth a]
FM [auth a]
LC [auth A]
MC [auth A]
RG [auth G]
EM [auth a],
FM [auth a],
LC [auth A],
MC [auth A],
RG [auth G],
SG [auth G]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR
Query on BCR
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AM [auth a]
AO [auth b]
BK [auth V]
BM [auth a]
BO [auth b]
AM [auth a],
AO [auth b],
BK [auth V],
BM [auth a],
BO [auth b],
CE [auth B],
CM [auth a],
DE [auth B],
DJ [auth L],
DM [auth a],
DO [auth b],
EE [auth B],
FC [auth A],
FE [auth B],
FJ [auth M],
GC [auth A],
GE [auth B],
GO [auth f],
HC [auth A],
HE [auth B],
IC [auth A],
IE [auth B],
II [auth H],
IO [auth f],
JC [auth A],
JI [auth H],
JJ [auth Q],
KC [auth A],
KE [auth B],
KI [auth H],
KO [auth i],
LG [auth G],
LI [auth H],
LJ [auth Q],
MG [auth G],
MI [auth H],
MJ [auth R],
NG [auth G],
NI [auth H],
NJ [auth R],
NO [auth j],
OE [auth F],
OG [auth G],
OJ [auth R],
OO [auth j],
PG [auth G],
PI [auth H],
QG [auth G],
QI [auth I],
QO [auth l],
RI [auth I],
RJ [auth S],
SJ [auth S],
SO [auth l],
TI [auth J],
UI [auth J],
VJ [auth U],
WN [auth b],
XN [auth b],
XO [auth l],
YI [auth L],
YL [auth a],
YN [auth b],
ZL [auth a],
ZN [auth b],
ZO [auth m]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN
Query on PQN
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BE [auth B]
DC [auth A]
HI [auth H]
JG [auth G]
VN [auth b]
BE [auth B],
DC [auth A],
HI [auth H],
JG [auth G],
VN [auth b],
WL [auth a]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4 (Subject of Investigation/LOI)
Query on SF4
Download Ideal Coordinates CCD File 
EC [auth A]
EO [auth c]
FO [auth c]
GJ [auth N]
HJ [auth N]
EC [auth A],
EO [auth c],
FO [auth c],
GJ [auth N],
HJ [auth N],
KG [auth G],
LE [auth C],
ME [auth C],
XL [auth a]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
TO [auth l],
WJ [auth U],
ZI [auth L]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE- AC02-06CH11357
Department of Energy (DOE, United States)United StatesDE-FG02-05ER15646
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM140174

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-30
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection
  • Version 1.2: 2025-05-14
    Changes: Data collection, Database references