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

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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 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.

Macromolecule Content 

  • Total Structure Weight: 1,079.91 kDa 
  • Atom Count: 71,694 
  • Modeled Residue Count: 6,786 
  • Deposited Residue Count: 7,029 
  • Unique protein chains: 12

Macromolecules

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|  3D Structure
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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Reference Sequence
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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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Reference Sequence
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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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Reference Sequence
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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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Reference Sequence
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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
Find proteins for A0A2D2Q1I4 (Parathermosynechococcus lividus PCC 6715)
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Reference Sequence
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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
Find proteins for A0A2D2PYV7 (Parathermosynechococcus lividus PCC 6715)
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Reference Sequence
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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
Find proteins for A0A2D2Q0W5 (Parathermosynechococcus lividus PCC 6715)
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Reference Sequence
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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 
UniProt
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Reference Sequence
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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
Find proteins for A0A2D2Q0K8 (Parathermosynechococcus lividus PCC 6715)
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Reference Sequence
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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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Reference Sequence
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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
Find proteins for A0A3B7MIX8 (Thermosynechococcus sichuanensis E542)
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
PhosphorylaseJA [auth x],
W,
X		36Parathermosynechococcus lividusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2D2Q2C6 (Parathermosynechococcus lividus PCC 6715)
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Reference Sequence

Small Molecules

Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA

Query on CLA


Download:Ideal Coordinates CCD File
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
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
LMG

Query on LMG


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
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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View more in-depth experimental data

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