10KF | pdb_000010kf

Cryo-EM structure of a chemically treated Cyanobacterial Photosystem I core with bound platinum nanoparticles


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Molecular Design Principles for Photosystem I-Based Biohybrid Solar Fuel Catalysts.

Emerson, M.D.Damaraju, S.N.S.Short, A.H.Alvord, Z.B.Palmer, Z.A.Mehra, H.S.Brininger, C.M.Vermaas, J.V.Utschig, L.M.Gisriel, C.J.

(2026) ACS Nano 20: 23893-23906

  • DOI: https://doi.org/10.1021/acsnano.6c07948
  • Primary Citation Related Structures: 
    10KF

  • PubMed Abstract: 

    Direct solar-to-chemical conversion offers a compelling route to clean, dispatchable energy. Photosystem I (PSI), an evolutionarily optimized light-driven oxidoreductase, can be repurposed for solar-fuel production by coupling its photochemistry to catalytic interfaces. However, the molecular determinants that govern productive electron transfer to abiotic catalysts remain poorly understood. Here, we present molecular structures of active PSI-Pt nanoparticle (PtNP) biohybrids that reveal how protein architecture controls catalyst access, binding geometry, and photocatalytic efficiency. Removal of stromal subunits exposes the electron transfer chain and enables PtNP binding proximal to the FX cluster, demonstrating that steric occlusion limits access to native acceptor regions in PSI. In contrast, in trimeric PSI, PtNPs bind at multiple sites per monomer, but only a subset are positioned within electron transfer distance of terminal cofactors, resulting in a heterogeneous population of productive and nonproductive configurations. Structural analyses and molecular dynamics simulations define the interface topology, electrostatics, and cofactor-to-nanoparticle distances that govern catalyst binding and electron transfer. These results establish that catalytic inefficiency arises not only from intrinsic electron transfer constraints but also from the distribution of binding geometries imposed by the protein scaffold. Together, these findings provide a molecular framework linking protein structure to biohybrid function and define design principles for engineering PSI-based solar fuel systems and protein-nanomaterial interfaces for light-driven catalysis.


  • Organizational Affiliation
    • Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin53706, United States.

Macromolecule Content 

  • Total Structure Weight: 290.43 kDa 
  • Atom Count: 18,035 
  • Modeled Residue Count: 1,716 
  • Deposited Residue Count: 1,847 
  • Unique protein chains: 7

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1763Synechococcus elongatus PCC 6301Mutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for Q5N0D6 (Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1))
Explore Q5N0D6 
Go to UniProtKB:  Q5N0D6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5N0D6
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2734Synechococcus elongatus PCC 6301Mutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for Q5N0D5 (Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1))
Explore Q5N0D5 
Go to UniProtKB:  Q5N0D5
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UniProt GroupQ5N0D5
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIC [auth F]159Synechococcus elongatus PCC 6301Mutation(s): 0 
UniProt
Find proteins for P31083 (Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1))
Explore P31083 
Go to UniProtKB:  P31083
Entity Groups
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UniProt GroupP31083
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIID [auth I]38Synechococcus elongatus PCC 6301Mutation(s): 0 
UniProt
Find proteins for A0A0H3K775 (Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1))
Explore A0A0H3K775 
Go to UniProtKB:  A0A0H3K775
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UniProt GroupA0A0H3K775
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXE [auth J]44Synechococcus elongatus PCC 6301Mutation(s): 0 
UniProt
Find proteins for Q5N5C7 (Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1))
Explore Q5N5C7 
Go to UniProtKB:  Q5N5C7
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UniProt GroupQ5N5C7
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaKF [auth K]80Synechococcus elongatus PCC 6301Mutation(s): 0 
UniProt
Find proteins for A0A0H3K593 (Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1))
Explore A0A0H3K593 
Go to UniProtKB:  A0A0H3K593
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIG [auth M]29Synechococcus elongatus PCC 6301Mutation(s): 0 
UniProt
Find proteins for Q5MZZ8 (Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1))
Explore Q5MZZ8 
Go to UniProtKB:  Q5MZZ8
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UniProt GroupQ5MZZ8
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL0

Query on CL0



Download:Ideal Coordinates CCD File
H [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
CLA
(Subject of Investigation/LOI)

Query on CLA



Download:Ideal Coordinates CCD File
AA [auth A]
AC [auth B]
BA [auth A]
BC [auth B]
CA [auth A]
AA [auth A],
AC [auth B],
BA [auth A],
BC [auth B],
CA [auth A],
CC [auth B],
DA [auth A],
DC [auth B],
EA [auth A],
EC [auth B],
FA [auth A],
FC [auth B],
FD [auth I],
GA [auth A],
GC [auth B],
GD [auth K],
HA [auth A],
HC [auth B],
I [auth A],
IA [auth A],
IB [auth B],
IC [auth B],
J [auth A],
JA [auth A],
JB [auth B],
JC [auth B],
K [auth A],
KA [auth A],
KB [auth B],
KC [auth B],
L [auth A],
LA [auth A],
LB [auth B],
LC [auth B],
M [auth A],
MA [auth A],
MB [auth B],
MC [auth B],
N [auth A],
NA [auth A],
NB [auth B],
NC [auth B],
O [auth A],
OA [auth A],
OB [auth B],
OC [auth B],
P [auth A],
PA [auth A],
PB [auth B],
PC [auth B],
Q [auth A],
QA [auth A],
QB [auth B],
QC [auth B],
R [auth A],
RA [auth A],
RB [auth B],
RC [auth B],
S [auth A],
SA [auth A],
SB [auth B],
SC [auth B],
T [auth A],
TA [auth A],
TB [auth B],
TC [auth B],
U [auth A],
UA [auth A],
UB [auth B],
UC [auth B],
V [auth A],
VA [auth A],
VB [auth B],
VC [auth B],
W [auth A],
WA [auth A],
WB [auth B],
X [auth A],
XA [auth A],
XB [auth B],
Y [auth A],
YA [auth A],
YB [auth B],
Z [auth A],
ZB [auth B]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG

Query on LMG



Download:Ideal Coordinates CCD File
DD [auth B]1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG

Query on LHG



Download:Ideal Coordinates CCD File
GB [auth A],
HB [auth A]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR

Query on BCR



Download:Ideal Coordinates CCD File
AD [auth B]
BB [auth A]
BD [auth B]
CB [auth A]
CD [auth B]
AD [auth B],
BB [auth A],
BD [auth B],
CB [auth A],
CD [auth B],
DB [auth A],
EB [auth A],
ED [auth F],
FB [auth A],
HD [auth M],
XC [auth B],
YC [auth B],
ZC [auth B]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN

Query on PQN



Download:Ideal Coordinates CCD File
WC [auth B],
ZA [auth A]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4

Query on SF4



Download:Ideal Coordinates CCD File
AB [auth A]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2026-09-02
    Type: Initial release
  • Version 1.1: 2026-09-16
    Changes: Data collection, Database references, Structure summary