8VU3

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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Literature

The cryo-EM structure of a biohybrid photosystem I photocatalyst reveals the locations of bound platinum nanoparticles

Gisriel, C.J.Malavath, T.Brudvig, G.W.Utschig, L.M.

To be published.

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
UniProt
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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
UniProt
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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
UniProt
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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
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVCA [auth e],
E,
P
75Parathermosynechococcus lividusMutation(s): 0 
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 
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 
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 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaKGA [auth k],
K,
T
83Parathermosynechococcus lividusMutation(s): 0 
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 
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 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
PhosphorylaseJA [auth x],
W,
X
36Parathermosynechococcus lividusMutation(s): 0 
UniProt
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Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
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
CL0
Query on CL0

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EK [auth a],
KA [auth A],
QE [auth G]
CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-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

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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

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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

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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