8ZWB | pdb_00008zwb

1.8 A resolution structure of the Photosystem I assembly intermediate lacking stromal subunits.

  • Classification: PHOTOSYNTHESIS
  • Organism(s): Synechocystis
  • Mutation(s): No 

  • Deposited: 2024-06-12 Released: 2025-06-18 
  • Deposition Author(s): Naschberger, A., Komenda, J.
  • Funding Organization(s): Grant Agency of the Czech Republic, European Research Council (ERC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

1.8 A resolution structure of the Photosystem I assembly intermediate lacking stromal subunits

Charras, Q.Gupta, S.Tichy, M.Al-Amoudi, A.Lukes, M.Konik, P.Sobotka, R.Novak, P.Komenda, J.Naschberger, A.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1751SynechocystisMutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for P29254 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2731SynechocystisMutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for P29255 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIC [auth F]165SynechocystisMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIID [auth I]40SynechocystisMutation(s): 0 
UniProt
Find proteins for Q55330 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXE [auth J]40SynechocystisMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaK 1F [auth K]86SynechocystisMutation(s): 0 
UniProt
Find proteins for P72712 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIG [auth M]31SynechocystisMutation(s): 0 
UniProt
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Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA (Subject of Investigation/LOI)
Query on CLA

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AA [auth A]
AB [auth A]
AC [auth B]
AD [auth B]
BA [auth A]
AA [auth A],
AB [auth A],
AC [auth B],
AD [auth B],
BA [auth A],
BC [auth B],
BD [auth B],
CA [auth A],
CC [auth B],
CD [auth B],
DA [auth A],
DC [auth B],
DD [auth B],
EA [auth A],
EC [auth B],
ED [auth B],
FA [auth A],
FC [auth B],
FD [auth B],
GA [auth A],
GC [auth B],
GD [auth B],
GE [auth F],
HA [auth A],
HC [auth B],
HD [auth B],
HE [auth F],
IA [auth A],
IC [auth B],
ID [auth B],
JA [auth A],
JC [auth B],
JD [auth B],
K [auth A],
KA [auth A],
KC [auth B],
KD [auth B],
L [auth A],
LA [auth A],
LC [auth B],
LD [auth B],
MA [auth A],
MC [auth B],
N [auth A],
NA [auth A],
NC [auth B],
O [auth A],
OA [auth A],
OC [auth B],
OE [auth J],
P [auth A],
PA [auth A],
PB [auth A],
PC [auth B],
PE [auth J],
Q [auth A],
QA [auth A],
QC [auth B],
R [auth A],
RA [auth A],
RB [auth A],
RC [auth B],
S [auth A],
SA [auth A],
SC [auth B],
T [auth A],
TA [auth A],
TC [auth B],
TE [auth K],
U [auth A],
UA [auth A],
UC [auth B],
UE [auth K],
V [auth A],
VA [auth A],
VB [auth B],
VC [auth B],
VE [auth K],
W [auth A],
WA [auth A],
WB [auth B],
WC [auth B],
X [auth A],
XA [auth A],
XB [auth B],
XC [auth B],
Y [auth A],
YA [auth A],
YC [auth B],
Z [auth A],
ZA [auth A],
ZC [auth B]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0 (Subject of Investigation/LOI)
Query on CL0

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J [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
LMG (Subject of Investigation/LOI)
Query on LMG

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GB [auth A],
SD [auth B]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG (Subject of Investigation/LOI)
Query on LHG

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H [auth A],
I [auth A],
TD [auth B]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
5X6
Query on 5X6

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UD [auth B]Zeaxanthin
C40 H56 O2
JKQXZKUSFCKOGQ-AYORJBSZSA-N
ECH
Query on ECH

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FB [auth A],
IE [auth F],
OD [auth B],
TB [auth A],
XE [auth M]
beta,beta-caroten-4-one
C40 H54 O
QXNWZXMBUKUYMD-QQGJMDNJSA-N
BCR
Query on BCR

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BB [auth A]
CB [auth A]
DB [auth A]
EB [auth A]
FE [auth F]
BB [auth A],
CB [auth A],
DB [auth A],
EB [auth A],
FE [auth F],
LE [auth I],
MD [auth B],
ND [auth B],
PD [auth B],
QD [auth B],
QE [auth J],
RD [auth B],
UB [auth A],
WE [auth K]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT (Subject of Investigation/LOI)
Query on LMT

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AE [auth B]
BE [auth B]
CE [auth B]
DE [auth B]
EE [auth F]
AE [auth B],
BE [auth B],
CE [auth B],
DE [auth B],
EE [auth F],
HB [auth A],
IB [auth A],
JB [auth A],
JE [auth F],
KB [auth A],
KE [auth F],
LB [auth A],
MB [auth A],
ME [auth I],
NB [auth A],
NE [auth I],
OB [auth A],
RE [auth J],
SB [auth A],
SE [auth J],
VD [auth B],
WD [auth B],
XD [auth B],
YD [auth B],
YE [auth M],
ZD [auth B]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN
Query on PQN

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M [auth A],
YB [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

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ZB [auth B]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
CL
Query on CL

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QB [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Grant Agency of the Czech RepublicCzech Republic24-10227S
European Research Council (ERC)European Union854126

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-18
    Type: Initial release