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- PDB-6nwa: The structure of the photosystem I IsiA super-complex -

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Entry
Database: PDB / ID: 6nwa
TitleThe structure of the photosystem I IsiA super-complex
Components
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 8
  • Iron stress-induced chlorophyll-binding protein
  • Photosystem I iron-sulfur center
KeywordsPHOTOSYNTHESIS / Photosystem / Antenna / Chlorophyll / Membrane
Function / homology
Function and homology information


plasma membrane-derived photosystem I / ec:1.97.1.12: / photosynthetic electron transport in photosystem I / photosystem I reaction center / thylakoid / photosystem I / chlorophyll binding / thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding ...plasma membrane-derived photosystem I / ec:1.97.1.12: / photosynthetic electron transport in photosystem I / photosystem I reaction center / thylakoid / photosystem I / chlorophyll binding / thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / protein-chromophore linkage / electron transfer activity / magnesium ion binding / integral component of membrane / metal ion binding
Photosystem II protein / Photosystem I reaction centre subunit VIII / Photosystem I PsaA/PsaB, conserved site / Photosystem I, reaction centre subunit XI / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaA/PsaB superfamily / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I PsaL, reaction centre subunit XI superfamily ...Photosystem II protein / Photosystem I reaction centre subunit VIII / Photosystem I PsaA/PsaB, conserved site / Photosystem I, reaction centre subunit XI / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaA/PsaB superfamily / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I psaA/psaB protein / Photosystem I psaG / psaK / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I reaction centre subunit IV / PsaE / Photosystem I reaction centre subunit III / PsaD / Photosystem I reaction centre subunit XI / Photosystem I protein M (PsaM) / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / Photosystem I psaA and psaB proteins signature. / Photosystem I psaG and psaK proteins signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I PsaK, reaction centre / Photosystem I PsaM, reaction centre / Electron transport accessory-like domain superfamily / Photosystem I PsaB / Photosystem I PsaA / Photosystem I protein PsaC / Photosystem I PsaL, reaction centre subunit XI / Photosystem I PsaD / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaE, reaction centre subunit IV / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit VIII / Photosystem I PsaA/PsaB / Photosystem I PsaG/PsaK protein
Photosystem I reaction center subunit II / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit III / Photosystem I iron-sulfur center / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit PsaK 1 / Photosystem I reaction center subunit XII / un:q55274: / Photosystem I reaction center subunit IX ...Photosystem I reaction center subunit II / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit III / Photosystem I iron-sulfur center / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit PsaK 1 / Photosystem I reaction center subunit XII / un:q55274: / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IV
Biological speciesSynechocystis sp. PCC 6803 (Cyanobacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.48 Å
AuthorsToporik, H. / Li, J. / Williams, D. / Chiu, P.L. / Mazor, Y.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2019
Title: The structure of the stress-induced photosystem I-IsiA antenna supercomplex.
Authors: Hila Toporik / Jin Li / Dewight Williams / Po-Lin Chiu / Yuval Mazor /
Abstract: Photochemical conversion in oxygenic photosynthesis takes place in two large protein-pigment complexes named photosystem II and photosystem I (PSII and PSI, respectively). Photosystems associate with ...Photochemical conversion in oxygenic photosynthesis takes place in two large protein-pigment complexes named photosystem II and photosystem I (PSII and PSI, respectively). Photosystems associate with antennae in vivo to increase the size of photosynthetic units to hundreds or thousands of pigments. Regulation of the interactions between antennae and photosystems allows photosynthetic organisms to adapt to their environment. In low-iron environments, cyanobacteria express IsiA, a PSI antenna, critical to their survival. Here we describe the structure of the PSI-IsiA complex isolated from the mesophilic cyanobacterium Synechocystis sp. PCC 6803. This 2-MDa photosystem-antenna supercomplex structure reveals more than 700 pigments coordinated by 51 subunits, as well as the mechanisms facilitating the self-assembly and association of IsiA with multiple PSI assemblies.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 6, 2019 / Release: May 29, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0May 29, 2019Structure modelrepositoryInitial release
1.1Jun 12, 2019Structure modelData collection / Database referencescitation / citation_author_citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
1.2Jun 19, 2019Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Assembly

Deposited unit
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: Photosystem I reaction center subunit II
E: Photosystem I reaction center subunit IV
F: Photosystem I reaction center subunit III
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
W: Iron stress-induced chlorophyll-binding protein
X: Iron stress-induced chlorophyll-binding protein
Y: Iron stress-induced chlorophyll-binding protein
Z: Iron stress-induced chlorophyll-binding protein
g: Iron stress-induced chlorophyll-binding protein
y: Iron stress-induced chlorophyll-binding protein
a: Photosystem I P700 chlorophyll a apoprotein A1
b: Photosystem I P700 chlorophyll a apoprotein A2
d: Photosystem I reaction center subunit II
i: Photosystem I reaction center subunit VIII
k: Photosystem I reaction center subunit PsaK 1
l: Photosystem I reaction center subunit XI
m: Photosystem I reaction center subunit XII
n: Iron stress-induced chlorophyll-binding protein
o: Iron stress-induced chlorophyll-binding protein
p: Iron stress-induced chlorophyll-binding protein
q: Iron stress-induced chlorophyll-binding protein
r: Iron stress-induced chlorophyll-binding protein
h: Iron stress-induced chlorophyll-binding protein
H: Photosystem I P700 chlorophyll a apoprotein A1
G: Photosystem I P700 chlorophyll a apoprotein A2
O: Photosystem I reaction center subunit II
R: Photosystem I reaction center subunit VIII
U: Photosystem I reaction center subunit XI
V: Photosystem I reaction center subunit XII
t: Iron stress-induced chlorophyll-binding protein
u: Iron stress-induced chlorophyll-binding protein
s: Iron stress-induced chlorophyll-binding protein
w: Iron stress-induced chlorophyll-binding protein
x: Iron stress-induced chlorophyll-binding protein
v: Iron stress-induced chlorophyll-binding protein
e: Photosystem I reaction center subunit IV
P: Photosystem I reaction center subunit IV
f: Photosystem I reaction center subunit III
Q: Photosystem I reaction center subunit III
j: Photosystem I reaction center subunit IX
S: Photosystem I reaction center subunit IX
c: Photosystem I iron-sulfur center
N: Photosystem I iron-sulfur center
K: Photosystem I reaction center subunit PsaK 1
T: Photosystem I reaction center subunit PsaK 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,055,659822
Polymers1,429,29451
Non-polymers626,365771
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 6 molecules AaHBbG

#1: Protein/peptide Photosystem I P700 chlorophyll a apoprotein A1 / / PsaA


Mass: 83022.375 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. PCC 6803 (Cyanobacteria)
References: UniProt: P29254, EC: 1.97.1.12
#2: Protein/peptide Photosystem I P700 chlorophyll a apoprotein A2 / / PsaB


Mass: 81369.531 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. PCC 6803 (Cyanobacteria)
References: UniProt: P29255, EC: 1.97.1.12

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Protein/peptide , 2 types, 21 molecules CcNWXYZgynopqrhtuswxv

#3: Protein/peptide Photosystem I iron-sulfur center / / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8837.261 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. PCC 6803 (Cyanobacteria)
References: UniProt: P32422, EC: 1.97.1.12
#11: Protein/peptide
Iron stress-induced chlorophyll-binding protein / CP43'


Mass: 37250.734 Da / Num. of mol.: 18 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. PCC 6803 (Cyanobacteria)
References: UniProt: Q55274

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Photosystem I reaction center subunit ... , 8 types, 24 molecules DdOEePFfQIiRJjSLlUMmVkKT

#4: Protein/peptide Photosystem I reaction center subunit II / / Photosystem I 16 kDa polypeptide / PSI-D


Mass: 15663.749 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. PCC 6803 (Cyanobacteria)
References: UniProt: P19569
#5: Protein/peptide Photosystem I reaction center subunit IV / / Photosystem I 8.1 kDa protein / p30 protein


Mass: 8154.086 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. PCC 6803 (Cyanobacteria)
References: UniProt: P12975
#6: Protein/peptide Photosystem I reaction center subunit III / / PSI-F


Mass: 18267.082 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. PCC 6803 (Cyanobacteria)
References: UniProt: P29256
#7: Protein/peptide Photosystem I reaction center subunit VIII /


Mass: 4414.148 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. PCC 6803 (Cyanobacteria)
References: UniProt: Q55330
#8: Protein/peptide Photosystem I reaction center subunit IX /


Mass: 4535.415 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. PCC 6803 (Cyanobacteria)
References: UniProt: Q55329
#9: Protein/peptide Photosystem I reaction center subunit XI / / PSI subunit V / PSI-L


Mass: 16631.795 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. PCC 6803 (Cyanobacteria)
References: UniProt: P37277
#10: Protein/peptide Photosystem I reaction center subunit XII / / PSI-M


Mass: 3382.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. PCC 6803 (Cyanobacteria)
References: UniProt: P72986
#12: Protein/peptide Photosystem I reaction center subunit PsaK 1 / / Photosystem I subunit X 1


Mass: 8649.268 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. PCC 6803 (Cyanobacteria)
References: UniProt: P72712

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Non-polymers , 9 types, 771 molecules

#13: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C38H75O10P
#14: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C45H86O10
#15: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


Mass: 893.489 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#16: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 588 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Chlorophyll a
#17: Chemical
ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C31H46O2 / Phytomenadione
#18: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Fe4S4 / Iron–sulfur cluster
#19: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 135 / Source method: obtained synthetically / Formula: C40H56 / Beta-Carotene
#20: Chemical ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Mass: 510.615 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent *YM
#21: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Calcium

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: PSI-IsiA / Type: COMPLEX / Details: PSI-IsiA from cyanobacteria / Entity ID: 1,2,3,4,5,6,7,8,9,10 / Source: NATURAL
Molecular weightValue: 2 MDa / Experimental value: NO
Source (natural)Organism: Synechocystis sp. PCC 6803 (Cyanobacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1.6 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.14_3260refinement
PHENIX1.14_3260refinement
EM software
IDNameVersionCategoryDetails
4CTFFINDCTF correction
7PHENIX1.14-3260model fitting
9RELION3initial Euler assignment
10RELION3final Euler assignment
11RELIONclassification
12RELION3D reconstruction3
13PHENIX1.14-3260model refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 572000
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74000 / Algorithm: BACK PROJECTION / Num. of class averages: 95 / Symmetry type: POINT
Atomic model buildingB value: 16.43 / Protocol: OTHER / Space: REAL
RefinementStereochemistry target values: CDL v1.2
Refine LS restraints

Refinement-ID: ELECTRON MICROSCOPY

TypeDev idealNumber
f_bond_d0.0048145615
f_angle_d0.8896207381
f_chiral_restr0.055117595
f_plane_restr0.006219922
f_dihedral_angle_d13.700767613

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