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- PDB-6uzv: The structure of a red shifted photosystem I complex -

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Basic information

Entry
Database: PDB / ID: 6uzv
TitleThe structure of a red shifted photosystem I complex
Components
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 8
  • Photosystem I iron-sulfur center
KeywordsPHOTOSYNTHESIS / Photosystem / Antenna / Chlorophyll / Membrane
Function / homology
Function and homology information


plasma membrane-derived photosystem I / photosystem I reaction center / photosystem I / photosystem I / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthetic electron transport in photosystem I / photosynthesis / 4 iron, 4 sulfur cluster binding / oxidoreductase activity ...plasma membrane-derived photosystem I / photosystem I reaction center / photosystem I / photosystem I / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthetic electron transport in photosystem I / photosynthesis / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI ...Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Photosystem I protein PsaC / Photosystem I PsaA / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Electron transport accessory-like domain superfamily / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit II / Photosystem I P700 chlorophyll a apoprotein A1 ...BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I reaction center subunit IV / 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 XII / Photosystem I reaction center subunit PsaK 2 / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit VIII
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsToporik, H. / Williams, D. / Chiu, P.L. / Mazor, Y.
CitationJournal: Nat Commun / Year: 2020
Title: The structure of a red-shifted photosystem I reveals a red site in the core antenna.
Authors: Hila Toporik / Anton Khmelnitskiy / Zachary Dobson / Reece Riddle / Dewight Williams / Su Lin / Ryszard Jankowiak / Yuval Mazor /
Abstract: Photosystem I coordinates more than 90 chlorophylls in its core antenna while achieving near perfect quantum efficiency. Low energy chlorophylls (also known as red chlorophylls) residing in the ...Photosystem I coordinates more than 90 chlorophylls in its core antenna while achieving near perfect quantum efficiency. Low energy chlorophylls (also known as red chlorophylls) residing in the antenna are important for energy transfer dynamics and yield, however, their precise location remained elusive. Here, we construct a chimeric Photosystem I complex in Synechocystis PCC 6803 that shows enhanced absorption in the red spectral region. We combine Cryo-EM and spectroscopy to determine the structurefunction relationship in this red-shifted Photosystem I complex. Determining the structure of this complex reveals the precise architecture of the low energy site as well as large scale structural heterogeneity which is probably universal to all trimeric Photosystem I complexes. Identifying the structural elements that constitute red sites can expand the absorption spectrum of oxygenic photosynthetic and potentially modulate light harvesting efficiency.
History
DepositionNov 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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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
K: Photosystem I reaction center subunit PsaK 2
a: Photosystem I P700 chlorophyll a apoprotein A1
1: Photosystem I P700 chlorophyll a apoprotein A1
c: Photosystem I iron-sulfur center
3: Photosystem I iron-sulfur center
b: Photosystem I P700 chlorophyll a apoprotein A2
2: Photosystem I P700 chlorophyll a apoprotein A2
d: Photosystem I reaction center subunit II
4: Photosystem I reaction center subunit II
e: Photosystem I reaction center subunit IV
5: Photosystem I reaction center subunit IV
f: Photosystem I reaction center subunit III
6: Photosystem I reaction center subunit III
i: Photosystem I reaction center subunit VIII
h: Photosystem I reaction center subunit VIII
j: Photosystem I reaction center subunit IX
7: Photosystem I reaction center subunit IX
k: Photosystem I reaction center subunit PsaK 2
8: Photosystem I reaction center subunit PsaK 2
l: Photosystem I reaction center subunit XI
0: Photosystem I reaction center subunit XI
m: Photosystem I reaction center subunit XII
9: Photosystem I reaction center subunit XII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,086,840441
Polymers762,61633
Non-polymers324,224408
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "L"
d_2ens_1chain "0"
d_3ens_1chain "l"
d_1ens_2chain "A"
d_2ens_2chain "1"
d_3ens_2chain "a"
d_1ens_3chain "B"
d_2ens_3chain "2"
d_3ens_3chain "b"
d_1ens_4chain "3"
d_2ens_4chain "C"
d_3ens_4chain "c"
d_1ens_5chain "4"
d_2ens_5chain "D"
d_3ens_5chain "d"
d_1ens_6chain "E"
d_2ens_6chain "5"
d_3ens_6chain "e"
d_1ens_7chain "F"
d_2ens_7chain "6"
d_3ens_7chain "f"
d_1ens_8chain "j"
d_2ens_8chain "7"
d_3ens_8chain "J"
d_1ens_9chain "K"
d_2ens_9chain "8"
d_3ens_9chain "k"
d_1ens_10chain "M"
d_2ens_10chain "9"
d_3ens_10chain "m"
d_1ens_11chain "i"
d_2ens_11chain "h"
d_3ens_11chain "I"

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4
ens_5
ens_6
ens_7
ens_8
ens_9
ens_10
ens_11

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Components

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Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 6 molecules Aa1Bb2

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


Mass: 83036.398 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P29254, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2


Mass: 81971.188 Da / Num. of mol.: 3 / Mutation: Red_a / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
References: UniProt: P29255*PLUS

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Photosystem I reaction center subunit ... , 8 types, 24 molecules Dd4Ee5Ff6IihJj7Ll0Mm9Kk8

#4: Protein 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. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P19569
#5: Protein 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. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P12975
#6: Protein 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. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / 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. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / 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. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: Q55329
#9: Protein 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. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / 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. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P72986
#11: Protein Photosystem I reaction center subunit PsaK 2 / Photosystem I subunit X 2


Mass: 9312.122 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P74564

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Protein / Sugars , 2 types, 9 molecules Cc3

#19: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#3: Protein 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. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P32422, photosystem I

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Non-polymers , 8 types, 402 molecules

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


Mass: 722.970 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#13: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


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


Mass: 893.489 Da / Num. of mol.: 288 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#15: 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
#16: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Fe4S4
#17: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 69 / Source method: obtained synthetically / Formula: C40H56
#18: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C45H86O10
#20: Chemical ChemComp-CA / CALCIUM ION


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

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Details

Has ligand of interestY

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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 / Type: COMPLEX / Details: PSI from cyanobacteria / Entity ID: #1-#11 / Source: NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
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 FIELD
Image recordingElectron dose: 1.6 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.18.2_3874refinement
PHENIX1.18.2_3874refinement
EM software
IDNameVersionCategoryDetails
4CTFFINDCTF correction
7PHENIX1.16-3549model fitting
9RELION3initial Euler assignment
10RELION3final Euler assignment
11RELIONclassification
12RELION3D reconstruction3
13PHENIX1.16-3549model refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 972010
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 196181 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building
IDPDB-IDPdb chain-ID 3D fitting-ID
15OY0

5oy0

1
26KIG

6kig

K1
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 35.52 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.009276683
ELECTRON MICROSCOPYf_angle_d0.9556108723
ELECTRON MICROSCOPYf_chiral_restr0.05599345
ELECTRON MICROSCOPYf_plane_restr0.024910500
ELECTRON MICROSCOPYf_dihedral_angle_d22.113113206

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