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- PDB-9au4: Cryo-EM structure of a photosystem I variant containing an unusua... -

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Basic information

Entry
Database: PDB / ID: 9au4
TitleCryo-EM structure of a photosystem I variant containing an unusual plastoquinone derivative in its electron transfer chain
Components
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 8
  • Photosystem I iron-sulfur center
KeywordsPHOTOSYNTHESIS / cyanobacteria / photosystem I / MenB / phylloquinone / plastoquinone / benzoquinone / naphthoquinone / redox potential
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity ...photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding / plasma membrane
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 PsaE, reaction centre subunit IV / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I protein PsaC / Photosystem I PsaA / 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,beta-carotene-4,4'-dione / : / BETA-CAROTENE / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / beta,beta-caroten-4-one / (3'R)-3'-hydroxy-beta,beta-caroten-4-one / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / IRON/SULFUR CLUSTER ...beta,beta-carotene-4,4'-dione / : / BETA-CAROTENE / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / beta,beta-caroten-4-one / (3'R)-3'-hydroxy-beta,beta-caroten-4-one / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / IRON/SULFUR CLUSTER / Chem-SQD / Chem-ZEX / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit II / Photosystem I P700 chlorophyll a apoprotein A1 / 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. PCC 6803 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.03 Å
AuthorsGisriel, C.J. / Vasily, K. / Iwig, D.F. / Russell, B.P. / Vinyard, D.J. / Golbeck, J.H. / Brudvig, G.W. / Lakshmi, K.V.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM140174 United States
Department of Energy (DOE, United States)DE-FG02-07ER15903 United States
Department of Energy (DOE, United States)DE-SC0010575 United States
Department of Energy (DOE, United States)DE-FG02-05ER15646 United States
Department of Energy (DOE, United States)DE-SC0020119 United States
CitationJournal: Sci Adv / Year: 2024
Title: Cryo-EM structure of a photosystem I variant containing an unusual plastoquinone derivative in its electron transfer chain.
Authors: Christopher J Gisriel / Vasily Kurashov / David F Iwig / Brandon P Russell / David J Vinyard / Gary W Brudvig / John H Golbeck / K V Lakshmi /
Abstract: Photosystem I (PS I) is a light-driven oxidoreductase responsible for converting photons into chemical bond energy. Its application for renewable energy was revolutionized by the creation of the MenB ...Photosystem I (PS I) is a light-driven oxidoreductase responsible for converting photons into chemical bond energy. Its application for renewable energy was revolutionized by the creation of the MenB deletion (Δ) variant in the cyanobacterium sp. PCC 6803, in which phylloquinone is replaced by plastoquinone-9 with a low binding affinity. This permits its exchange with exogenous quinones covalently coupled to dihydrogen catalysts that bind with high affinity, thereby converting PS I into a stable solar fuel catalyst. Here, we reveal the 2.03-Å-resolution cryo-EM structure of a recent MenB variant of PS I. The quinones and their binding environment are analyzed in the context of previous biophysical data, thereby enabling a protocol to solve future PS I hybrids and constructs from this genetically tractable cyanobacterium.
History
DepositionFeb 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Photosystem I P700 chlorophyll a apoprotein A1
H: Photosystem I P700 chlorophyll a apoprotein A2
N: Photosystem I iron-sulfur center
O: Photosystem I reaction center subunit II
P: Photosystem I reaction center subunit IV
Q: Photosystem I reaction center subunit III
R: Photosystem I reaction center subunit VIII
S: Photosystem I reaction center subunit IX
T: Photosystem I reaction center subunit PsaK 2
U: Photosystem I reaction center subunit XI
V: Photosystem I reaction center subunit XII
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
k: Photosystem I reaction center subunit PsaK 2
l: Photosystem I reaction center subunit XI
m: Photosystem I reaction center subunit XII
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
K: Photosystem I reaction center subunit PsaK 2
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,077,744435
Polymers760,59833
Non-polymers317,147402
Water16,376909
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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

#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. PCC 6803 (bacteria) / References: UniProt: P29254, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2


Mass: 81298.453 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: photosystem I

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Protein , 1 types, 3 molecules NcC

#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. PCC 6803 (bacteria) / References: UniProt: P32422, photosystem I

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

#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. PCC 6803 (bacteria) / 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. PCC 6803 (bacteria) / 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. PCC 6803 (bacteria) / 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 (bacteria) / 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 (bacteria) / References: UniProt: Q55329
#9: 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. PCC 6803 (bacteria) / References: UniProt: P74564
#10: 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. PCC 6803 (bacteria) / References: UniProt: P37277
#11: 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 (bacteria) / References: UniProt: P72986

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Sugars , 2 types, 6 molecules

#25: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C51H96O15
#26: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 14 types, 1305 molecules

#12: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 282 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#13: Chemical
ChemComp-A1AGD / 2,3-dimethyl-5-[(2E,7R,11R)-3,7,11,15-tetramethylhexadec-2-en-1-yl]cyclohexa-2,5-diene-1,4-dione


Mass: 414.664 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C28H46O2
#14: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


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


Mass: 536.873 Da / Num. of mol.: 45 / Source method: obtained synthetically / Formula: C40H56
#16: 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
#17: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C45H86O10
#18: Chemical ChemComp-45D / beta,beta-carotene-4,4'-dione / Isomer of Canthaxanthin


Mass: 564.840 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C40H52O2
#19: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#20: Chemical
ChemComp-ECH / beta,beta-caroten-4-one / echinenone


Mass: 550.856 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C40H54O
#21: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#22: Chemical ChemComp-EQ3 / (3'R)-3'-hydroxy-beta,beta-caroten-4-one / 3'-Hydroxyechinenone / 3'-OH-Echinenone


Mass: 566.856 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C40H54O2
#23: Chemical
ChemComp-ZEX / (1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol


Mass: 568.871 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C40H56O2
#24: Chemical
ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C41H78O12S
#27: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 909 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: MenB Photosystem I / Type: COMPLEX / Entity ID: #1-#11 / Source: NATURAL
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Buffer solutionpH: 8.3
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40.2 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 375816 / Symmetry type: POINT

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