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- PDB-7sa3: Structure of a monomeric photosystem II core complex from a cyano... -

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Basic information

Entry
Database: PDB / ID: 7sa3
TitleStructure of a monomeric photosystem II core complex from a cyanobacterium acclimated to far-red light
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 5
  • Photosystem q(B) protein
  • Unknown
KeywordsPHOTOSYNTHESIS / Photosystem II / far-red light photoacclimation / chlorophyll f / chlorophyll d / bicarbonate / photoactivation / cyanobacteria
Function / homology
Function and homology information


oxygen evolving activity / photosystem II / photosystem II reaction center / : / photosynthetic electron transport chain / response to herbicide / photosystem II / photosynthetic electron transport in photosystem II / chlorophyll binding / plasma membrane-derived thylakoid membrane ...oxygen evolving activity / photosystem II / photosystem II reaction center / : / photosynthetic electron transport chain / response to herbicide / photosystem II / photosynthetic electron transport in photosystem II / chlorophyll binding / plasma membrane-derived thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / electron transfer activity / membrane => GO:0016020 / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosystem II CP43 reaction centre protein superfamily / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II CP47 reaction centre protein / Photosystem II PsbI / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II protein D1 ...Photosystem II CP43 reaction centre protein superfamily / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II CP47 reaction centre protein / Photosystem II PsbI / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Cytochrome b559 subunits heme-binding site signature. / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
BETA-CAROTENE / CHLOROPHYLL D / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chlorophyll F / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHEOPHYTIN A ...BETA-CAROTENE / CHLOROPHYLL D / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chlorophyll F / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHEOPHYTIN A / Chem-PL9 / Cytochrome b559 subunit alpha / Photosystem q(B) protein / Photosystem II CP47 reaction center protein / Photosystem II CP43 reaction center protein / Photosystem II D2 protein / Cytochrome b559 subunit beta / Photosystem II reaction center protein I / Photosystem II reaction center protein K
Similarity search - Component
Biological speciesSynechococcus sp. PCC 7335 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.25 Å
AuthorsGisriel, C.J. / Bryant, D.A. / Brudvig, G.W.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM140174 United States
National Science Foundation (NSF, United States)MCB-1613022 United States
Department of Energy (DOE, United States)DE-FG02-05ER15646 United States
CitationJournal: J Biol Chem / Year: 2022
Title: Structure of a monomeric photosystem II core complex from a cyanobacterium acclimated to far-red light reveals the functions of chlorophylls d and f.
Authors: Christopher J Gisriel / Gaozhong Shen / Ming-Yang Ho / Vasily Kurashov / David A Flesher / Jimin Wang / William H Armstrong / John H Golbeck / Marilyn R Gunner / David J Vinyard / Richard J ...Authors: Christopher J Gisriel / Gaozhong Shen / Ming-Yang Ho / Vasily Kurashov / David A Flesher / Jimin Wang / William H Armstrong / John H Golbeck / Marilyn R Gunner / David J Vinyard / Richard J Debus / Gary W Brudvig / Donald A Bryant /
Abstract: Far-red light (FRL) photoacclimation in cyanobacteria provides a selective growth advantage for some terrestrial cyanobacteria by expanding the range of photosynthetically active radiation to include ...Far-red light (FRL) photoacclimation in cyanobacteria provides a selective growth advantage for some terrestrial cyanobacteria by expanding the range of photosynthetically active radiation to include far-red/near-infrared light (700-800 nm). During this photoacclimation process, photosystem II (PSII), the water:plastoquinone photooxidoreductase involved in oxygenic photosynthesis, is modified. The resulting FRL-PSII is comprised of FRL-specific core subunits and binds chlorophyll (Chl) d and Chl f molecules in place of several of the Chl a molecules found when cells are grown in visible light. These new Chls effectively lower the energy canonically thought to define the "red limit" for light required to drive photochemical catalysis of water oxidation. Changes to the architecture of FRL-PSII were previously unknown, and the positions of Chl d and Chl f molecules had only been proposed from indirect evidence. Here, we describe the 2.25 Å resolution cryo-EM structure of a monomeric FRL-PSII core complex from Synechococcus sp. PCC 7335 cells that were acclimated to FRL. We identify one Chl d molecule in the Chl position of the electron transfer chain and four Chl f molecules in the core antenna. We also make observations that enhance our understanding of PSII biogenesis, especially on the acceptor side of the complex where a bicarbonate molecule is replaced by a glutamate side chain in the absence of the assembly factor Psb28. In conclusion, these results provide a structural basis for the lower energy limit required to drive water oxidation, which is the gateway for most solar energy utilization on earth.
History
DepositionSep 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 29, 2021Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

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Assembly

Deposited unit
A: Photosystem q(B) protein
B: Photosystem II CP47 reaction center protein
C: Photosystem II CP43 reaction center protein
D: Photosystem II D2 protein
E: Cytochrome b559 subunit alpha
F: Cytochrome b559 subunit beta
I: Photosystem II reaction center protein I
K: Photosystem II reaction center protein K
N: Unknown
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,67865
Polymers213,9609
Non-polymers42,71856
Water4,143230
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Photosystem II ... , 5 types, 5 molecules BCDIK

#2: Protein Photosystem II CP47 reaction center protein / / PSII 47 kDa protein / Protein CP-47


Mass: 56440.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WKI1
#3: Protein Photosystem II CP43 reaction center protein / / PSII 43 kDa protein / Protein CP-43


Mass: 52375.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WKI2
#4: Protein Photosystem II D2 protein / / PSII D2 protein / Photosystem Q(A) protein


Mass: 39596.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WKI3, photosystem II
#7: Protein/peptide Photosystem II reaction center protein I / / PSII-I / PSII 4.4 kDa protein


Mass: 4229.917 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WM03
#8: Protein/peptide Photosystem II reaction center protein K / / PSII-K


Mass: 5069.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WR12

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Cytochrome b559 subunit ... , 2 types, 2 molecules EF

#5: Protein Cytochrome b559 subunit alpha / / PSII reaction center subunit V


Mass: 9136.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WII1
#6: Protein/peptide Cytochrome b559 subunit beta / / PSII reaction center subunit VI


Mass: 5023.960 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WKJ2

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Protein / Protein/peptide , 2 types, 2 molecules AN

#1: Protein Photosystem q(B) protein


Mass: 40111.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WKH9
#9: Protein/peptide Unknown


Mass: 1975.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria)

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Sugars , 2 types, 8 molecules

#16: 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
#18: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C51H96O15

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Non-polymers , 13 types, 278 molecules

#10: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#11: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#12: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: C55H72MgN4O5
#13: Chemical ChemComp-CL7 / CHLOROPHYLL D / Chlorophyll d


Mass: 895.462 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C54H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#14: Chemical ChemComp-PHO / PHEOPHYTIN A / Pheophytin


Mass: 871.200 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C55H74N4O5
#15: Chemical
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C40H56
#17: Chemical
ChemComp-F6C / Chlorophyll F / [methyl 9-ethenyl-14-ethyl-8-formyl-4,13,18-trimethyl-20-oxo-3-{3-oxo-3-[(3,7,11,15-tetramethylhexadec-2-en-1-yl)oxy]propyl}-3,4,23,25-tetradehydro-24,26-dihydrophorbine-21-carboxylatato(2-)-kappa~4~N~23~,N~24~,N~25~,N~26~]magnesium / Chlorophyll f


Mass: 905.457 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C55H68MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#19: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C45H86O10
#20: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Fe
#21: Chemical ChemComp-PL9 / 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE / PLASTOQUINONE 9 / Plastoquinone


Mass: 749.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C53H80O2
#22: Chemical ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C38H75O10P / Comment: phospholipid*YM
#23: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C34H32FeN4O4
#24: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O

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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: Monomeric photosystem II from cyanobacteria acclimated to far-red light
Type: COMPLEX / Entity ID: #1-#9 / Source: NATURAL
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria)
Buffer solutionpH: 6.5
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 25 mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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: 40.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 315307 / Symmetry type: POINT

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