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- EMDB-24821: Structure of photosystem I with bound ferredoxin from Synechococc... -

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Basic information

Entry
Database: EMDB / ID: EMD-24821
TitleStructure of photosystem I with bound ferredoxin from Synechococcus sp. PCC 7335 acclimated to far-red light
Map data
SampleFar-red light-acclimated Photosystem I from Synechococcus sp. PCC 7335
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • PsaC
  • Photosystem I 16 kDa polypeptide
  • (Photosystem I reaction center subunit ...) x 3
  • PSI-F
  • PsaI2
  • PSI subunit V
  • PsaM
  • 2Fe-2S ferredoxin-type domain-containing protein
  • (ligand) x 13
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / protein-chromophore linkage / electron transfer activity ...photosystem I reaction center / photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / protein-chromophore linkage / electron transfer activity / magnesium ion binding / integral component of membrane / metal ion binding
Similarity search - Function
Photosystem I PsaK, reaction centre / Photosystem I reaction centre subunit PsaK / Photosystem I reaction centre subunit PsaK superfamily / Ferredoxin [2Fe-2S], plant / Photosystem I PsaG/PsaK protein / Photosystem I psaG / psaK / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaL, reaction centre subunit XI / Photosystem I reaction centre subunit III / Photosystem I reaction centre subunit XI ...Photosystem I PsaK, reaction centre / Photosystem I reaction centre subunit PsaK / Photosystem I reaction centre subunit PsaK superfamily / Ferredoxin [2Fe-2S], plant / Photosystem I PsaG/PsaK protein / Photosystem I psaG / psaK / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaL, reaction centre subunit XI / Photosystem I reaction centre subunit III / Photosystem I reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I, reaction centre subunit XI / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaD / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaE, reaction centre subunit IV / Photosystem I psaA and psaB proteins signature. / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I PsaA / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Electron transport accessory-like domain superfamily / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Beta-grasp domain superfamily
Similarity search - Domain/homology
PSI subunit V / Photosystem I reaction center subunit IX / PSI-F / Uncharacterized protein / 2Fe-2S ferredoxin-type domain-containing protein / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit PsaK / Photosystem I 16 kDa polypeptide / Photosystem I reaction center subunit IV
Similarity search - Component
Biological speciesSynechococcus sp. PCC 7335 (Cyanobacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsGisriel CJ / Flesher DA / Shen G / Wang J / Ho M / Brudvig GW / Bryant DA
Funding support United States, 2 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FG02-05ER15646 United States
National Science Foundation (NSF, United States)MCB-1613022 United States
CitationJournal: J Biol Chem / Year: 2021
Title: Structure of a photosystem I-ferredoxin complex from a marine cyanobacterium provides insights into far-red light photoacclimation.
Authors: Christopher J Gisriel / David A Flesher / Gaozhong Shen / Jimin Wang / Ming-Yang Ho / Gary W Brudvig / Donald A Bryant /
Abstract: Far-red light photoacclimation (FaRLiP) exhibited by some cyanobacteria allows these organisms to use light of the far-red region of the solar spectrum (700 to 800 nm) for photosynthesis. Part of ...Far-red light photoacclimation (FaRLiP) exhibited by some cyanobacteria allows these organisms to use light of the far-red region of the solar spectrum (700 to 800 nm) for photosynthesis. Part of this process includes the replacement of six photosystem I (PSI) subunits with isoforms that confer the binding of chlorophyll (Chl) f molecules that are synthesized by chlorophyll f synthase and that absorb far-red light. However, the exact sites at which Chl f molecules are bound are still challenging to determine. To aid in the identification of Chl f-binding sites, we solved the cryo-EM structure of PSI from far-red light-acclimated cells (FRL-PSI) of the cyanobacterium Synechococcus sp. PCC 7335. We identified six sites that bind Chl f with high specificity, and three additional sites that are likely to bind Chl f at lower specificity. All of these binding sites are in the core antenna regions of PSI, and Chl f was not observed among the electron transport cofactors. This structural analysis also reveals both conserved and non-conserved Chl f-binding sites, the latter of which exemplify the diversity in FRL-PSI among species. We found that the FRL-PSI structure also contains a bound soluble ferredoxin, PetF1, at low occupancy, which suggests that ferredoxin binds less transiently than expected according to the canonical view of ferredoxin-binding to facilitate electron transfer. We suggest that this may result from structural changes in FRL-PSI that occur specifically during FaRLiP.
History
DepositionSep 5, 2021-
Header (metadata) releaseNov 24, 2021-
Map releaseNov 24, 2021-
UpdateDec 1, 2021-
Current statusDec 1, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0302
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0302
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7s3d
  • Surface level: 0.0302
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7s3d
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_24821.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 316.8 Å
0.83 Å/pix.
x 384 pix.
= 316.8 Å
0.83 Å/pix.
x 384 pix.
= 316.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density
Contour LevelBy AUTHOR: 0.0302 / Movie #1: 0.0302
Minimum - Maximum-0.20111874 - 0.31543994
Average (Standard dev.)0.00018521286 (±0.010041001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 316.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8250.8250.825
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z316.800316.800316.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.2010.3150.000

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Supplemental data

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Additional map: Unsharpened map for Far-red light-acclimated PSI from Synechococcus...

Fileemd_24821_additional_1.map
AnnotationUnsharpened map for Far-red light-acclimated PSI from Synechococcus sp. PCC 7335
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Far-red light-acclimated Photosystem I from Synechococcus sp. PCC 7335

EntireName: Far-red light-acclimated Photosystem I from Synechococcus sp. PCC 7335
Number of Components: 26

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Component #1: protein, Far-red light-acclimated Photosystem I from Synechococcu...

ProteinName: Far-red light-acclimated Photosystem I from Synechococcus sp. PCC 7335
Recombinant expression: No
SourceSpecies: Synechococcus sp. PCC 7335 (Cyanobacteria)

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Component #2: protein, Photosystem I P700 chlorophyll a apoprotein A1

ProteinName: Photosystem I P700 chlorophyll a apoprotein A1 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 86.411227 kDa
SourceSpecies: Synechococcus sp. PCC 7335 (Cyanobacteria) / Strain: ATCC 29403 / PCC 7335

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Component #3: protein, Photosystem I P700 chlorophyll a apoprotein A2

ProteinName: Photosystem I P700 chlorophyll a apoprotein A2 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 83.207648 kDa
SourceSpecies: Synechococcus sp. PCC 7335 (Cyanobacteria) / Strain: ATCC 29403 / PCC 7335

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Component #4: protein, PsaC

ProteinName: PsaC / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 8.809169 kDa
SourceSpecies: Synechococcus sp. PCC 7335 (Cyanobacteria)

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Component #5: protein, Photosystem I 16 kDa polypeptide

ProteinName: Photosystem I 16 kDa polypeptide / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 17.051336 kDa
SourceSpecies: Synechococcus sp. PCC 7335 (Cyanobacteria) / Strain: ATCC 29403 / PCC 7335

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Component #6: protein, Photosystem I reaction center subunit IV

ProteinName: Photosystem I reaction center subunit IV / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 7.955112 kDa
SourceSpecies: Synechococcus sp. PCC 7335 (Cyanobacteria) / Strain: ATCC 29403 / PCC 7335

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Component #7: protein, PSI-F

ProteinName: PSI-F / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 18.569213 kDa
SourceSpecies: Synechococcus sp. PCC 7335 (Cyanobacteria) / Strain: ATCC 29403 / PCC 7335

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Component #8: protein, PsaI2

ProteinName: PsaI2 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 7.668838 kDa
SourceSpecies: Synechococcus sp. PCC 7335 (Cyanobacteria) / Strain: ATCC 29403 / PCC 7335

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Component #9: protein, Photosystem I reaction center subunit IX

ProteinName: Photosystem I reaction center subunit IX / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 5.170094 kDa
SourceSpecies: Synechococcus sp. PCC 7335 (Cyanobacteria) / Strain: ATCC 29403 / PCC 7335

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Component #10: protein, Photosystem I reaction center subunit PsaK

ProteinName: Photosystem I reaction center subunit PsaK / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 8.195834 kDa
SourceSpecies: Synechococcus sp. PCC 7335 (Cyanobacteria) / Strain: ATCC 29403 / PCC 7335

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Component #11: protein, PSI subunit V

ProteinName: PSI subunit V / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 18.632201 kDa
SourceSpecies: Synechococcus sp. PCC 7335 (Cyanobacteria) / Strain: ATCC 29403 / PCC 7335

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Component #12: protein, PsaM

ProteinName: PsaM / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 3.366065 kDa
SourceSpecies: Synechococcus sp. PCC 7335 (Cyanobacteria)

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Component #13: protein, 2Fe-2S ferredoxin-type domain-containing protein

ProteinName: 2Fe-2S ferredoxin-type domain-containing protein / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 10.835725 kDa
SourceSpecies: Synechococcus sp. PCC 7335 (Cyanobacteria) / Strain: ATCC 29403 / PCC 7335

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Component #14: ligand, CHLOROPHYLL A ISOMER

LigandName: CHLOROPHYLL A ISOMER / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.893489 kDa

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Component #15: ligand, CHLOROPHYLL A

LigandName: CHLOROPHYLL A / Number of Copies: 255 / Recombinant expression: No
MassTheoretical: 0.893489 kDa

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Component #16: ligand, Chlorophyll F

LigandName: Chlorophyll F / Number of Copies: 18 / Recombinant expression: No
MassTheoretical: 0.905457 kDa

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Component #17: ligand, PHYLLOQUINONE

LigandName: PHYLLOQUINONEPhytomenadione / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.450696 kDa

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Component #18: ligand, IRON/SULFUR CLUSTER

LigandName: IRON/SULFUR CLUSTERIron–sulfur cluster / Number of Copies: 9 / Recombinant expression: No
MassTheoretical: 0.35164 kDa

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Component #19: ligand, BETA-CAROTENE

LigandName: BETA-CAROTENEΒ-Carotene / Number of Copies: 57 / Recombinant expression: No
MassTheoretical: 0.536873 kDa

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Component #20: ligand, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

LigandName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 0.72297 kDa

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Component #21: ligand, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

LigandName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Number of Copies: 9 / Recombinant expression: No
MassTheoretical: 0.787158 kDa

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Component #22: ligand, DODECYL-BETA-D-MALTOSIDE

LigandName: DODECYL-BETA-D-MALTOSIDE / Number of Copies: 39 / Recombinant expression: No
MassTheoretical: 0.510615 kDa

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Component #23: ligand, CHLORIDE ION

LigandName: CHLORIDE IONChloride / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 3.545305 MDa

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Component #24: ligand, CALCIUM ION

LigandName: CALCIUM IONCalcium / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 4.007805 MDa

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Component #25: ligand, FE2/S2 (INORGANIC) CLUSTER

LigandName: FE2/S2 (INORGANIC) CLUSTER / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.17582 kDa

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Component #26: ligand, water

LigandName: water / Number of Copies: 333 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 6.5
VitrificationCryogen Name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 40.8 e/Å2 / Illumination Mode: FLOOD BEAM
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Number of Projections: 286672
3D reconstructionResolution: 2.91 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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