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- EMDB-30420: Structure of the far-red light utilizing photosystem I of Acaryoc... -

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Basic information

Entry
Database: EMDB / ID: EMD-30420
TitleStructure of the far-red light utilizing photosystem I of Acaryochloris marina
Map data
SamplePhotosystem I complex from Acaryochloris marina
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • Photosystem I iron-sulfur center
  • (Photosystem I protein ...) x 5
  • (Photosystem I reaction center subunit ...) x 3
  • (ligand) x 9
Function / homology
Function and homology information


photosystem I reaction center / photosynthetic electron transport in photosystem I / photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / protein-chromophore linkage / electron transfer activity ...photosystem I reaction center / photosynthetic electron transport in photosystem I / photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived 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
Similarity search - Function
Photosystem I PsaK, reaction centre / Photosystem I reaction centre subunit PsaK / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG / psaK / Photosystem I PsaG/PsaK protein / Photosystem I, reaction centre subunit XI / Photosystem I PsaF, reaction centre subunit III / Photosystem I reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I PsaL, reaction centre subunit XI ...Photosystem I PsaK, reaction centre / Photosystem I reaction centre subunit PsaK / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG / psaK / Photosystem I PsaG/PsaK protein / Photosystem I, reaction centre subunit XI / Photosystem I PsaF, reaction centre subunit III / Photosystem I reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I PsaL, reaction centre subunit XI / Photosystem I reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I PsaJ, reaction centre subunit IX / 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/PsaB, conserved site / Photosystem I PsaB / Photosystem I psaA and psaB proteins signature. / Photosystem I PsaA / Photosystem I PsaA/PsaB superfamily / Photosystem I PsaA/PsaB / 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
Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit IV / PSI subunit V / Photosystem I reaction center subunit IX / PSI-F / Photosystem I 16 kDa polypeptide / Photosystem I reaction center subunit PsaK / Photosystem I iron-sulfur center
Similarity search - Component
Biological speciesAcaryochloris marina (Cyanobacteria) / Acaryochloris marina MBIC11017 (Cyanobacteria) / Acaryochloris marina MBIC110017 (Cyanobacteria) / Acaryochloris marina MBIC 11017 (Cyanobacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsKawakami K / Yonekura K / Hamaguchi T / Kashino Y / Shinzawa-Itoh K / Inoue-Kashino N / Itoh S / Ifuku K / Yamashita E
Funding support Japan, 5 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H05175 Japan
Japan Society for the Promotion of Science (JSPS)16H04757 Japan
Japan Society for the Promotion of Science (JSPS)16H06554 Japan
Japan Society for the Promotion of Science (JSPS)20K06684 Japan
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: Nat Commun / Year: 2021
Title: Structure of the far-red light utilizing photosystem I of Acaryochloris marina.
Authors: Tasuku Hamaguchi / Keisuke Kawakami / Kyoko Shinzawa-Itoh / Natsuko Inoue-Kashino / Shigeru Itoh / Kentaro Ifuku / Eiki Yamashita / Kou Maeda / Koji Yonekura / Yasuhiro Kashino /
Abstract: Acaryochloris marina is one of the cyanobacterial species that can use far-red light to drive photochemical reactions for oxygenic photosynthesis. Here, we report the structure of A. marina ...Acaryochloris marina is one of the cyanobacterial species that can use far-red light to drive photochemical reactions for oxygenic photosynthesis. Here, we report the structure of A. marina photosystem I (PSI) reaction center, determined by cryo-electron microscopy at 2.58 Å resolution. The structure reveals an arrangement of electron carriers and light-harvesting pigments distinct from other type I reaction centers. The paired chlorophyll, or special pair (also referred to as P740 in this case), is a dimer of chlorophyll d and its epimer chlorophyll d'. The primary electron acceptor is pheophytin a, a metal-less chlorin. We show the architecture of this PSI reaction center is composed of 11 subunits and we identify key components that help explain how the low energy yield from far-red light is efficiently utilized for driving oxygenic photosynthesis.
History
DepositionAug 5, 2020-
Header (metadata) releaseMar 31, 2021-
Map releaseMar 31, 2021-
UpdateMay 5, 2021-
Current statusMay 5, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0064
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0064
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7coy
  • Surface level: 0.0055
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7coy
  • 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_30420.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 330 pix.
= 356.4 Å
1.08 Å/pix.
x 330 pix.
= 356.4 Å
1.08 Å/pix.
x 330 pix.
= 356.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.00637 / Movie #1: 0.0064
Minimum - Maximum-0.046826307 - 0.07514111
Average (Standard dev.)2.1081954e-05 (±0.0014213339)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions330330330
Spacing330330330
CellA=B=C: 356.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z330330330
origin x/y/z0.0000.0000.000
length x/y/z356.400356.400356.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS330330330
D min/max/mean-0.0470.0750.000

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Supplemental data

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Additional map: Local resolution map

Fileemd_30420_additional_1.map
AnnotationLocal_resolution_map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: run half1 class001 unfil.mrc

Fileemd_30420_half_map_1.map
Annotationrun_half1_class001_unfil.mrc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: run half2 class001 unfil.mrc

Fileemd_30420_half_map_2.map
Annotationrun_half2_class001_unfil.mrc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Photosystem I complex from Acaryochloris marina

EntireName: Photosystem I complex from Acaryochloris marina / Number of Components: 21

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Component #1: protein, Photosystem I complex from Acaryochloris marina

ProteinName: Photosystem I complex from Acaryochloris marina / Recombinant expression: No
SourceSpecies: Acaryochloris marina (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: 83.470539 kDa
SourceSpecies: Acaryochloris marina MBIC11017 (Cyanobacteria) / Strain: MBIC 11017

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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: 82.210555 kDa
SourceSpecies: Acaryochloris marina MBIC110017 (Cyanobacteria) / Strain: MBIC 11017

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Component #4: protein, Photosystem I iron-sulfur center

ProteinName: Photosystem I iron-sulfur center / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 8.825207 kDa
SourceSpecies: Acaryochloris marina MBIC110017 (Cyanobacteria) / Strain: MBIC 11017

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Component #5: protein, Photosystem I protein PsaD

ProteinName: Photosystem I protein PsaD / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 15.114146 kDa
SourceSpecies: Acaryochloris marina MBIC110017 (Cyanobacteria) / Strain: MBIC 11017

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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: 9.560822 kDa
SourceSpecies: Acaryochloris marina MBIC110017 (Cyanobacteria) / Strain: MBIC 11017

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Component #7: protein, Photosystem I protein PsaF

ProteinName: Photosystem I protein PsaF / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 17.844621 kDa
SourceSpecies: Acaryochloris marina MBIC110017 (Cyanobacteria) / Strain: MBIC 11017

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Component #8: protein, Photosystem I protein Psa27

ProteinName: Photosystem I protein Psa27 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 3.648337 kDa
SourceSpecies: Acaryochloris marina MBIC11017 (Cyanobacteria) / Strain: MBIC 11017

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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: 5.900939 kDa
SourceSpecies: Acaryochloris marina MBIC110017 (Cyanobacteria) / Strain: MBIC 11017

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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: 9.289071 kDa
SourceSpecies: Acaryochloris marina MBIC 11017 (Cyanobacteria) / Strain: MBIC 11017

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Component #11: protein, Photosystem I protein PsaL

ProteinName: Photosystem I protein PsaL / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 15.349588 kDa
SourceSpecies: Acaryochloris marina MBIC 11017 (Cyanobacteria) / Strain: MBIC 11017

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Component #12: protein, Photosystem I protein PsaM

ProteinName: Photosystem I protein PsaM / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 3.190899 kDa
SourceSpecies: Acaryochloris marina MBIC11017 (Cyanobacteria) / Strain: MBIC 11017

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Component #13: ligand, CHLOROPHYLL D ISOMER

LigandName: CHLOROPHYLL D ISOMER / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.895462 kDa

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Component #14: ligand, PHEOPHYTIN A

LigandName: PHEOPHYTIN A / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.8712 kDa

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Component #15: ligand, CHLOROPHYLL D

LigandName: CHLOROPHYLL D / Number of Copies: 210 / Recombinant expression: No
MassTheoretical: 0.895462 kDa

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Component #16: ligand, UNKNOWN LIGAND

LigandName: UNKNOWN LIGAND / Number of Copies: 36 / Recombinant expression: No

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Component #17: ligand, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

LigandName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.72297 kDa

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Component #18: ligand, PHYLLOQUINONE

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

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Component #19: 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 #20: ligand, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

LigandName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.787158 kDa

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Component #21: ligand, water

LigandName: water / Number of Copies: 84 / 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: NITROGEN

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Electron microscopy imaging

ImagingMicroscope: JEOL CRYO ARM 300
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 85.7 e/Å2 / Illumination Mode: FLOOD BEAM
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of Projections: 86419
3D reconstructionResolution: 2.5 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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