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- EMDB-0727: Structure of PSI from H. hongdechloris grown under far-red light ... -

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Basic information

Entry
Database: EMDB / ID: EMD-0727
TitleStructure of PSI from H. hongdechloris grown under far-red light condition
Map data
Samplefar-red PSI
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • Photosystem I iron-sulfur center
  • (Photosystem I reaction center subunit ...) x 6
  • (ligand) x 12
Function / homology
Function and homology information


thylakoid membrane / 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 ...thylakoid membrane / 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 / oxidoreductase 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 psaG and psaK proteins signature. / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I PsaG/PsaK protein / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI / Photosystem I reaction centre subunit XI ...Photosystem I PsaK, reaction centre / Photosystem I reaction centre subunit PsaK / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I PsaG/PsaK protein / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I PsaD / PsaD / 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-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
Photosystem I 16 kDa polypeptide / Photosystem I reaction center subunit IV / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit VIII / Photosystem I P700 chlorophyll a apoprotein A1 / PSI subunit V / Photosystem I iron-sulfur center / Photosystem I reaction center subunit PsaK
Similarity search - Component
Biological speciesHalomicronema hongdechloris (Cyanobacteria) / Halomicronema hongdechloris C2206 (Cyanobacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.41 Å
AuthorsKato K / Nagao R / Shen JR / Miyazaki N / Akita F
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis for the adaptation and function of chlorophyll f in photosystem I.
Authors: Koji Kato / Toshiyuki Shinoda / Ryo Nagao / Seiji Akimoto / Takehiro Suzuki / Naoshi Dohmae / Min Chen / Suleyman I Allakhverdiev / Jian-Ren Shen / Fusamichi Akita / Naoyuki Miyazaki / Tatsuya Tomo /
Abstract: Chlorophylls (Chl) play pivotal roles in energy capture, transfer and charge separation in photosynthesis. Among Chls functioning in oxygenic photosynthesis, Chl f is the most red-shifted type first ...Chlorophylls (Chl) play pivotal roles in energy capture, transfer and charge separation in photosynthesis. Among Chls functioning in oxygenic photosynthesis, Chl f is the most red-shifted type first found in a cyanobacterium Halomicronema hongdechloris. The location and function of Chl f in photosystems are not clear. Here we analyzed the high-resolution structures of photosystem I (PSI) core from H. hongdechloris grown under white or far-red light by cryo-electron microscopy. The structure showed that, far-red PSI binds 83 Chl a and 7 Chl f, and Chl f are associated at the periphery of PSI but not in the electron transfer chain. The appearance of Chl f is well correlated with the expression of PSI genes induced under far-red light. These results indicate that Chl f functions to harvest the far-red light and enhance uphill energy transfer, and changes in the gene sequences are essential for the binding of Chl f.
History
DepositionAug 1, 2019-
Header (metadata) releaseJan 15, 2020-
Map releaseJan 15, 2020-
UpdateJan 29, 2020-
Current statusJan 29, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6kmx
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0727.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 360 pix.
= 313.2 Å
0.87 Å/pix.
x 360 pix.
= 313.2 Å
0.87 Å/pix.
x 360 pix.
= 313.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.30953747 - 0.91508144
Average (Standard dev.)0.0009085082 (±0.013346554)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 313.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.870.870.87
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z313.200313.200313.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.3100.9150.001

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Supplemental data

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Sample components

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Entire far-red PSI

EntireName: far-red PSI / Number of Components: 22

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Component #1: protein, far-red PSI

ProteinName: far-red PSI / Recombinant expression: No
SourceSpecies: Halomicronema hongdechloris (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: 87.406258 kDa
SourceSpecies: Halomicronema hongdechloris C2206 (Cyanobacteria)

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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: 83.287695 kDa
SourceSpecies: Halomicronema hongdechloris C2206 (Cyanobacteria)

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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: 8.782184 kDa
SourceSpecies: Halomicronema hongdechloris C2206 (Cyanobacteria)

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Component #5: protein, Photosystem I reaction center subunit II

ProteinName: Photosystem I reaction center subunit II / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 15.7238 kDa
SourceSpecies: Halomicronema hongdechloris C2206 (Cyanobacteria)

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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: 7.907028 kDa
SourceSpecies: Halomicronema hongdechloris C2206 (Cyanobacteria)

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Component #7: protein, Photosystem I reaction center subunit VIII

ProteinName: Photosystem I reaction center subunit VIII / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 7.136356 kDa
SourceSpecies: Halomicronema hongdechloris C2206 (Cyanobacteria)

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Component #8: protein, Photosystem I reaction center subunit PsaK

ProteinName: Photosystem I reaction center subunit PsaK / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 9.726539 kDa
SourceSpecies: Halomicronema hongdechloris C2206 (Cyanobacteria)

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

ProteinName: Photosystem I reaction center subunit XI / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 20.191928 kDa
SourceSpecies: Halomicronema hongdechloris C2206 (Cyanobacteria)

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

ProteinName: Photosystem I reaction center subunit XII / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 3.440141 kDa
SourceSpecies: Halomicronema hongdechloris C2206 (Cyanobacteria)

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Component #11: ligand, CHLOROPHYLL A ISOMER

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

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Component #12: ligand, CHLOROPHYLL A

LigandName: CHLOROPHYLL A / Number of Copies: 246 / Recombinant expression: No
MassTheoretical: 0.893489 kDa

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Component #13: ligand, Chlorophyll F

LigandName: Chlorophyll F / Number of Copies: 21 / Recombinant expression: No
MassTheoretical: 0.905457 kDa

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Component #14: ligand, PHYLLOQUINONE

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

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Component #15: 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 #16: ligand, BETA-CAROTENE

LigandName: BETA-CAROTENEΒ-Carotene / Number of Copies: 51 / Recombinant expression: No
MassTheoretical: 0.536873 kDa

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

LigandName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.72297 kDa

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Component #18: ligand, DODECYL-BETA-D-MALTOSIDE

LigandName: DODECYL-BETA-D-MALTOSIDE / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.510615 kDa

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Component #19: 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 #20: ligand, UNKNOWN LIGAND

LigandName: UNKNOWN LIGAND / Number of Copies: 15 / Recombinant expression: No

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Component #21: ligand, CALCIUM ION

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

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Component #22: ligand, water

LigandName: water / Number of Copies: 636 / 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 solutionSpecimen conc.: 0.071 mg/mL / pH: 6.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: ETHANE / Temperature: 277 K / Humidity: 100 %

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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: 47 e/Å2 / Illumination Mode: FLOOD BEAM
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C3 (3 fold cyclic) / Number of Projections: 311993
3D reconstructionSoftware: RELION / Resolution: 2.41 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Target Criteria: Correlation coefficient
Input PDB model: 1JB0
Output model

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