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- EMDB-0524: The structure of the photosystem I IsiA super-complex -

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Basic information

Entry
Database: EMDB / ID: EMD-0524
TitleThe structure of the photosystem I IsiA super-complex
Map data
SamplePSI-IsiA
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • Photosystem I iron-sulfur center
  • (Photosystem I reaction center subunit ...) x 8
  • Iron stress-induced chlorophyll-binding protein
  • (ligand) x 9
Function / homology
Function and homology information


plasma membrane-derived photosystem I / ec:1.97.1.12: / photosynthetic electron transport in photosystem I / photosystem I reaction center / photosystem I / thylakoid / chlorophyll binding / thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding ...plasma membrane-derived photosystem I / ec:1.97.1.12: / photosynthetic electron transport in photosystem I / photosystem I reaction center / photosystem I / thylakoid / chlorophyll binding / 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
Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I PsaA/PsaB, conserved site / Photosystem I PsaB / Electron transport accessory-like domain superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein PsaC / Photosystem I PsaK, reaction centre / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / Photosystem I, reaction centre subunit XI ...Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I PsaA/PsaB, conserved site / Photosystem I PsaB / Electron transport accessory-like domain superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein PsaC / Photosystem I PsaK, reaction centre / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaA/PsaB superfamily / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit PsaK / Photosystem I PsaA / Photosystem I PsaD / Photosystem I psaA/psaB protein / Photosystem I reaction centre subunit III / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / Photosystem I psaG and psaK proteins signature. / Photosystem I psaA and psaB proteins signature. / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S dicluster domain / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit XI / PsaD / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I reaction centre subunit IV / PsaE / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I psaG / psaK / Photosystem I PsaG/PsaK protein / Photosystem I PsaA/PsaB / Photosystem I reaction centre subunit VIII / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaE, reaction centre subunit IV
Photosystem I reaction center subunit IV / Photosystem I reaction center subunit II / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit III / Photosystem I iron-sulfur center / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit PsaK 1 / Photosystem I reaction center subunit XII / un:q55274: ...Photosystem I reaction center subunit IV / Photosystem I reaction center subunit II / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit III / Photosystem I iron-sulfur center / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit PsaK 1 / Photosystem I reaction center subunit XII / un:q55274: / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit VIII
Biological speciesSynechocystis sp. PCC 6803 (Cyanobacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.48 Å
AuthorsToporik H / Li J / Williams D / Chiu PL / Mazor Y
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2019
Title: The structure of the stress-induced photosystem I-IsiA antenna supercomplex.
Authors: Hila Toporik / Jin Li / Dewight Williams / Po-Lin Chiu / Yuval Mazor /
Abstract: Photochemical conversion in oxygenic photosynthesis takes place in two large protein-pigment complexes named photosystem II and photosystem I (PSII and PSI, respectively). Photosystems associate with ...Photochemical conversion in oxygenic photosynthesis takes place in two large protein-pigment complexes named photosystem II and photosystem I (PSII and PSI, respectively). Photosystems associate with antennae in vivo to increase the size of photosynthetic units to hundreds or thousands of pigments. Regulation of the interactions between antennae and photosystems allows photosynthetic organisms to adapt to their environment. In low-iron environments, cyanobacteria express IsiA, a PSI antenna, critical to their survival. Here we describe the structure of the PSI-IsiA complex isolated from the mesophilic cyanobacterium Synechocystis sp. PCC 6803. This 2-MDa photosystem-antenna supercomplex structure reveals more than 700 pigments coordinated by 51 subunits, as well as the mechanisms facilitating the self-assembly and association of IsiA with multiple PSI assemblies.
Validation ReportPDB-ID: 6nwa

SummaryFull reportAbout validation report
DateDeposition: Feb 6, 2019 / Header (metadata) release: Apr 24, 2019 / Map release: May 29, 2019 / Update: Jun 19, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0125
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0125
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6nwa
  • Surface level: 0.0125
  • 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_0524.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 500 pix.
= 512. Å
1.02 Å/pix.
x 500 pix.
= 512. Å
1.02 Å/pix.
x 500 pix.
= 512. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.024 Å
Density
Contour LevelBy AUTHOR: 0.0125 / Movie #1: 0.0125
Minimum - Maximum-0.049302652 - 0.15141094
Average (Standard dev.)0.00014315994 (±0.0019637637)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 512.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0241.0241.024
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z512.000512.000512.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS500500500
D min/max/mean-0.0490.1510.000

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Supplemental data

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Sample components

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Entire PSI-IsiA

EntireName: PSI-IsiA / Details: PSI-IsiA from cyanobacteria / Number of components: 22

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Component #1: protein, PSI-IsiA

ProteinName: PSI-IsiA / Details: PSI-IsiA from cyanobacteria / Recombinant expression: No
MassTheoretical: 2 MDa
SourceSpecies: Synechocystis sp. PCC 6803 (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: 83.022375 kDa
SourceSpecies: Synechocystis sp. PCC 6803 (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: 81.369531 kDa
SourceSpecies: Synechocystis sp. PCC 6803 (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: 8.837261 kDa
SourceSpecies: Synechocystis sp. PCC 6803 (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: 15.663749 kDa
SourceSpecies: Synechocystis sp. PCC 6803 (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: 8.154086 kDa
SourceSpecies: Synechocystis sp. PCC 6803 (Cyanobacteria)

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

ProteinName: Photosystem I reaction center subunit III / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 18.267082 kDa
SourceSpecies: Synechocystis sp. PCC 6803 (Cyanobacteria)

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

ProteinName: Photosystem I reaction center subunit VIII / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 4.414148 kDa
SourceSpecies: Synechocystis sp. PCC 6803 (Cyanobacteria)

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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: 4.535415 kDa
SourceSpecies: Synechocystis sp. PCC 6803 (Cyanobacteria)

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

ProteinName: Photosystem I reaction center subunit XI / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 16.631795 kDa
SourceSpecies: Synechocystis sp. PCC 6803 (Cyanobacteria)

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Component #11: protein, Photosystem I reaction center subunit XII

ProteinName: Photosystem I reaction center subunit XII / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 3.382063 kDa
SourceSpecies: Synechocystis sp. PCC 6803 (Cyanobacteria)

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Component #12: protein, Iron stress-induced chlorophyll-binding protein

ProteinName: Iron stress-induced chlorophyll-binding protein / Number of Copies: 18 / Recombinant expression: No
MassTheoretical: 37.250734 kDa
SourceSpecies: Synechocystis sp. PCC 6803 (Cyanobacteria)

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Component #13: protein, Photosystem I reaction center subunit PsaK 1

ProteinName: Photosystem I reaction center subunit PsaK 1 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 8.649268 kDa
SourceSpecies: Synechocystis sp. PCC 6803 (Cyanobacteria)

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Component #14: ligand, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

LigandName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Number of Copies: 9 / Recombinant expression: No
MassTheoretical: 0.72297 kDa

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Component #15: ligand, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

LigandName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Number of Copies: 15 / Recombinant expression: No
MassTheoretical: 0.787158 kDa

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Component #16: ligand, CHLOROPHYLL A ISOMER

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

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Component #17: ligand, CHLOROPHYLL A

LigandName: CHLOROPHYLL A / Number of Copies: 588 / Recombinant expression: No
MassTheoretical: 0.893489 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, BETA-CAROTENE

LigandName: BETA-CAROTENE / Number of Copies: 135 / Recombinant expression: No
MassTheoretical: 0.536873 kDa

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Component #21: 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 #22: ligand, CALCIUM ION

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

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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: 1.6 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 / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 74000
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION / Resolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement space: REAL / Overall bvalue: 16.43
Output model

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