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- EMDB-6929: Cryo-EM structure of the red algal PSI-LHCR -

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Basic information

Entry
Database: EMDB / ID: 6929
TitleCryo-EM structure of the red algal PSI-LHCR
Map data
SamplePSI-5Lhcr:
PsaA / PsaB / PsaC / PsaD / PsaE / PsaF / PsaI / PsaJ / PsaKPosek / PsaL ...PsaA / PsaB / PsaC / PsaD / PsaE / PsaF / PsaI / PsaJ / PsaKPosek / PsaL / PsaMPalm Springs Air Museum / PsaO / Lhcr1 / Lhcr2 / Lhcr3 / (ligand) x 11
Function / homologyChlorophyll a/b binding domain superfamily / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Photosystem I PsaD / Photosystem I PsaL, reaction centre subunit XI / Photosystem I PsaA / Photosystem I PsaB / Electron transport accessory-like domain superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein PsaC / Photosystem I PsaO ...Chlorophyll a/b binding domain superfamily / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Photosystem I PsaD / Photosystem I PsaL, reaction centre subunit XI / Photosystem I PsaA / Photosystem I PsaB / Electron transport accessory-like domain superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein PsaC / Photosystem I PsaO / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / Photosystem I PsaE, reaction centre subunit IV / Photosystem I PsaA/PsaB, conserved site / Chlorophyll A-B binding protein / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaA/PsaB superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I reaction centre subunit IV / PsaE / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 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 reaction centre subunit III / Photosystem I reaction centre subunit IX / PsaJ / Chlorophyll A-B binding protein, plant / Photosystem I psaG / psaK / Photosystem I reaction centre subunit VIII / Chlorophyll A-B binding protein / Photosystem I psaA/psaB protein / Photosystem I PsaM, reaction centre superfamily / Photosystem I reaction centre subunit PsaK / Photosystem I PsaG/PsaK protein / Photosystem I PsaA/PsaB / Photosystem I reaction centre subunit VIII / Photosystem I PsaF, reaction centre subunit III superfamily / photosystem I / photosystem I reaction center / photosynthetic electron transport in photosystem I / photosynthesis, light harvesting / photosystem I / chlorophyll binding / chloroplast envelope / thylakoid membrane / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / protein-chromophore linkage / electron transfer activity / protein domain specific binding / magnesium ion binding / integral component of membrane / metal ion binding / Similar to chlorophyll a/b-binding protein, CP24 / Uncharacterized protein / Similar to light harvesting protein / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit II / Photosystem I p700 chlorophyll A apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I iron-sulfur center subunit VII / Photosystem I iron-sulfur center / Photosystem I reaction center subunit X / Photosystem I reaction center subunit XII
Function and homology information
SourceCyanidioschyzon merolae (eukaryote) / Red alga (eukaryote)
Methodsingle particle reconstruction / cryo EM / 3.63 Å resolution
AuthorsPi X
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Unique organization of photosystem I-light-harvesting supercomplex revealed by cryo-EM from a red alga.
Authors: Xiong Pi / Lirong Tian / Huai-En Dai / Xiaochun Qin / Lingpeng Cheng / Tingyun Kuang / Sen-Fang Sui / Jian-Ren Shen
Validation ReportPDB-ID: 5zgb

SummaryFull reportAbout validation report
DateDeposition: Mar 8, 2018 / Header (metadata) release: Apr 11, 2018 / Map release: Apr 25, 2018 / Last update: May 9, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0562
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0562
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5zgb
  • Surface level: 0.0562
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6929.map.gz (map file in CCP4 format, 87809 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
280 pix
1.05 Å/pix.
= 294. Å
280 pix
1.05 Å/pix.
= 294. Å
280 pix
1.05 Å/pix.
= 294. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density
Contour Level:0.0562 (by author), 0.0562 (movie #1):
Minimum - Maximum-0.17014694 - 0.6529895
Average (Standard dev.)0.00007548861 (0.013605257)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions280280280
Origin0.00.00.0
Limit279.0279.0279.0
Spacing280280280
CellA=B=C: 294.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z294.000294.000294.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.1700.6530.000

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Supplemental data

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Sample components

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Entire PSI-5Lhcr

EntireName: PSI-5Lhcr / Number of components: 27

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Component #1: protein, PSI-5Lhcr

ProteinName: PSI-5Lhcr / Recombinant expression: No
SourceSpecies: Cyanidioschyzon merolae (eukaryote)

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Component #2: protein, PsaA

ProteinName: PsaA / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 82.763461 kDa
SourceSpecies: Red alga (eukaryote) / Strain: 10D

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Component #3: protein, PsaB

ProteinName: PsaB / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 82.107852 kDa
SourceSpecies: Red alga (eukaryote) / Strain: 10D

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Component #4: protein, PsaC

ProteinName: PsaC / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.822272 kDa
SourceSpecies: Red alga (eukaryote) / Strain: 10D

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Component #5: protein, PsaD

ProteinName: PsaD / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.698932 kDa
SourceSpecies: Red alga (eukaryote) / Strain: 10D

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Component #6: protein, PsaE

ProteinName: PsaE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.545162 kDa
SourceSpecies: Red alga (eukaryote) / Strain: 10D

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Component #7: protein, PsaF

ProteinName: PsaF / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.239318 kDa
SourceSpecies: Red alga (eukaryote) / Strain: 10D

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Component #8: protein, PsaI

ProteinName: PsaI / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 3.408184 kDa
SourceSpecies: Red alga (eukaryote) / Strain: 10D

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Component #9: protein, PsaJ

ProteinName: PsaJ / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.410245 kDa
SourceSpecies: Red alga (eukaryote) / Strain: 10D

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Component #10: protein, PsaK

ProteinName: PsaKPosek / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.295657 kDa
SourceSpecies: Red alga (eukaryote) / Strain: 10D

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Component #11: protein, PsaL

ProteinName: PsaL / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.157522 kDa
SourceSpecies: Red alga (eukaryote) / Strain: 10D

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Component #12: protein, PsaM

ProteinName: PsaMPalm Springs Air Museum / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 3.139878 kDa
SourceSpecies: Red alga (eukaryote) / Strain: 10D

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Component #13: protein, PsaO

ProteinName: PsaO / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.744471 kDa
SourceSpecies: Red alga (eukaryote) / Strain: 10D

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Component #14: protein, Lhcr1

ProteinName: Lhcr1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 19.808818 kDa
SourceSpecies: Red alga (eukaryote) / Strain: 10D

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Component #15: protein, Lhcr2

ProteinName: Lhcr2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 21.960398 kDa
SourceSpecies: Red alga (eukaryote) / Strain: 10D

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Component #16: protein, Lhcr3

ProteinName: Lhcr3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.458535 kDa
SourceSpecies: Red alga (eukaryote) / Strain: 10D

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Component #17: ligand, CHLOROPHYLL A ISOMER

LigandName: CHLOROPHYLL A ISOMER / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.893489 kDa

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Component #18: ligand, CHLOROPHYLL A

LigandName: CHLOROPHYLL A / Number of Copies: 157 / Recombinant expression: No
MassTheoretical: 0.893489 kDa

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Component #19: ligand, PHYLLOQUINONE

LigandName: PHYLLOQUINONEPhytomenadione / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.450696 kDa

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

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

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Component #21: ligand, BETA-CAROTENE

LigandName: BETA-CAROTENE / Number of Copies: 21 / Recombinant expression: No
MassTheoretical: 0.536873 kDa

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Component #22: ligand, IRON/SULFUR CLUSTER

LigandName: IRON/SULFUR CLUSTERIron–sulfur cluster / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.35164 kDa

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Component #23: ligand, BETA-D-GLUCOSE

LigandName: BETA-D-GLUCOSEGlucose / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

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Component #24: ligand, DIGALACTOSYL DIACYL GLYCEROL (DGDG)

LigandName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.949299 kDa

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Component #25: ligand, (2S)-2,3-dihydroxypropyl octadecanoate

LigandName: (2S)-2,3-dihydroxypropyl octadecanoate / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.358556 kDa

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Component #26: ligand, (1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hy...

LigandName: (1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol
Number of Copies: 25 / Recombinant expression: No
MassTheoretical: 0.568871 kDa

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Component #27: ligand, 1-DODECANOL

LigandName: 1-DODECANOL / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.186334 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 3 mg/ml / pH: 7.4
VitrificationCryogen name: NITROGEN / 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: 2.17 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 124279
3D reconstructionSoftware: RELION / Resolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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