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- EMDB-9670: Structure of PSI-LHCI -

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Basic information

Entry
Database: EMDB / ID: 9670
TitleStructure of PSI-LHCI
Map dataPSI-LHCI
SamplePSI-LHCI
  • PsaA
  • PsaB
  • PsaC
  • PsaD
  • PsaE
  • PsaF
  • PsaG
  • PsaH
  • PsaI
  • PsaJ
  • PsaK
  • PsaL
  • Lhca-a
  • Lhca-c
  • Lhca-d
  • Lhca-b
  • Lhca-g
  • Lhca-h
  • Lhca-i
  • Lhca-j
  • Photosystem I reaction center subunit XII
  • (ligand) x 10
Function / homologyPhotosystem I PsaM, reaction centre / Photosystem I PsaM, reaction centre superfamily / Photosystem I protein M (PsaM) / photosystem I / chloroplast thylakoid membrane / photosynthesis / integral component of membrane / Photosystem I reaction center subunit XII
Function and homology information
SourceBryopsis corticulans (plant) / Spinacia oleracea (spinach) / Green alga (plant)
Methodsingle particle reconstruction / cryo EM / 3.49 Å resolution
AuthorsXiong P / Xiaochun Q
CitationJournal: Nat Plants / Year: 2019
Title: Structure of a green algal photosystem I in complex with a large number of light-harvesting complex I subunits.
Authors: Xiaochun Qin / Xiong Pi / Wenda Wang / Guangye Han / Lixia Zhu / Mingmei Liu / Linpeng Cheng / Jian-Ren Shen / Tingyun Kuang / Sen-Fang Sui
Validation ReportPDB-ID: 6igz

SummaryFull reportAbout validation report
DateDeposition: Sep 27, 2018 / Header (metadata) release: Feb 13, 2019 / Map release: Feb 13, 2019 / Last update: Feb 13, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.034
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.034
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6igz
  • Surface level: 0.034
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9670.map.gz (map file in CCP4 format, 389345 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
460 pix
0.87 Å/pix.
= 401.442 Å
460 pix
0.87 Å/pix.
= 401.442 Å
460 pix
0.87 Å/pix.
= 401.442 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8727 Å
Density
Contour Level:0.034 (by author), 0.034 (movie #1):
Minimum - Maximum-0.060164515 - 0.18709584
Average (Standard dev.)0.0019334673 (0.0052781226)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions460460460
Origin0.00.00.0
Limit459.0459.0459.0
Spacing460460460
CellA=B=C: 401.442 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.87270.87270.8727
M x/y/z460460460
origin x/y/z0.0000.0000.000
length x/y/z401.442401.442401.442
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS460460460
D min/max/mean-0.0600.1870.002

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Supplemental data

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Sample components

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Entire PSI-LHCI

EntireName: PSI-LHCI / Number of components: 32

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Component #1: protein, PSI-LHCI

ProteinName: PSI-LHCI / Recombinant expression: No
SourceSpecies: Bryopsis corticulans (plant)

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Component #2: protein, PsaA

ProteinName: PsaA / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 83.412336 kDa
SourceSpecies: Bryopsis corticulans (plant)

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Component #3: protein, PsaB

ProteinName: PsaB / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 82.164461 kDa
SourceSpecies: Bryopsis corticulans (plant)

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Component #4: protein, PsaC

ProteinName: PsaC / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.880307 kDa
SourceSpecies: Bryopsis corticulans (plant)

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Component #5: protein, PsaD

ProteinName: PsaD / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.733045 kDa
SourceSpecies: Bryopsis corticulans (plant)

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Component #6: protein, PsaE

ProteinName: PsaE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.096458 kDa
SourceSpecies: Bryopsis corticulans (plant)

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Component #7: protein, PsaF

ProteinName: PsaF / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.129158 kDa
SourceSpecies: Bryopsis corticulans (plant)

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Component #8: protein, PsaG

ProteinName: PsaG / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.2266 kDa
SourceSpecies: Spinacia oleracea (spinach)

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Component #9: protein, PsaH

ProteinName: PsaH / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.40036 kDa
SourceSpecies: Bryopsis corticulans (plant)

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Component #10: protein, PsaI

ProteinName: PsaI / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 3.859615 kDa
SourceSpecies: Bryopsis corticulans (plant)

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Component #11: protein, PsaJ

ProteinName: PsaJ / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.744679 kDa
SourceSpecies: Bryopsis corticulans (plant)

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Component #12: protein, PsaK

ProteinName: PsaK / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.487672 kDa
SourceSpecies: Bryopsis corticulans (plant)

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Component #13: protein, PsaL

ProteinName: PsaL / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.338602 kDa
SourceSpecies: Bryopsis corticulans (plant)

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Component #14: protein, Lhca-a

ProteinName: Lhca-a / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 24.458012 kDa
SourceSpecies: Bryopsis corticulans (plant)

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Component #15: protein, Lhca-c

ProteinName: Lhca-c / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.808264 kDa
SourceSpecies: Bryopsis corticulans (plant)

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Component #16: protein, Lhca-d

ProteinName: Lhca-d / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.409689 kDa
SourceSpecies: Bryopsis corticulans (plant)

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Component #17: protein, Lhca-b

ProteinName: Lhca-b / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 26.575912 kDa
SourceSpecies: Bryopsis corticulans (plant)

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Component #18: protein, Lhca-g

ProteinName: Lhca-g / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.30068 kDa
SourceSpecies: Bryopsis corticulans (plant)

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Component #19: protein, Lhca-h

ProteinName: Lhca-h / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.621643 kDa
SourceSpecies: Bryopsis corticulans (plant)

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Component #20: protein, Lhca-i

ProteinName: Lhca-i / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.152645 kDa
SourceSpecies: Bryopsis corticulans (plant)

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Component #21: protein, Lhca-j

ProteinName: Lhca-j / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.910092 kDa
SourceSpecies: Bryopsis corticulans (plant)

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Component #22: protein, Photosystem I reaction center subunit XII

ProteinName: Photosystem I reaction center subunit XII / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 3.505114 kDa
SourceSpecies: Green alga (plant)

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Component #23: ligand, CHLOROPHYLL A

LigandName: CHLOROPHYLL A / Number of Copies: 218 / Recombinant expression: No
MassTheoretical: 0.893489 kDa

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Component #24: ligand, PHYLLOQUINONE

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

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Component #25: ligand, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

LigandName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Number of Copies: 11 / Recombinant expression: No
MassTheoretical: 0.72297 kDa

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Component #26: ligand, (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihy...

LigandName: (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene
Number of Copies: 34 / Recombinant expression: No
MassTheoretical: 0.536873 kDa

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Component #27: ligand, HEPTYL 1-THIOHEXOPYRANOSIDE

LigandName: HEPTYL 1-THIOHEXOPYRANOSIDE / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.294408 kDa

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Component #28: 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 #29: 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 #30: ligand, CHLOROPHYLL B

LigandName: CHLOROPHYLL B / Number of Copies: 26 / Recombinant expression: No
MassTheoretical: 0.907472 kDa

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Component #31: ligand, (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRA...

LigandName: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
Number of Copies: 20 / Recombinant expression: No
MassTheoretical: 0.60087 kDa

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Component #32: 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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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 3 mg/ml / pH: 7.8
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: 1.852 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 / Number of projections: 59525
3D reconstructionResolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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