[English] 日本語
Yorodumi
- EMDB-6932: Structure of photosystem I supercomplex with light-harvesting com... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 6932
TitleStructure of photosystem I supercomplex with light-harvesting complexes I and II
Map data
SampleSupercomplex of plant PSI-LHCI-LHCII from Zea Mays
  • (Chlorophyll a-b binding protein, ...Light-harvesting complexes of green plants) x 5
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • photosystem I subunit VII
  • (Photosystem I reaction center subunit ...) x 10
  • 16kDa membrane protein
  • Chlorophyll a-b binding protein 1, chloroplastic
  • (ligand) x 13
Function / homologyPhotosystem I, reaction centre subunit XI / Photosystem I protein PsaC / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaD / Photosystem I PsaL, reaction centre subunit XI / Photosystem I PsaH, reaction centre subunit VI / Photosystem I PsaA / Photosystem I PsaB / Photosystem I reaction centre subunit N, chloroplastic / Electron transport accessory-like domain superfamily ...Photosystem I, reaction centre subunit XI / Photosystem I protein PsaC / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaD / Photosystem I PsaL, reaction centre subunit XI / Photosystem I PsaH, reaction centre subunit VI / Photosystem I PsaA / Photosystem I PsaB / Photosystem I reaction centre subunit N, chloroplastic / Electron transport accessory-like domain superfamily / Photosystem I PsaG/PsaK, plant / Photosystem I reaction centre subunit psaK, chloroplastic / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaG, plant / Photosystem I PsaO / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / Photosystem I PsaA/PsaB, conserved site / Chlorophyll A-B binding protein / Photosystem I PsaA/PsaB superfamily / Chlorophyll a/b binding domain superfamily / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I PsaE, reaction centre subunit IV / Chlorophyll A-B binding protein, plant / Photosystem I reaction centre subunit VIII superfamily / Photosystem I reaction centre subunit IV / PsaE / 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. / Photosystem I reaction centre subunit N (PSAN or PSI-N) / Photosystem I reaction centre subunit VI / Photosystem I reaction centre subunit XI / PsaD / Photosystem I reaction centre subunit III / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I reaction centre subunit VIII / Photosystem I psaG / psaK / Photosystem I reaction centre subunit VIII / Chlorophyll A-B binding protein / Photosystem I psaA/psaB protein / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I PsaG/PsaK protein / Photosystem I PsaA/PsaB / Photosystem I PsaJ, reaction centre subunit IX superfamily / photosynthesis, light harvesting in photosystem I / plastoglobule / photosystem I / photosystem I reaction center / photosynthetic electron transport in photosystem I / photosynthesis, light harvesting / photosystem I / plastid / thylakoid / photosystem II / chlorophyll binding / chloroplast envelope / thylakoid membrane / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / 4 iron, 4 sulfur cluster binding / protein-chromophore linkage / electron transfer activity / magnesium ion binding / integral component of membrane / metal ion binding / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit VIII / Chlorophyll a-b binding protein 1, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit VI, chloroplastic / Photosystem I reaction center subunit V / Photosystem I reaction center subunit N / Photosystem I reaction center subunit psaK / Chlorophyll a-b binding protein, chloroplastic / Photosystem I iron-sulfur center / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit XI / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit III / 16kDa membrane protein / Photosystem I reaction center subunit II / Photosystem I reaction center subunit IV A / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit IX
Function and homology information
SourceZea mays (maize) / Maize (maize)
Methodsingle particle reconstruction / cryo EM / 3.3 Å resolution
AuthorsPan XW / Ma J / Su XD / Cao P / Liu ZF / Zhang XZ / Li M
CitationJournal: Science / Year: 2018
Title: Structure of the maize photosystem I supercomplex with light-harvesting complexes I and II.
Authors: Xiaowei Pan / Jun Ma / Xiaodong Su / Peng Cao / Wenrui Chang / Zhenfeng Liu / Xinzheng Zhang / Mei Li
Abstract: Plants regulate photosynthetic light harvesting to maintain balanced energy flux into photosystems I and II (PSI and PSII). Under light conditions favoring PSII excitation, the PSII antenna, ...Plants regulate photosynthetic light harvesting to maintain balanced energy flux into photosystems I and II (PSI and PSII). Under light conditions favoring PSII excitation, the PSII antenna, light-harvesting complex II (LHCII), is phosphorylated and forms a supercomplex with PSI core and the PSI antenna, light-harvesting complex I (LHCI). Both LHCI and LHCII then transfer excitation energy to the PSI core. We report the structure of maize PSI-LHCI-LHCII solved by cryo-electron microscopy, revealing the recognition site between LHCII and PSI. The PSI subunits PsaN and PsaO are observed at the PSI-LHCI interface and the PSI-LHCII interface, respectively. Each subunit relays excitation to PSI core through a pair of chlorophyll molecules, thus revealing previously unseen paths for energy transfer between the antennas and the PSI core.
Validation ReportPDB-ID: 5zji

SummaryFull reportAbout validation report
DateDeposition: Mar 20, 2018 / Header (metadata) release: Jun 20, 2018 / Map release: Jun 20, 2018 / Last update: Jun 20, 2018

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5zji
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_6932.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
1.06 Å/pix.
= 296.8 Å
280 pix
1.06 Å/pix.
= 296.8 Å
280 pix
1.06 Å/pix.
= 296.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour Level:0.05 (by author), 0.05 (movie #1):
Minimum - Maximum-0.11124071 - 0.29227716
Average (Standard dev.)0.0006920389 (0.011263453)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions280280280
Origin-140.0-140.0-140.0
Limit139.0139.0139.0
Spacing280280280
CellA=B=C: 296.8 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z296.800296.800296.800
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-140-140-140
NC/NR/NS280280280
D min/max/mean-0.1110.2920.001

-
Supplemental data

-
Sample components

+
Entire Supercomplex of plant PSI-LHCI-LHCII from Zea Mays

EntireName: Supercomplex of plant PSI-LHCI-LHCII from Zea Mays / Number of components: 34

+
Component #1: protein, Supercomplex of plant PSI-LHCI-LHCII from Zea Mays

ProteinName: Supercomplex of plant PSI-LHCI-LHCII from Zea Mays / Recombinant expression: No
SourceSpecies: Zea mays (maize)

+
Component #2: protein, Chlorophyll a-b binding protein, chloroplastic

ProteinName: Chlorophyll a-b binding protein, chloroplastic / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.335127 kDa
SourceSpecies: Maize (maize)

+
Component #3: protein, Chlorophyll a-b binding protein, chloroplastic

ProteinName: Chlorophyll a-b binding protein, chloroplastic / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.237975 kDa
SourceSpecies: Maize (maize)

+
Component #4: protein, Chlorophyll a-b binding protein, chloroplastic

ProteinName: Chlorophyll a-b binding protein, chloroplastic / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.011234 kDa
SourceSpecies: Maize (maize)

+
Component #5: protein, Chlorophyll a-b binding protein, chloroplastic

ProteinName: Chlorophyll a-b binding protein, chloroplastic / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.406082 kDa
SourceSpecies: Maize (maize)

+
Component #6: protein, Photosystem I P700 chlorophyll a apoprotein A1

ProteinName: Photosystem I P700 chlorophyll a apoprotein A1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 83.193156 kDa
SourceSpecies: Maize (maize)

+
Component #7: protein, Photosystem I P700 chlorophyll a apoprotein A2

ProteinName: Photosystem I P700 chlorophyll a apoprotein A2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 82.648797 kDa
SourceSpecies: maize (maize)

+
Component #8: protein, photosystem I subunit VII

ProteinName: photosystem I subunit VII / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.909345 kDa
SourceSpecies: maize (maize)

+
Component #9: protein, Photosystem I reaction center subunit II

ProteinName: Photosystem I reaction center subunit II / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.603672 kDa
SourceSpecies: Maize (maize)

+
Component #10: protein, Photosystem I reaction center subunit IV A

ProteinName: Photosystem I reaction center subunit IV A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.429237 kDa
SourceSpecies: Maize (maize)

+
Component #11: protein, Photosystem I reaction center subunit III

ProteinName: Photosystem I reaction center subunit III / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.833559 kDa
SourceSpecies: Maize (maize)

+
Component #12: protein, Photosystem I reaction center subunit V

ProteinName: Photosystem I reaction center subunit V / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.329372 kDa
SourceSpecies: Maize (maize)

+
Component #13: protein, Photosystem I reaction center subunit VI, chloroplastic

ProteinName: Photosystem I reaction center subunit VI, chloroplastic
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.948259 kDa
SourceSpecies: Maize (maize)

+
Component #14: protein, Photosystem I reaction center subunit VIII

ProteinName: Photosystem I reaction center subunit VIII / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.029889 kDa
SourceSpecies: Maize (maize)

+
Component #15: protein, Photosystem I reaction center subunit IX

ProteinName: Photosystem I reaction center subunit IX / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.74762 kDa
SourceSpecies: Maize (maize)

+
Component #16: protein, Photosystem I reaction center subunit psaK

ProteinName: Photosystem I reaction center subunit psaK / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.668812 kDa
SourceSpecies: Maize (maize)

+
Component #17: protein, Photosystem I reaction center subunit XI

ProteinName: Photosystem I reaction center subunit XI / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.347809 kDa
SourceSpecies: Maize (maize)

+
Component #18: protein, 16kDa membrane protein

ProteinName: 16kDa membrane protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.381669 kDa
SourceSpecies: Maize (maize)

+
Component #19: protein, Photosystem I reaction center subunit N

ProteinName: Photosystem I reaction center subunit N / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.663827 kDa
SourceSpecies: Maize (maize)

+
Component #20: protein, Chlorophyll a-b binding protein 1, chloroplastic

ProteinName: Chlorophyll a-b binding protein 1, chloroplastic / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 24.879148 kDa
SourceSpecies: Maize (maize)

+
Component #21: protein, Chlorophyll a-b binding protein, chloroplastic

ProteinName: Chlorophyll a-b binding protein, chloroplastic / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.7809 kDa
SourceSpecies: Maize (maize)

+
Component #22: ligand, CHLOROPHYLL B

LigandName: CHLOROPHYLL B / Number of Copies: 30 / Recombinant expression: No
MassTheoretical: 0.907472 kDa

+
Component #23: ligand, CHLOROPHYLL A

LigandName: CHLOROPHYLL A / Number of Copies: 171 / Recombinant expression: No
MassTheoretical: 0.893489 kDa

+
Component #24: ligand, (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-...

LigandName: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
Number of Copies: 11 / Recombinant expression: No
MassTheoretical: 0.568871 kDa

+
Component #25: 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: 7 / Recombinant expression: No
MassTheoretical: 0.60087 kDa

+
Component #26: ligand, BETA-CAROTENE

LigandName: BETA-CAROTENE / Number of Copies: 26 / Recombinant expression: No
MassTheoretical: 0.536873 kDa

+
Component #27: ligand, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

LigandName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 0.72297 kDa

+
Component #28: ligand, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

LigandName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 0.787158 kDa

+
Component #29: ligand, CHLOROPHYLL A ISOMER

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

+
Component #30: ligand, PHYLLOQUINONE

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

+
Component #31: ligand, IRON/SULFUR CLUSTER

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

+
Component #32: ligand, DODECYL-ALPHA-D-MALTOSIDE

LigandName: DODECYL-ALPHA-D-MALTOSIDE / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.510615 kDa

+
Component #33: ligand, DIGALACTOSYL DIACYL GLYCEROL (DGDG)

LigandName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.949299 kDa

+
Component #34: ligand, (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4...

LigandName: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL
Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.60087 kDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

-
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: 5 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 635845
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at EBI / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more