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- EMDB-30935: LHCII-2 in the state transition supercomplex PSI-LHCI-LHCII from ... -

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Basic information

Entry
Database: EMDB / ID: EMD-30935
TitleLHCII-2 in the state transition supercomplex PSI-LHCI-LHCII from the double phosphatase mutant pph1;pbcp of Chlamydomonas reinhardti.
Map dataLocal refined map of LHCII-2 in the PSI-LHCI-LHCII supercomplex from pph1;pbcp mutant of Chlamydomonas reinhardtii
Sample
  • Complex: LHCII-2 in the state transition complex PSI-LHCI-LHCII from pph1;pbcp mutant of Chlamydomonas reinhardtii
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
  • Ligand: CHLOROPHYLL B
  • Ligand: CHLOROPHYLL A
  • Ligand: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: (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
  • Ligand: (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
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
Function / homology
Function and homology information


photosynthesis, light harvesting in photosystem I / photosystem I / photosystem II / chloroplast thylakoid membrane / chlorophyll binding / response to light stimulus
Similarity search - Function
Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein
Similarity search - Domain/homology
Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant) / Chlamydomonas smithii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsPan XW / Li AJ / Liu ZF / Li M
Funding support China, Japan, 8 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2017YFA0503702 China
Chinese Academy of SciencesXDB27020106 China
Chinese Academy of SciencesXDB37020101 China
National Natural Science Foundation of China (NSFC)31925024 China
National Natural Science Foundation of China (NSFC)31930064 China
Chinese Academy of SciencesZDBS-LY-SM003 China
Japan Society for the Promotion of Science (JSPS)16H06553 Japan
Japan Society for the Promotion of Science (JSPS)JP15H05599 Japan
CitationJournal: Nat Plants / Year: 2021
Title: Structural basis of LhcbM5-mediated state transitions in green algae.
Authors: Xiaowei Pan / Ryutaro Tokutsu / Anjie Li / Kenji Takizawa / Chihong Song / Kazuyoshi Murata / Tomohito Yamasaki / Zhenfeng Liu / Jun Minagawa / Mei Li /
Abstract: In green algae and plants, state transitions serve as a short-term light-acclimation process in the regulation of the light-harvesting capacity of photosystems I and II (PSI and PSII, respectively). ...In green algae and plants, state transitions serve as a short-term light-acclimation process in the regulation of the light-harvesting capacity of photosystems I and II (PSI and PSII, respectively). During the process, a portion of light-harvesting complex II (LHCII) is phosphorylated, dissociated from PSII and binds with PSI to form the supercomplex PSI-LHCI-LHCII. Here, we report high-resolution structures of PSI-LHCI-LHCII from Chlamydomonas reinhardtii, revealing the mechanism of assembly between the PSI-LHCI complex and two phosphorylated LHCII trimers containing all four types of LhcbM protein. Two specific LhcbM isoforms, namely LhcbM1 and LhcbM5, directly interact with the PSI core through their phosphorylated amino terminal regions. Furthermore, biochemical and functional studies on mutant strains lacking either LhcbM1 or LhcbM5 indicate that only LhcbM5 is indispensable in supercomplex formation. The results unravel the specific interactions and potential excitation energy transfer routes between green algal PSI and two phosphorylated LHCIIs.
History
DepositionJan 28, 2021-
Header (metadata) releaseJun 30, 2021-
Map releaseJun 30, 2021-
UpdateSep 1, 2021-
Current statusSep 1, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7e0k
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7e0k
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30935.png

Downloads & links

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Map

FileDownload / File: emd_30935.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal refined map of LHCII-2 in the PSI-LHCI-LHCII supercomplex from pph1;pbcp mutant of Chlamydomonas reinhardtii
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 480 pix.
= 480. Å		1 Å/pix.
x 480 pix.
= 480. Å		1 Å/pix.
x 480 pix.
= 480. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.09340475 - 0.17072734
Average (Standard dev.)1.9861456e-05 (±0.0015114322)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 480.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z480.000480.000480.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.0930.1710.000

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Supplemental data

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Sample components

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Entire : LHCII-2 in the state transition complex PSI-LHCI-LHCII from pph1;...

EntireName: LHCII-2 in the state transition complex PSI-LHCI-LHCII from pph1;pbcp mutant of Chlamydomonas reinhardtii
Components
  • Complex: LHCII-2 in the state transition complex PSI-LHCI-LHCII from pph1;pbcp mutant of Chlamydomonas reinhardtii
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
  • Ligand: CHLOROPHYLL B
  • Ligand: CHLOROPHYLL A
  • Ligand: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: (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
  • Ligand: (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
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

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Supramolecule #1: LHCII-2 in the state transition complex PSI-LHCI-LHCII from pph1;...

SupramoleculeName: LHCII-2 in the state transition complex PSI-LHCI-LHCII from pph1;pbcp mutant of Chlamydomonas reinhardtii
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Chlamydomonas reinhardtii (plant)

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Macromolecule #1: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 27.405008 KDa
SequenceString: MAFALSFSRK ALQVSAKATG KKGTGKTAAK QAPASSGIEF YGPNRAKWLG PYSENATPAY LTGEFPGDYG WDTAGLSADP ETFKRYREL ELIHARWAML GALGCITPEL LAKSGTQFGE AVWFKAGAQI FSEGGLDYLG NPSLVHAQNI VATLAVQVIL M GLVEGYRV ...String:
MAFALSFSRK ALQVSAKATG KKGTGKTAAK QAPASSGIEF YGPNRAKWLG PYSENATPAY LTGEFPGDYG WDTAGLSADP ETFKRYREL ELIHARWAML GALGCITPEL LAKSGTQFGE AVWFKAGAQI FSEGGLDYLG NPSLVHAQNI VATLAVQVIL M GLVEGYRV NGGPAGEGLD PLYPGESFDP LGLADDPDTF AELKVKEIKN GRLAMFSMFG FFVQAIVTGK GPIQNLDDHL SN PTVNNAF AFATKFTPSA

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Macromolecule #2: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 28.796824 KDa
SequenceString: MMLSRTVVNV QAKLTKKGGA PKKAAPASAQ KK(TPO)IREKAGW WSNGGNEKLS AFYGPDRGLW LGPLSGTTPA YLTGEF PGD YGWDSAGLSA DPETFKRYRE LELIHARWAM LGALGCITPE LLAKNGTPIV EPVWFKAGAQ IFAEGGLDYL GNPGLVH AQ SILATLAVQV ...String:
MMLSRTVVNV QAKLTKKGGA PKKAAPASAQ KK(TPO)IREKAGW WSNGGNEKLS AFYGPDRGLW LGPLSGTTPA YLTGEF PGD YGWDSAGLSA DPETFKRYRE LELIHARWAM LGALGCITPE LLAKNGTPIV EPVWFKAGAQ IFAEGGLDYL GNPGLVH AQ SILATLAVQV ILMGAIEGYR VNGGPAGEGL DKLHPGGQFF DPLGLAEDPD AFAELKVKEI KNGRLAMFSM FGFFVQAI V TGKGPLANLD EHLASPFTSN AFTYAQKFTP Q

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Macromolecule #3: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 26.67535 KDa
SequenceString: MAAIMKSAVR SSVRPTVSGR SARVVPRAAI EWYGPDRPKF LGPFSEGDTP AYLTGEFPGD YGWDTAGLSA DPETFKRYRE LELIHARWA MLGALGCITP ELLAKNGIPF GEAVWFKAGA QIFAEGGLNY LGNENLIHAQ SIIATLAFQV VVMGLAEAYR A NGGPLGEG ...String:
MAAIMKSAVR SSVRPTVSGR SARVVPRAAI EWYGPDRPKF LGPFSEGDTP AYLTGEFPGD YGWDTAGLSA DPETFKRYRE LELIHARWA MLGALGCITP ELLAKNGIPF GEAVWFKAGA QIFAEGGLNY LGNENLIHAQ SIIATLAFQV VVMGLAEAYR A NGGPLGEG LDPLHPGGAF DPLGLADDPD TFAELKVKEI KNGRLAMFSM FGFFVQAIVT GKGPIQNLDD HLANPTAVNA FA YATKFTP SA

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Macromolecule #4: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 4 / Number of copies: 18 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B

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Macromolecule #5: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 5 / Number of copies: 24 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #6: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

MacromoleculeName: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
type: ligand / ID: 6 / Number of copies: 6 / Formula: LUT
Molecular weightTheoretical: 568.871 Da
Chemical component information

ChemComp-LUT:
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

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Macromolecule #7: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...

MacromoleculeName: (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
type: ligand / ID: 7 / Number of copies: 3 / Formula: XAT
Molecular weightTheoretical: 600.87 Da
Chemical component information

ChemComp-XAT:
(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

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Macromolecule #8: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY...

MacromoleculeName: (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
type: ligand / ID: 8 / Number of copies: 3 / Formula: NEX
Molecular weightTheoretical: 600.87 Da
Chemical component information

ChemComp-NEX:
(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

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Macromolecule #9: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 9 / Number of copies: 3 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

ChemComp-LHG:
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / phospholipid*YM

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Macromolecule #10: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 10 / Number of copies: 1 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

ChemComp-LMG:
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.5625 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 56601
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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