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- EMDB-6744: Structure of M-LHCII and CP24 complexes in the unstacked C2S2M2-t... -

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Basic information

Entry
Database: EMDB / ID: EMD-6744
TitleStructure of M-LHCII and CP24 complexes in the unstacked C2S2M2-type PSII-LHCII supercomplex from Pisum sativum
Map dataNone
Sample
  • Complex: M-LHCII and CP24 complexes in the unstacked C2S2M2-type PSII-LHCII supercomplex from Pisum sativum
    • Protein or peptide: Chlorophyll a-b binding protein 8, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Light harvesting chlorophyll a/b-binding protein Lhcb6, CP24
  • 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: BETA-CAROTENE
KeywordsPhotosystem II / M-LHCII and CP24 complexes / PSII-LHCII / C2S2M2 supercomplex / MEMBRANE PROTEIN
Function / homology
Function and homology information


photosynthesis, light harvesting / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / metal ion binding
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 8, chloroplastic / Chlorophyll a-b binding protein, chloroplastic
Similarity search - Component
Biological speciesPisum sativum (garden pea)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsSu XD / Ma J / Wei XP / Cao P / Zhu DJ / Chang WR / Liu ZF / Zhang XZ / Li M
Funding support China, 4 items
OrganizationGrant numberCountry
The Strategic Priority Research Program of CASXDB08020302 China
The Key Research Program of Frontier Sciences of CASQYZDB-SSW-SMC005 China
National 973 project grant2011CBA00900 China
National Natural Science Foundation of China31570724 and 31270793 China
CitationJournal: Science / Year: 2017
Title: Structure and assembly mechanism of plant CSM-type PSII-LHCII supercomplex.
Authors: Xiaodong Su / Jun Ma / Xuepeng Wei / Peng Cao / Dongjie Zhu / Wenrui Chang / Zhenfeng Liu / Xinzheng Zhang / Mei Li /
Abstract: In plants, the photosynthetic machinery photosystem II (PSII) consists of a core complex associated with variable numbers of light-harvesting complexes II (LHCIIs). The supercomplex, comprising a ...In plants, the photosynthetic machinery photosystem II (PSII) consists of a core complex associated with variable numbers of light-harvesting complexes II (LHCIIs). The supercomplex, comprising a dimeric core and two strongly bound and two moderately bound LHCIIs (CSM), is the dominant form in plants acclimated to limited light. Here we report cryo-electron microscopy structures of two forms of CSM (termed stacked and unstacked) from at 2.7- and 3.2-angstrom resolution, respectively. In each CSM, the moderately bound LHCII assembles specifically with a peripheral antenna complex CP24-CP29 heterodimer and the strongly bound LHCII, to establish a pigment network that facilitates light harvesting at the periphery and energy transfer into the core. The high mobility of peripheral antennae, including the moderately bound LHCII and CP24, provides insights into functional regulation of plant PSII.
History
DepositionMay 23, 2017-
Header (metadata) releaseSep 27, 2017-
Map releaseSep 27, 2017-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.028
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5xno
  • Surface level: 0.028
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6744.png

Downloads & links

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Map

FileDownload / File: emd_6744.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 150 pix.
= 156. Å		1.04 Å/pix.
x 150 pix.
= 156. Å		1.04 Å/pix.
x 150 pix.
= 156. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.028 / Movie #1: 0.028
Minimum - Maximum-0.039222088 - 0.0877881
Average (Standard dev.)0.00087074627 (±0.0068345955)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-75-75-75
Dimensions150150150
Spacing150150150
CellA=B=C: 156.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z150150150
origin x/y/z0.0000.0000.000
length x/y/z156.000156.000156.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-75-75-75
NC/NR/NS150150150
D min/max/mean-0.0390.0880.001

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Supplemental data

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Sample components

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Entire : M-LHCII and CP24 complexes in the unstacked C2S2M2-type PSII-LHCI...

EntireName: M-LHCII and CP24 complexes in the unstacked C2S2M2-type PSII-LHCII supercomplex from Pisum sativum
Components
  • Complex: M-LHCII and CP24 complexes in the unstacked C2S2M2-type PSII-LHCII supercomplex from Pisum sativum
    • Protein or peptide: Chlorophyll a-b binding protein 8, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Light harvesting chlorophyll a/b-binding protein Lhcb6, CP24
  • 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: BETA-CAROTENE

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Supramolecule #1: M-LHCII and CP24 complexes in the unstacked C2S2M2-type PSII-LHCI...

SupramoleculeName: M-LHCII and CP24 complexes in the unstacked C2S2M2-type PSII-LHCII supercomplex from Pisum sativum
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Pisum sativum (garden pea)

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Macromolecule #1: Chlorophyll a-b binding protein 8, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein 8, chloroplastic / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 24.952113 KDa
SequenceString: RKSATTKKVA SSGSPWYGPD RVKYLGPFSG ESPSYLTGEF PGDYGWDTAG LSADPETFSK NRELEVIHSR WAMLGALGCV FPELLSRNG VKFGEAVWFK AGSQIFSEGG LDYLGNPSLV HAQSILAIWA TQVILMGAVE GYRIAGGPLG EVVDPLYPGG S FDPLGLAD ...String:
RKSATTKKVA SSGSPWYGPD RVKYLGPFSG ESPSYLTGEF PGDYGWDTAG LSADPETFSK NRELEVIHSR WAMLGALGCV FPELLSRNG VKFGEAVWFK AGSQIFSEGG LDYLGNPSLV HAQSILAIWA TQVILMGAVE GYRIAGGPLG EVVDPLYPGG S FDPLGLAD DPEAFAELKV KELKNGRLAM FSMFGFFVQA IVTGKGPLEN LADHLSDPVN NNAWSYATNF VPGK

UniProtKB: Chlorophyll a-b binding protein 8, chloroplastic

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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: Pisum sativum (garden pea)
Molecular weightTheoretical: 26.54524 KDa
SequenceString: RKSANPLRDV VAMGTSKFTM GNDLWYGPDR VKYLGPFSAQ TPSYLTGEFP GDYGWDTAGL SADPEAFAKN RALEVIHGRW AMLGALGCI TPEVLQKWVR VDFKEPVWFK AGSQIFSEGG LDYLGNPNLV HAQSILAVLG FQIVLMGLVE GFRINGLPDV G EGNDLYPG ...String:
RKSANPLRDV VAMGTSKFTM GNDLWYGPDR VKYLGPFSAQ TPSYLTGEFP GDYGWDTAGL SADPEAFAKN RALEVIHGRW AMLGALGCI TPEVLQKWVR VDFKEPVWFK AGSQIFSEGG LDYLGNPNLV HAQSILAVLG FQIVLMGLVE GFRINGLPDV G EGNDLYPG GQYFDPLGLA DDPVTFAELK VKEIKNGRLA MFSMFGFFVQ AIVTGKGPLE NLLDHLDNPV ANNAWVYATK FV PGA

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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Macromolecule #3: Light harvesting chlorophyll a/b-binding protein Lhcb6, CP24

MacromoleculeName: Light harvesting chlorophyll a/b-binding protein Lhcb6, CP24
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 22.858957 KDa
SequenceString: AASAPKKSWI PGVSFGGNLV DPEWLDGSLP GDFGFDPLGL GKDPAFLKWY REAELIHGRW AMAAVLGIFV GQAWSGVPWF EAGADPNAI APFSFGTLLG TQLILMGWVE SKRWVDFFNP DSQSVEWATP WSKTAENFVN STGEQGYPGG KFFDPLSLAG T IENGVYIP ...String:
AASAPKKSWI PGVSFGGNLV DPEWLDGSLP GDFGFDPLGL GKDPAFLKWY REAELIHGRW AMAAVLGIFV GQAWSGVPWF EAGADPNAI APFSFGTLLG TQLILMGWVE SKRWVDFFNP DSQSVEWATP WSKTAENFVN STGEQGYPGG KFFDPLSLAG T IENGVYIP DTDKLERLKL AEIKHARLAM LAMLIFYFEA GQGKTPLGAL GL

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Macromolecule #4: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 4 / Number of copies: 23 / 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: 30 / 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: 7 / 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: 4 / 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: 4 / 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: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 10 / Number of copies: 1 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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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

Concentration3.0 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 50237
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-5xno:
Structure of M-LHCII and CP24 complexes in the unstacked C2S2M2-type PSII-LHCII supercomplex from Pisum sativum

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