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- EMDB-32588: The Cryo-EM structure of siphonaxanthin chlorophyll a/b type ligh... -

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Basic information

Entry
Database: EMDB / ID: EMD-32588
TitleThe Cryo-EM structure of siphonaxanthin chlorophyll a/b type light-harvesting complex II
Map data
Sample
  • Complex: siphonaxanthin chlorophyll a/b-type light-harvesting complex II
    • Protein or peptide: siphonaxanthin chlorophyll a/b binding light-harvesting complex II
  • Ligand: CHLOROPHYLL B
  • Ligand: CHLOROPHYLL A
  • 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: Siphonein
  • Ligand: Siphonaxanthin
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: water
Biological speciesCodium fragile (dead man's fingers)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsSeki S / Nakaniwa T / Castro-Hartmann P / Sader K / Kawamoto A / Tanaka H / Qian P / Kurisu G / Fujii R
Funding support1 items
OrganizationGrant numberCountry
Other privateSasakura Enviro-Science Foundation 2020
CitationJournal: BBA Adv / Year: 2022
Title: Structural insights into blue-green light utilization by marine green algal light harvesting complex II at 2.78 Å.
Authors: Soichiro Seki / Tetsuko Nakaniwa / Pablo Castro-Hartmann / Kasim Sader / Akihiro Kawamoto / Hideaki Tanaka / Pu Qian / Genji Kurisu / Ritsuko Fujii /
Abstract: Light-harvesting complex II (LHCII) present in plants and green algae absorbs solar energy to promote photochemical reactions. A marine green macroalga, , exhibits the unique characteristic of ...Light-harvesting complex II (LHCII) present in plants and green algae absorbs solar energy to promote photochemical reactions. A marine green macroalga, , exhibits the unique characteristic of absorbing blue-green light from the sun during photochemical reactions while being underwater owing to the presence of pigment-altered LHCII called siphonaxanthin-chlorophyll binding protein (SCP). In this study, we determined the structure of SCP at a resolution of 2.78 Å using cryogenic electron microscopy. SCP has a trimeric structure, wherein each monomer containing two lutein and two chlorophyll molecules in the plant-type LHCII are replaced by siphonaxanthin and its ester and two chlorophyll molecules, respectively. Siphonaxanthin occupies the binding site in SCP having a polarity in the trimeric inner core, and exhibits a distorted conjugated chain comprising a carbonyl group hydrogen bonded to a cysteine residue of apoprotein. These features suggest that the siphonaxanthin molecule is responsible for the characteristic green absorption of SCP. The replaced chlorophyll molecules extend the region of the stromal side chlorophyll cluster, spanning two adjacent monomers.
History
DepositionJan 13, 2022-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateMay 3, 2023-
Current statusMay 3, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32588.png

Downloads & links

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Map

FileDownload / File: emd_32588.map.gz / Format: CCP4 / Size: 134.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.662 Å
Density
Contour LevelBy AUTHOR: 0.0528
Minimum - Maximum-0.19495443 - 0.3746698
Average (Standard dev.)0.0005438575 (±0.008236589)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions328328328
Spacing328328328
CellA=B=C: 217.136 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : siphonaxanthin chlorophyll a/b-type light-harvesting complex II

EntireName: siphonaxanthin chlorophyll a/b-type light-harvesting complex II
Components
  • Complex: siphonaxanthin chlorophyll a/b-type light-harvesting complex II
    • Protein or peptide: siphonaxanthin chlorophyll a/b binding light-harvesting complex II
  • Ligand: CHLOROPHYLL B
  • Ligand: CHLOROPHYLL A
  • 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: Siphonein
  • Ligand: Siphonaxanthin
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: water

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Supramolecule #1: siphonaxanthin chlorophyll a/b-type light-harvesting complex II

SupramoleculeName: siphonaxanthin chlorophyll a/b-type light-harvesting complex II
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Codium fragile (dead man's fingers)
Molecular weightTheoretical: 119 KDa

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Macromolecule #1: siphonaxanthin chlorophyll a/b binding light-harvesting complex II

MacromoleculeName: siphonaxanthin chlorophyll a/b binding light-harvesting complex II
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Codium fragile (dead man's fingers) / Strain: KU-0654
Molecular weightTheoretical: 24.190102 KDa
SequenceString: IEFYGPDRAL WLGPYSEGAV PSYLTGEFPG DYGWDSAGLS ADPETFAANR ELELIHARWA MLGVVGCLTP EALEKYSGVE FGEATWFKA GSQIFAEGGI DYLGNPSLVH AQSILAIVWS QVVLMGLAEG YRVSGGPLGE ATDPLYPGEA FDPFGFADDP E TFSELKIK ...String:
IEFYGPDRAL WLGPYSEGAV PSYLTGEFPG DYGWDSAGLS ADPETFAANR ELELIHARWA MLGVVGCLTP EALEKYSGVE FGEATWFKA GSQIFAEGGI DYLGNPSLVH AQSILAIVWS QVVLMGLAEG YRVSGGPLGE ATDPLYPGEA FDPFGFADDP E TFSELKIK EIKNGRLAMF AMFGFFVQAL QTGKGPVECW ASHIEDPVAN NGFVYATKFF GAQIF

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Macromolecule #2: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 2 / Number of copies: 24 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B / Chlorophyll b

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Macromolecule #3: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 3 / Number of copies: 15 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A / Chlorophyll a

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Macromolecule #4: (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: 4 / 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 #5: Siphonein

MacromoleculeName: Siphonein / type: ligand / ID: 5 / Number of copies: 3 / Formula: 0UR
Molecular weightTheoretical: 781.157 Da
Chemical component information

ChemComp-0UR:
Siphonein

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Macromolecule #6: Siphonaxanthin

MacromoleculeName: Siphonaxanthin / type: ligand / ID: 6 / Number of copies: 3 / Formula: 0IE
Molecular weightTheoretical: 600.87 Da
Chemical component information

ChemComp-0IE:
Siphonaxanthin

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Macromolecule #7: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 7 / Number of copies: 3 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 54 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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

Concentration10 mg/mL
BufferpH: 8.2
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3trishydroxylmethylaminomethane
0.03 %C24H46O11n-Dodecyl-beta-D-maltoside
GridMaterial: COPPER
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 120000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 2 / Number real images: 8935 / Average electron dose: 50.75 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2336076
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 10 / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 250633
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1rwt


Chain - Chain ID: B / Chain - Residue range: 14-231
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7wlm:
The Cryo-EM structure of siphonaxanthin chlorophyll a/b type light-harvesting complex II

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