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- EMDB-54697: Chlorophyll synthase in complex with the LHC-like protein HliD, G... -

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Basic information

Entry
Database: EMDB / ID: EMD-54697
TitleChlorophyll synthase in complex with the LHC-like protein HliD, GGPP-bound state
Map dataChlG-HliD dimer GGPP-bound half-map B local refinement
Sample
  • Complex: Chlorophyll synthase ChlG in complex with the LHC-like protein HliD, GGPP-bound state
    • Protein or peptide: High light-inducible protein HliD
    • Protein or peptide: Chlorophyll a synthase
  • Ligand: CHLOROPHYLL A
  • Ligand: Zeaxanthin
  • Ligand: GERANYLGERANYL DIPHOSPHATE
  • Ligand: (2~{S},3~{R},4~{R},5~{R},6~{S})-2-[(3~{R},4~{E},6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},24~{E})-2,6,10,14,19,23-hexamethyl-2-oxidanyl-25-[(4~{S})-2,2,6-trimethyl-4-oxidanyl-cyclohexyl]pentacosa-4,6,8,10,12,14,16,18,20,22,24-undecaen-3-yl]oxy-6-methyl-oxane-3,4,5-triol
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE
Keywordschlorophyll biosynthesis / complex / chlorophyll synthase / light harvesting / high light-inducible protein / prenyltransferase / transmembrane protein / PHOTOSYNTHESIS
Function / homology
Function and homology information


chlorophyll synthetase activity / energy quenching / photoprotection / vitamin K biosynthetic process / pigment binding / chlorophyll biosynthetic process / prenyltransferase activity / menaquinone biosynthetic process / ubiquinone biosynthetic process / photosystem II ...chlorophyll synthetase activity / energy quenching / photoprotection / vitamin K biosynthetic process / pigment binding / chlorophyll biosynthetic process / prenyltransferase activity / menaquinone biosynthetic process / ubiquinone biosynthetic process / photosystem II / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthesis / membrane
Similarity search - Function
Bacteriochlorophyll/chlorophyll synthetase / Chlorophyll synthase, ChlG / : / UbiA prenyltransferase family / UbiA prenyltransferase superfamily / UbiA prenyltransferase family
Similarity search - Domain/homology
High light-inducible protein HliD / Chlorophyll a synthase
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsShvarev D / Hitchcock A / Sobotka R
Funding support Germany, European Union, Czech Republic, United Kingdom, 7 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SH 1664/2-1 Germany
German Research Foundation (DFG)SFB1557 Germany
German Research Foundation (DFG)INST190/196-1 FUGG Germany
European Research Council (ERC)Synergy Award 854126European Union
Czech Science Foundation22-03092S Czech Republic
Ministry of Education (MoE, Czech Republic)PHOTOMACHINES, CZ.02.01.01/00/22_008/0004624 Czech Republic
Royal SocietyURF-R-241006 United Kingdom
CitationJournal: To Be Published
Title: Structure of chlorophyll synthase in complex with the LHC-like protein HliD
Authors: Shvarev D / Wysocka A / Morey-Burrows F / Panas K / Pazuki A / Kulik N / Proctor M / Pilny J / Hunter N / Hitchcock A / Sobotka R
History
DepositionAug 7, 2025-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54697.png

Downloads & links

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Map

FileDownload / File: emd_54697.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationChlG-HliD dimer GGPP-bound half-map B local refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 512 pix.
= 348.16 Å		0.68 Å/pix.
x 512 pix.
= 348.16 Å		0.68 Å/pix.
x 512 pix.
= 348.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.073113255 - 0.16590013
Average (Standard dev.)0.00007742527 (±0.002994537)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 348.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: ChlG-HliD dimer GGPP-bound half-map B local refinement

Fileemd_54697_half_map_1.map
AnnotationChlG-HliD dimer GGPP-bound half-map B local refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ChlG-HliD dimer GGPP-bound half-map B local refinement

Fileemd_54697_half_map_2.map
AnnotationChlG-HliD dimer GGPP-bound half-map B local refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Chlorophyll synthase ChlG in complex with the LHC-like protein Hl...

EntireName: Chlorophyll synthase ChlG in complex with the LHC-like protein HliD, GGPP-bound state
Components
  • Complex: Chlorophyll synthase ChlG in complex with the LHC-like protein HliD, GGPP-bound state
    • Protein or peptide: High light-inducible protein HliD
    • Protein or peptide: Chlorophyll a synthase
  • Ligand: CHLOROPHYLL A
  • Ligand: Zeaxanthin
  • Ligand: GERANYLGERANYL DIPHOSPHATE
  • Ligand: (2~{S},3~{R},4~{R},5~{R},6~{S})-2-[(3~{R},4~{E},6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},24~{E})-2,6,10,14,19,23-hexamethyl-2-oxidanyl-25-[(4~{S})-2,2,6-trimethyl-4-oxidanyl-cyclohexyl]pentacosa-4,6,8,10,12,14,16,18,20,22,24-undecaen-3-yl]oxy-6-methyl-oxane-3,4,5-triol
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE

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Supramolecule #1: Chlorophyll synthase ChlG in complex with the LHC-like protein Hl...

SupramoleculeName: Chlorophyll synthase ChlG in complex with the LHC-like protein HliD, GGPP-bound state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)

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Macromolecule #1: High light-inducible protein HliD

MacromoleculeName: High light-inducible protein HliD / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 4.592385 KDa
Recombinant expressionOrganism: Synechocystis sp. PCC 6803 (bacteria)
SequenceString:
PKFGFNNYAE KLNGRAAMVG FLLILVIEYF TNQGVLAWLG L

UniProtKB: High light-inducible protein HliD

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Macromolecule #2: Chlorophyll a synthase

MacromoleculeName: Chlorophyll a synthase / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 32.152812 KDa
Recombinant expressionOrganism: Synechocystis sp. PCC 6803 (bacteria)
SequenceString: IWKIRLQLMK PITWIPLIWG VVCGAASSGG YIWSVEDFLK ALTCMLLSGP LMTGYTQTLN DFYDRDIDAI NEPYRPIPSG AISVPQVVT QILILLVAGI GVAYGLDVWA QHDFPIMMVL TLGGAFVAYI YSAPPLKLKQ NGWLGNYALG ASYIALPWWA G HALFGTLN ...String:
IWKIRLQLMK PITWIPLIWG VVCGAASSGG YIWSVEDFLK ALTCMLLSGP LMTGYTQTLN DFYDRDIDAI NEPYRPIPSG AISVPQVVT QILILLVAGI GVAYGLDVWA QHDFPIMMVL TLGGAFVAYI YSAPPLKLKQ NGWLGNYALG ASYIALPWWA G HALFGTLN PTIMVLTLIY SLAGLGIAVV NDFKSVEGDR QLGLKSLPVM FGIGTAAWIC VIMIDVFQAG IAGYLIYVHQ QL YATIVLL LLIPQITFQD MYFLRNPLEN DVKYQASAQP FLVFGMLATG LALGHAG

UniProtKB: Chlorophyll a synthase

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Macromolecule #3: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 3 / Number of copies: 4 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #4: Zeaxanthin

MacromoleculeName: Zeaxanthin / type: ligand / ID: 4 / Number of copies: 2 / Formula: 5X6
Molecular weightTheoretical: 568.871 Da
Chemical component information

ChemComp-K3I:
Zeaxanthin

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Macromolecule #5: GERANYLGERANYL DIPHOSPHATE

MacromoleculeName: GERANYLGERANYL DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: GRG
Molecular weightTheoretical: 450.443 Da
Chemical component information

ChemComp-GRG:
GERANYLGERANYL DIPHOSPHATE

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Macromolecule #6: (2~{S},3~{R},4~{R},5~{R},6~{S})-2-[(3~{R},4~{E},6~{E},8~{E},10~{E...

MacromoleculeName: (2~{S},3~{R},4~{R},5~{R},6~{S})-2-[(3~{R},4~{E},6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},24~{E})-2,6,10,14,19,23-hexamethyl-2-oxidanyl-25-[(4~{S})-2,2,6-trimethyl-4-oxidanyl- ...Name: (2~{S},3~{R},4~{R},5~{R},6~{S})-2-[(3~{R},4~{E},6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},24~{E})-2,6,10,14,19,23-hexamethyl-2-oxidanyl-25-[(4~{S})-2,2,6-trimethyl-4-oxidanyl-cyclohexyl]pentacosa-4,6,8,10,12,14,16,18,20,22,24-undecaen-3-yl]oxy-6-methyl-oxane-3,4,5-triol
type: ligand / ID: 6 / Number of copies: 2 / Formula: A1JR2
Molecular weightTheoretical: 733.028 Da

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Macromolecule #7: Lauryl Maltose Neopentyl Glycol

MacromoleculeName: Lauryl Maltose Neopentyl Glycol / type: ligand / ID: 7 / Number of copies: 2 / Formula: LMN
Molecular weightTheoretical: 1.005188 KDa
Chemical component information

ChemComp-AV0:
Lauryl Maltose Neopentyl Glycol

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Macromolecule #8: (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL...

MacromoleculeName: (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE
type: ligand / ID: 8 / Number of copies: 2 / Formula: MGE
Molecular weightTheoretical: 688.972 Da
Chemical component information

ChemComp-MGE:
(1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE

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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 / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4) / Number images used: 254925
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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