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- EMDB-54701: Chlorophyll synthase in complex with the LHC-like protein HliD, C... -

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Basic information

Entry
Database: EMDB / ID: EMD-54701
TitleChlorophyll synthase in complex with the LHC-like protein HliD, ChlGx1-HliDx2 complex, GGPP sample
Map dataChlG monomer in complex with HliD dimer, GGPP sample
Sample
  • Complex: Chlorophyll synthase ChlG in complex with the LHC-like protein HliD, ChlGx1-HliDx2 complex, GGPP sample
Keywordschlorophyll biosynthesis / complex / chlorophyll synthase / light harvesting / high light-inducible protein / prenyltransferase / transmembrane protein / PHOTOSYNTHESIS
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.1 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_54701.png

Downloads & links

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Map

FileDownload / File: emd_54701.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationChlG monomer in complex with HliD dimer, GGPP sample
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: 0.2
Minimum - Maximum-0.5898593 - 0.83037263
Average (Standard dev.)-0.000040777777 (±0.0089548435)
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 monomer in complex with HliD dimer half-map A, GGPP sample

Fileemd_54701_half_map_1.map
AnnotationChlG monomer in complex with HliD dimer half-map A, GGPP sample
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ChlG monomer in complex with HliD dimer half-map B, GGPP sample

Fileemd_54701_half_map_2.map
AnnotationChlG monomer in complex with HliD dimer half-map B, GGPP sample
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, ChlGx1-HliDx2 complex, GGPP sample
Components
  • Complex: Chlorophyll synthase ChlG in complex with the LHC-like protein HliD, ChlGx1-HliDx2 complex, GGPP sample

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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, ChlGx1-HliDx2 complex, GGPP sample
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)

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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: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4) / Number images used: 164515
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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