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- PDB-9sau: Chlorophyll synthase in complex with the LHC-like protein HliD, G... -

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Basic information

Entry
Database: PDB / ID: 9sau
TitleChlorophyll synthase in complex with the LHC-like protein HliD, GGPP-bound state
Components
  • Chlorophyll a synthase
  • High light-inducible protein HliD
KeywordsPHOTOSYNTHESIS / chlorophyll biosynthesis / complex / chlorophyll synthase / light harvesting / high light-inducible protein / prenyltransferase / transmembrane protein
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
: / : / CHLOROPHYLL A / GERANYLGERANYL DIPHOSPHATE / Chem-MGE / High light-inducible protein HliD / Chlorophyll a synthase
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsShvarev, D. / Hitchcock, A. / Sobotka, R.
Funding support Germany, European Union, Czech Republic, United Kingdom, 7items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: High light-inducible protein HliD
B: High light-inducible protein HliD
C: Chlorophyll a synthase
D: Chlorophyll a synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,95718
Polymers73,4904
Non-polymers10,46714
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein/peptide / Protein , 2 types, 4 molecules ABCD

#1: Protein/peptide High light-inducible protein HliD / Small Cab-like protein ScpE


Mass: 4592.385 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: hliD, hliA, scpE, ssr1789 / Production host: Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P72932
#2: Protein Chlorophyll a synthase


Mass: 32152.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: chlG / Production host: Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: Q55145

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Non-polymers , 6 types, 14 molecules

#3: Chemical
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-5X6 / Zeaxanthin / (1R)-4-[(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4R)-4-hydroxy-2,6,6-trimethylcyclohexen-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaenyl]-3,5,5-trimethylcyclohex-3-en-1-ol


Mass: 568.871 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H56O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GRG / GERANYLGERANYL DIPHOSPHATE


Mass: 450.443 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H36O7P2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-A1JR2 / (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


Mass: 733.028 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C46H68O7 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-LMN / Lauryl Maltose Neopentyl Glycol / 2,2-didecylpropane-1,3-bis-b-D-maltopyranoside


Mass: 1005.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C47H88O22 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
#8: Chemical ChemComp-MGE / (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE / MONOGALACTOSYL-DIACYLGLYCEROL


Mass: 688.972 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C38H72O10 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Chlorophyll synthase ChlG in complex with the LHC-like protein HliD, GGPP-bound state
Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4particle selection
2PHENIX1.21.2_5419:model refinement
13cryoSPARCv43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 254925 / Symmetry type: POINT
RefinementHighest resolution: 3.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0046114
ELECTRON MICROSCOPYf_angle_d1.2088386
ELECTRON MICROSCOPYf_dihedral_angle_d14.4831330
ELECTRON MICROSCOPYf_chiral_restr0.042928
ELECTRON MICROSCOPYf_plane_restr0.0061072

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