9SAU | pdb_00009sau

Chlorophyll synthase in complex with the LHC-like protein HliD, GGPP-bound state

PDB DOI: https://doi.org/10.2210/pdb9SAU/pdb
EM Map EMD-54697: EMDB EMDataResource

Classification: PHOTOSYNTHESIS
Organism(s): Synechocystis sp. PCC 6803
Expression System: Synechocystis sp. PCC 6803
Mutation(s): No

Deposited: 2025-08-07 Released: 2026-08-19
Deposition Author(s): Shvarev, D., Hitchcock, A., Sobotka, R.
Funding Organization(s): German Research Foundation (DFG), European Research Council (ERC), Czech Science Foundation, Ministry of Education (MoE, Czech Republic), Royal Society

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure of chlorophyll synthase in complex with the LHC-like protein HliD

Shvarev, D., Wysocka, A., Morey-Burrows, F., Panas, K., Pazuki, A., Kulik, N., Proctor, M., Pilny, J., Hunter, N., Hitchcock, A., Sobotka, R.

To be published.

Macromolecule Content

Total Structure Weight: 83.96 kDa
Atom Count: 5,930
Modeled Residue Count: 670
Deposited Residue Count: 670
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
High light-inducible protein HliD	A, B	41	Synechocystis sp. PCC 6803	Mutation(s): 0 Gene Names: hliD, hliA, scpE, ssr1789
UniProt
Find proteins for P72932 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore P72932 Go to UniProtKB: P72932
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P72932
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll a synthase	C, D	294	Synechocystis sp. PCC 6803	Mutation(s): 0 Gene Names: chlG
UniProt
Find proteins for Q55145 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore Q55145 Go to UniProtKB: Q55145
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q55145
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LMN (Subject of Investigation/LOI) Query on LMN Download:Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain Q [auth D] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth D]	M [auth C], Q [auth D]	Lauryl Maltose Neopentyl Glycol C₄₇ H₈₈ O₂₂ MADJBYLAYPCCOO-XYPZXBMFSA-N		Interactions Focus chain M [auth C] Focus chain Q [auth D] Interactions & Density Focus chain M [auth C] Focus chain Q [auth D]
CLA (Subject of Investigation/LOI) Query on CLA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	E [auth A], F [auth A], H [auth B], I [auth B]	CHLOROPHYLL A C₅₅ H₇₂ Mg N₄ O₅ ATNHDLDRLWWWCB-AENOIHSZSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B]
A1JR2( Subject of Investigation/LOI) Query on A1JR2 Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain P [auth D] MOL2 format, chain L [auth C] MOL2 format, chain P [auth D] mmCIF format, chain L [auth C] mmCIF format, chain P [auth D]	L [auth C], P [auth D]	(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 C₄₆ H₆₈ O₇ WYZZQKLBLCPJSJ-XVXQRKMDSA-N		Interactions Focus chain L [auth C] Focus chain P [auth D] Interactions & Density Focus chain L [auth C] Focus chain P [auth D]
MGE (Subject of Investigation/LOI) Query on MGE Download:Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain R [auth D] MOL2 format, chain N [auth C] MOL2 format, chain R [auth D] mmCIF format, chain N [auth C] mmCIF format, chain R [auth D]	N [auth C], R [auth D]	(1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE C₃₈ H₇₂ O₁₀ FIJGNIAJTZSERN-DQQGJSMTSA-N		Interactions Focus chain N [auth C] Focus chain R [auth D] Interactions & Density Focus chain N [auth C] Focus chain R [auth D]
5X6 (Subject of Investigation/LOI) Query on 5X6 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B]	G [auth A], J [auth B]	Zeaxanthin C₄₀ H₅₆ O₂ JKQXZKUSFCKOGQ-AYORJBSZSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth B]
GRG (Subject of Investigation/LOI) Query on GRG Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain O [auth D] MOL2 format, chain K [auth C] MOL2 format, chain O [auth D] mmCIF format, chain K [auth C] mmCIF format, chain O [auth D]	K [auth C], O [auth D]	GERANYLGERANYL DIPHOSPHATE C₂₀ H₃₆ O₇ P₂ OINNEUNVOZHBOX-QIRCYJPOSA-N		Interactions Focus chain K [auth C] Focus chain O [auth D] Interactions & Density Focus chain K [auth C] Focus chain O [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419:
RECONSTRUCTION	cryoSPARC	v4

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-19

Deposition Author(s):

Shvarev, D.

Hitchcock, A.

Sobotka, R.

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SH 1664/2-1
German Research Foundation (DFG)	Germany	SFB1557
German Research Foundation (DFG)	Germany	INST190/196-1 FUGG
European Research Council (ERC)	European Union	Synergy Award 854126
Czech Science Foundation	Czech Republic	22-03092S
Ministry of Education (MoE, Czech Republic)	Czech Republic	PHOTOMACHINES, CZ.02.01.01/00/22_008/0004624
Royal Society	United Kingdom	URF-R-241006

Revision History (Full details and data files)

Version 1.0: 2026-08-19
Type: Initial release

9SAU | pdb_00009sau

Chlorophyll synthase in complex with the LHC-like protein HliD, GGPP-bound state

Literature

Structure of chlorophyll synthase in complex with the LHC-like protein HliD

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2