8YDM | pdb_00008ydm

Cryo-EM structure of CaRC-LH complex from Chloroflexus aurantiacus

PDB DOI: https://doi.org/10.2210/pdb8YDM/pdb
EM Map EMD-39177: EMDB EMDataResource

Classification: PHOTOSYNTHESIS
Organism(s): Chloroflexus aurantiacus J-10-fl
Mutation(s): No
Membrane Protein: Yes PDBTM mpstruc

Deposited: 2024-02-20 Released: 2025-02-19
Deposition Author(s): Guoqiang, H., Shishang, D.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.05 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM structure of a minimal reaction center-light-harvesting complex from the phototrophic bacterium Chloroflexus aurantiacus.

Huang, G., Dong, S., Ma, L., Li, L., Ju, J., Wang, M.J., Zhang, J.P., Sui, S.F., Qin, X.

(2025) J Integr Plant Biol 67: 967-978

PubMed: 39912559 Search on PubMed
DOI: https://doi.org/10.1111/jipb.13853
Primary Citation Related Structures:
8YDM

PubMed Abstract:
Photosynthetic organisms have developed various light-harvesting antenna systems to capture light and transfer energy to reaction centers (RCs). Simultaneous utilization of the integral membrane light-harvesting antenna (LH complex) and the extrinsic antenna (chlorosomes) makes the phototrophic bacterium Chloroflexus (Cfx.) aurantiacus an ideal model for studying filamentous anoxygenic phototrophs (FAPs). Here, we determined the structure of a minimal RC-LH photocomplex from Cfx. aurantiacus J-10-fl (CaRC-LH) at 3.05-Å resolution. The CaRC-LH binds only to seven LH subunits, which form a crescent-shaped antenna surrounding the movable menaquinone-10 (Q _B) binding site of CaRC. In this complex with minimal LH units, an extra antenna is required to ensure sufficient light-gathering, providing a clear explanation for the presence of chlorosomes in Cfx. aurantiacus. More importantly, the semicircle of the antenna represents a novel RC-LH assembly pattern. Our structure provides a basis for understanding the existence of chlorosomes in Cfx. aurantiacus and the possible assembly pattern of RC-LH.

Organizational Affiliation

State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.

Macromolecule Content

Total Structure Weight: 246.99 kDa
Atom Count: 15,637
Modeled Residue Count: 1,662
Deposited Residue Count: 1,866
Unique protein chains: 6

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Light-harvesting protein B-808/866 alpha chain	A, D, F, H, J A, D, F, H, J, O, Q	57	Chloroflexus aurantiacus J-10-fl	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P07503 (Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl)) Explore P07503 Go to UniProtKB: P07503
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07503
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light-harvesting protein B-808/866 beta chain	B, E, G, I, K B, E, G, I, K, P, R	53	Chloroflexus aurantiacus J-10-fl	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P09927 (Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl)) Explore P09927 Go to UniProtKB: P09927
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09927
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Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c-554	C	414	Chloroflexus aurantiacus J-10-fl	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P33325 (Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl)) Explore P33325 Go to UniProtKB: P33325
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P33325
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Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein L chain	L	311	Chloroflexus aurantiacus J-10-fl	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P11695 (Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl)) Explore P11695 Go to UniProtKB: P11695
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11695
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Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein M chain	M	307	Chloroflexus aurantiacus J-10-fl	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P09438 (Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl)) Explore P09438 Go to UniProtKB: P09438
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09438
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Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein chain N	N	64	Chloroflexus aurantiacus J-10-fl	Mutation(s): 0

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MQE Query on MQE Download:Ideal Coordinates CCD File SDF format, chain VA [auth L] SDF format, chain AB [auth M] MOL2 format, chain VA [auth L] MOL2 format, chain AB [auth M] mmCIF format, chain VA [auth L] mmCIF format, chain AB [auth M]	AB [auth M], VA [auth L]	2-methyl-3-[(2E,6E,10E,14E,18E,22E,26E,30E,34E,38E)-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,1 4,18,22,26,30,34,38,42-undecaen-1-yl]naphthalene-1,4-dione C₆₆ H₉₆ O₂ YYDMANIEKFAEJC-RYZSZPJESA-N		Interactions Focus chain AB [auth M] Focus chain VA [auth L] Interactions & Density Focus chain AB [auth M] Focus chain VA [auth L]
BCL Query on BCL Download:Ideal Coordinates CCD File SDF format, chain ZA [auth M] SDF format, chain WA [auth L] SDF format, chain V [auth A] SDF format, chain UA [auth K] SDF format, chain U [auth A] SDF format, chain SA [auth K] SDF format, chain S [auth A] SDF format, chain QA [auth J] SDF format, chain PA [auth I] SDF format, chain OA [auth I] SDF format, chain NB [auth R] SDF format, chain MB [auth R] SDF format, chain LA [auth H] SDF format, chain KA [auth G] SDF format, chain JB [auth Q] SDF format, chain JA [auth G] SDF format, chain IB [auth P] SDF format, chain HA [auth F] SDF format, chain GB [auth O] SDF format, chain GA [auth E] SDF format, chain EB [auth O] SDF format, chain EA [auth D] SDF format, chain CB [auth M] SDF format, chain CA [auth D] MOL2 format, chain ZA [auth M] MOL2 format, chain WA [auth L] MOL2 format, chain V [auth A] MOL2 format, chain UA [auth K] MOL2 format, chain U [auth A] MOL2 format, chain SA [auth K] MOL2 format, chain S [auth A] MOL2 format, chain QA [auth J] MOL2 format, chain PA [auth I] MOL2 format, chain OA [auth I] MOL2 format, chain NB [auth R] MOL2 format, chain MB [auth R] MOL2 format, chain LA [auth H] MOL2 format, chain KA [auth G] MOL2 format, chain JB [auth Q] MOL2 format, chain JA [auth G] MOL2 format, chain IB [auth P] MOL2 format, chain HA [auth F] MOL2 format, chain GB [auth O] MOL2 format, chain GA [auth E] MOL2 format, chain EB [auth O] MOL2 format, chain EA [auth D] MOL2 format, chain CB [auth M] MOL2 format, chain CA [auth D] mmCIF format, chain ZA [auth M] mmCIF format, chain WA [auth L] mmCIF format, chain V [auth A] mmCIF format, chain UA [auth K] mmCIF format, chain U [auth A] mmCIF format, chain SA [auth K] mmCIF format, chain S [auth A] mmCIF format, chain QA [auth J] mmCIF format, chain PA [auth I] mmCIF format, chain OA [auth I] mmCIF format, chain NB [auth R] mmCIF format, chain MB [auth R] mmCIF format, chain LA [auth H] mmCIF format, chain KA [auth G] mmCIF format, chain JB [auth Q] mmCIF format, chain JA [auth G] mmCIF format, chain IB [auth P] mmCIF format, chain HA [auth F] mmCIF format, chain GB [auth O] mmCIF format, chain GA [auth E] mmCIF format, chain EB [auth O] mmCIF format, chain EA [auth D] mmCIF format, chain CB [auth M] mmCIF format, chain CA [auth D]	CA [auth D] CB [auth M] EA [auth D] EB [auth O] GA [auth E] CA [auth D], CB [auth M], EA [auth D], EB [auth O], GA [auth E], GB [auth O], HA [auth F], IB [auth P], JA [auth G], JB [auth Q], KA [auth G], LA [auth H], MB [auth R], NB [auth R], OA [auth I], PA [auth I], QA [auth J], S [auth A], SA [auth K], U [auth A], UA [auth K], V [auth A], WA [auth L], ZA [auth M]	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-AGGZHOMASA-M		Interactions Focus chain CA [auth D] Focus chain CB [auth M] Focus chain EA [auth D] Focus chain EB [auth O] Focus chain GA [auth E] Focus chain GB [auth O] Focus chain HA [auth F] Focus chain IB [auth P] Focus chain JA [auth G] Focus chain JB [auth Q] Focus chain KA [auth G] Focus chain LA [auth H] Focus chain MB [auth R] Focus chain NB [auth R] Focus chain OA [auth I] Focus chain PA [auth I] Focus chain QA [auth J] Focus chain S [auth A] Focus chain SA [auth K] Focus chain U [auth A] Focus chain UA [auth K] Focus chain V [auth A] Focus chain WA [auth L] Focus chain ZA [auth M] Interactions & Density Focus chain CA [auth D] Focus chain CB [auth M] Focus chain EA [auth D] Focus chain EB [auth O] Focus chain GA [auth E] Focus chain GB [auth O] Focus chain HA [auth F] Focus chain IB [auth P] Focus chain JA [auth G] Focus chain JB [auth Q] Focus chain KA [auth G] Focus chain LA [auth H] Focus chain MB [auth R] Focus chain NB [auth R] Focus chain OA [auth I] Focus chain PA [auth I] Focus chain QA [auth J] Focus chain S [auth A] Focus chain SA [auth K] Focus chain U [auth A] Focus chain UA [auth K] Focus chain V [auth A] Focus chain WA [auth L] Focus chain ZA [auth M]
BPH Query on BPH Download:Ideal Coordinates CCD File SDF format, chain YA [auth M] SDF format, chain XA [auth L] SDF format, chain DB [auth M] MOL2 format, chain YA [auth M] MOL2 format, chain XA [auth L] MOL2 format, chain DB [auth M] mmCIF format, chain YA [auth M] mmCIF format, chain XA [auth L] mmCIF format, chain DB [auth M]	DB [auth M], XA [auth L], YA [auth M]	BACTERIOPHEOPHYTIN A C₅₅ H₇₆ N₄ O₆ KWOZSBGNAHVCKG-SZQBJALDSA-N		Interactions Focus chain DB [auth M] Focus chain XA [auth L] Focus chain YA [auth M] Interactions & Density Focus chain DB [auth M] Focus chain XA [auth L] Focus chain YA [auth M]
PGV Query on PGV Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] MOL2 format, chain BA [auth C] mmCIF format, chain BA [auth C]	BA [auth C]	(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE C₄₀ H₇₇ O₁₀ P ADYWCMPUNIVOEA-GPJPVTGXSA-N		Interactions Focus chain BA [auth C] Interactions & Density Focus chain BA [auth C]
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain Y [auth C] SDF format, chain X [auth C] SDF format, chain AA [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain AA [auth C]	AA [auth C], X [auth C], Y [auth C], Z [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain AA [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
U4Z Query on U4Z Download:Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain TA [auth K] SDF format, chain T [auth A] SDF format, chain RA [auth K] SDF format, chain NA [auth I] SDF format, chain MA [auth I] SDF format, chain LB [auth R] SDF format, chain KB [auth Q] SDF format, chain IA [auth G] SDF format, chain HB [auth P] SDF format, chain FB [auth O] SDF format, chain FA [auth D] SDF format, chain DA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain TA [auth K] MOL2 format, chain T [auth A] MOL2 format, chain RA [auth K] MOL2 format, chain NA [auth I] MOL2 format, chain MA [auth I] MOL2 format, chain LB [auth R] MOL2 format, chain KB [auth Q] MOL2 format, chain IA [auth G] MOL2 format, chain HB [auth P] MOL2 format, chain FB [auth O] MOL2 format, chain FA [auth D] MOL2 format, chain DA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain TA [auth K] mmCIF format, chain T [auth A] mmCIF format, chain RA [auth K] mmCIF format, chain NA [auth I] mmCIF format, chain MA [auth I] mmCIF format, chain LB [auth R] mmCIF format, chain KB [auth Q] mmCIF format, chain IA [auth G] mmCIF format, chain HB [auth P] mmCIF format, chain FB [auth O] mmCIF format, chain FA [auth D] mmCIF format, chain DA [auth D]	DA [auth D] FA [auth D] FB [auth O] HB [auth P] IA [auth G] DA [auth D], FA [auth D], FB [auth O], HB [auth P], IA [auth G], KB [auth Q], LB [auth R], MA [auth I], NA [auth I], RA [auth K], T [auth A], TA [auth K], W [auth B]	gamma-Carotene C₄₀ H₅₆ HRQKOYFGHJYEFS-BXOLYSJBSA-N		Interactions Focus chain DA [auth D] Focus chain FA [auth D] Focus chain FB [auth O] Focus chain HB [auth P] Focus chain IA [auth G] Focus chain KB [auth Q] Focus chain LB [auth R] Focus chain MA [auth I] Focus chain NA [auth I] Focus chain RA [auth K] Focus chain T [auth A] Focus chain TA [auth K] Focus chain W [auth B] Interactions & Density Focus chain DA [auth D] Focus chain FA [auth D] Focus chain FB [auth O] Focus chain HB [auth P] Focus chain IA [auth G] Focus chain KB [auth Q] Focus chain LB [auth R] Focus chain MA [auth I] Focus chain NA [auth I] Focus chain RA [auth K] Focus chain T [auth A] Focus chain TA [auth K] Focus chain W [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain BB [auth M] MOL2 format, chain BB [auth M] mmCIF format, chain BB [auth M]	BB [auth M]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain BB [auth M] Interactions & Density Focus chain BB [auth M]