9W1C | pdb_00009w1c

LH2 complex from Ectothiorhodospira haloalkaliphila with inhibited carotenoid biosynthesis

PDB DOI: https://doi.org/10.2210/pdb9W1C/pdb
EM Map EMD-65526: EMDB EMDataResource

Classification: PHOTOSYNTHESIS
Organism(s): Ectothiorhodospira haloalkaliphila ATCC 51935
Mutation(s): No

Deposited: 2025-07-25 Released: 2025-10-22
Deposition Author(s): Burtseva, A.D., Baymukhametov, T.N., Popov, V.O., Ashikhmin, A.A., Boyko, K.M.
Funding Organization(s): Russian Science Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 1.92 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

Structural insights into LH2 complexes formed by a purple sulfur bacterium with inhibited carotenoid biosynthesis.

Burtseva, A.D., Baymukhametov, T.N., Bolshakov, M.A., Starodubov, A.S., Zhang, H., Popov, V.O., Ashikhmin, A.A., Boyko, K.M.

(2025) FEBS Lett

PubMed: 41313718 Search on PubMed
DOI: https://doi.org/10.1002/1873-3468.70242
Primary Citation of Related Structures:
9W1C

PubMed Abstract:
The LH2 complex is essential for light harvesting in many photosynthetic bacteria. To elucidate the specific structural role of carotenoids, we analyzed LH2 complexes from Ectothiorhodospira haloalkaliphila with inhibited carotenoid biosynthesis. This approach allowed us to study complexes incorporating the colorless carotenoid phytoene instead of the native, colored pigments. A 1.92 Å cryo-EM reconstruction revealed that phytoene fully substitutes for the native carotenoids while maintaining the octameric symmetry of the complex and the precise arrangement of bacteriochlorophylls. These results demonstrate that the architectural function of carotenoids in LH2 complexes is maintained even when their light-absorption capability is altered, providing new mechanistic insight into the structural basis of pigment-protein interactions in photosynthetic antenna complexes.

Organizational Affiliation

Bach Institute of Biochemistry, Research Center of Biotechnology Russian Academy of Sciences, Moscow, Russia.

Macromolecule Content

Total Structure Weight: 132.83 kDa
Atom Count: 8,480
Modeled Residue Count: 800
Deposited Residue Count: 928
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Light-harvesting protein B:800-850 subunit beta	A C [auth D] E [auth G] G [auth J] I [auth M] A, C [auth D], E [auth G], G [auth J], I [auth M], K [auth P], M [auth S], O [auth V]	46	Ectothiorhodospira haloalkaliphila ATCC 51935	Mutation(s): 0
UniProt
Find proteins for W8KQR0 (Ectothiorhodospira haloalkaliphila) Explore W8KQR0 Go to UniProtKB: W8KQR0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	W8KQR0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light-harvesting protein B-800/850 alpha chain	B [auth C] D [auth E] F [auth H] H [auth K] J [auth N] B [auth C], D [auth E], F [auth H], H [auth K], J [auth N], L [auth Q], N [auth T], P [auth W]	70	Ectothiorhodospira haloalkaliphila ATCC 51935	Mutation(s): 0
UniProt
Find proteins for W8KE12 (Ectothiorhodospira haloalkaliphila) Explore W8KE12 Go to UniProtKB: W8KE12
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	W8KE12
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BCL (Subject of Investigation/LOI) Query on BCL Download Ideal Coordinates CCD File SDF format, chain Z [auth G] SDF format, chain Y [auth G] SDF format, chain X [auth E] SDF format, chain W [auth E] SDF format, chain VA [auth W] SDF format, chain UA [auth W] SDF format, chain U [auth D] SDF format, chain TA [auth V] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain RA [auth T] SDF format, chain QA [auth T] SDF format, chain Q [auth A] SDF format, chain OA [auth S] SDF format, chain NA [auth Q] SDF format, chain MA [auth Q] SDF format, chain LA [auth P] SDF format, chain JA [auth N] SDF format, chain IA [auth N] SDF format, chain GA [auth M] SDF format, chain FA [auth K] SDF format, chain EA [auth K] SDF format, chain CA [auth J] SDF format, chain BA [auth H] MOL2 format, chain Z [auth G] MOL2 format, chain Y [auth G] MOL2 format, chain X [auth E] MOL2 format, chain W [auth E] MOL2 format, chain VA [auth W] MOL2 format, chain UA [auth W] MOL2 format, chain U [auth D] MOL2 format, chain TA [auth V] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain RA [auth T] MOL2 format, chain QA [auth T] MOL2 format, chain Q [auth A] MOL2 format, chain OA [auth S] MOL2 format, chain NA [auth Q] MOL2 format, chain MA [auth Q] MOL2 format, chain LA [auth P] MOL2 format, chain JA [auth N] MOL2 format, chain IA [auth N] MOL2 format, chain GA [auth M] MOL2 format, chain FA [auth K] MOL2 format, chain EA [auth K] MOL2 format, chain CA [auth J] MOL2 format, chain BA [auth H] mmCIF format, chain Z [auth G] mmCIF format, chain Y [auth G] mmCIF format, chain X [auth E] mmCIF format, chain W [auth E] mmCIF format, chain VA [auth W] mmCIF format, chain UA [auth W] mmCIF format, chain U [auth D] mmCIF format, chain TA [auth V] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain RA [auth T] mmCIF format, chain QA [auth T] mmCIF format, chain Q [auth A] mmCIF format, chain OA [auth S] mmCIF format, chain NA [auth Q] mmCIF format, chain MA [auth Q] mmCIF format, chain LA [auth P] mmCIF format, chain JA [auth N] mmCIF format, chain IA [auth N] mmCIF format, chain GA [auth M] mmCIF format, chain FA [auth K] mmCIF format, chain EA [auth K] mmCIF format, chain CA [auth J] mmCIF format, chain BA [auth H]	BA [auth H] CA [auth J] EA [auth K] FA [auth K] GA [auth M] BA [auth H], CA [auth J], EA [auth K], FA [auth K], GA [auth M], IA [auth N], JA [auth N], LA [auth P], MA [auth Q], NA [auth Q], OA [auth S], Q [auth A], QA [auth T], RA [auth T], S [auth C], T [auth C], TA [auth V], U [auth D], UA [auth W], VA [auth W], W [auth E], X [auth E], Y [auth G], Z [auth G]	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-AGGZHOMASA-M		Interactions Focus chain BA [auth H] Focus chain CA [auth J] Focus chain EA [auth K] Focus chain FA [auth K] Focus chain GA [auth M] Focus chain IA [auth N] Focus chain JA [auth N] Focus chain LA [auth P] Focus chain MA [auth Q] Focus chain NA [auth Q] Focus chain OA [auth S] Focus chain Q [auth A] Focus chain QA [auth T] Focus chain RA [auth T] Focus chain S [auth C] Focus chain T [auth C] Focus chain TA [auth V] Focus chain U [auth D] Focus chain UA [auth W] Focus chain VA [auth W] Focus chain W [auth E] Focus chain X [auth E] Focus chain Y [auth G] Focus chain Z [auth G] Interactions & Density Focus chain BA [auth H] Focus chain CA [auth J] Focus chain EA [auth K] Focus chain FA [auth K] Focus chain GA [auth M] Focus chain IA [auth N] Focus chain JA [auth N] Focus chain LA [auth P] Focus chain MA [auth Q] Focus chain NA [auth Q] Focus chain OA [auth S] Focus chain Q [auth A] Focus chain QA [auth T] Focus chain RA [auth T] Focus chain S [auth C] Focus chain T [auth C] Focus chain TA [auth V] Focus chain U [auth D] Focus chain UA [auth W] Focus chain VA [auth W] Focus chain W [auth E] Focus chain X [auth E] Focus chain Y [auth G] Focus chain Z [auth G]
A1MBA (Subject of Investigation/LOI) Query on A1MBA Download Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain SA [auth T] SDF format, chain R [auth A] SDF format, chain PA [auth S] SDF format, chain KA [auth N] SDF format, chain HA [auth M] SDF format, chain DA [auth J] SDF format, chain AA [auth G] MOL2 format, chain V [auth D] MOL2 format, chain SA [auth T] MOL2 format, chain R [auth A] MOL2 format, chain PA [auth S] MOL2 format, chain KA [auth N] MOL2 format, chain HA [auth M] MOL2 format, chain DA [auth J] MOL2 format, chain AA [auth G] mmCIF format, chain V [auth D] mmCIF format, chain SA [auth T] mmCIF format, chain R [auth A] mmCIF format, chain PA [auth S] mmCIF format, chain KA [auth N] mmCIF format, chain HA [auth M] mmCIF format, chain DA [auth J] mmCIF format, chain AA [auth G]	AA [auth G] DA [auth J] HA [auth M] KA [auth N] PA [auth S] AA [auth G], DA [auth J], HA [auth M], KA [auth N], PA [auth S], R [auth A], SA [auth T], V [auth D]	Phytoene C₄₀ H₆₄ YVLPJIGOMTXXLP-JPWSVPCBSA-N		Interactions Focus chain AA [auth G] Focus chain DA [auth J] Focus chain HA [auth M] Focus chain KA [auth N] Focus chain PA [auth S] Focus chain R [auth A] Focus chain SA [auth T] Focus chain V [auth D] Interactions & Density Focus chain AA [auth G] Focus chain DA [auth J] Focus chain HA [auth M] Focus chain KA [auth N] Focus chain PA [auth S] Focus chain R [auth A] Focus chain SA [auth T] Focus chain V [auth D]