9LTI | pdb_00009lti

Cryo-EM structure of LH1-RC from Ery. sanguineus

PDB DOI: https://doi.org/10.2210/pdb9LTI/pdb
EM Map EMD-63370: EMDB EMDataResource

Classification: PHOTOSYNTHESIS
Organism(s): Erythrobacter sanguineus
Mutation(s): No

Deposited: 2025-02-06 Released: 2025-12-10
Deposition Author(s): Yue, X.-Y., Wang, G.-L., Yu, L.-J.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.27 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

Cryo-EM structures of photocomplexes from the free-living aerobic anoxygenic phototrophic bacterium Erythrobacter sanguineus.

Yue, X.Y., Wang, G.L., Zou, M.J., Ma, F., Wang-Otomo, Z.Y., Madigan, M.T., Yu, L.J.

(2025) Structure

PubMed: 41274286 Search on PubMed
DOI: https://doi.org/10.1016/j.str.2025.10.017
Primary Citation of Related Structures:
9LT4, 9LTI

PubMed Abstract:
Aerobic anoxygenic phototrophic bacteria (AAPB) are widely distributed in nature and they are important members of the marine phototrophic community. However, a structural and functional understanding of the AAPB photosynthetic apparatus is still lacking. Here, we present cryo-EM structures of the LH1-RC (core) and LH2 (peripheral) photocomplexes from the model aerobic phototroph Erythrobacter (Ery.) sanguineus. The LH1 αβ-heterodimers bind the carotenoids bacteriorubixanthinal and caloxanthin-pigments that are absent from anaerobic anoxygenic phototrophs-to form a closed ring structure. Ery. sanguineus LH1-RC contains a lipid-anchored polypeptide unrelated to any of the auxiliary proteins identified in the core complexes of purple bacteria so far. The Ery. sanguineus LH2 complex shows unique absorption characteristics, with its Q _y transition being blue-shifted to 814 nm. This work provides structural insights into the unusual photosynthetic properties of AAPB and points to new avenues to further explore their biology.

Organizational Affiliation

Photosynthesis Research Center, State Key Laboratory of Forage Breeding-by-Design and Utilization, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.

Macromolecule Content

Total Structure Weight: 385.53 kDa
Atom Count: 22,831
Modeled Residue Count: 2,222
Deposited Residue Count: 2,856
Unique protein chains: 6

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Light-harvesting complex 1 alpha chain	A B C D E A, B, C, D, E, F, G, H [auth Q], I, J, K, L [auth R], M [auth S], N, O, P	64	Erythrobacter sanguineus	Mutation(s): 0
UniProt
Find proteins for A0A1M7RZ65 (Erythrobacter sanguineus) Explore A0A1M7RZ65 Go to UniProtKB: A0A1M7RZ65
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1M7RZ65
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antenna complex alpha/beta subunit	AA [auth d] BA [auth e] CA [auth f] DA [auth g] EA [auth q] AA [auth d], BA [auth e], CA [auth f], DA [auth g], EA [auth q], FA [auth i], Q [auth b], R [auth a], S [auth p], T [auth o], U [auth n], V [auth s], W [auth r], X [auth k], Y [auth j], Z [auth c]	52	Erythrobacter sanguineus	Mutation(s): 0
UniProt
Find proteins for A0A1M7RZ98 (Erythrobacter sanguineus) Explore A0A1M7RZ98 Go to UniProtKB: A0A1M7RZ98
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1M7RZ98
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein L chain	GA [auth L]	274	Erythrobacter sanguineus	Mutation(s): 0
UniProt
Find proteins for A0A1M7RZC0 (Erythrobacter sanguineus) Explore A0A1M7RZC0 Go to UniProtKB: A0A1M7RZC0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1M7RZC0
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic reaction center H subunit	HA [auth H]	268	Erythrobacter sanguineus	Mutation(s): 0
UniProt
Find proteins for A0A1M7RZD6 (Erythrobacter sanguineus) Explore A0A1M7RZD6 Go to UniProtKB: A0A1M7RZD6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1M7RZD6
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein M chain	IA [auth M]	323	Erythrobacter sanguineus	Mutation(s): 0
UniProt
Find proteins for A0A1M7RZG6 (Erythrobacter sanguineus) Explore A0A1M7RZG6 Go to UniProtKB: A0A1M7RZG6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1M7RZG6
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Secreted protein	JA [auth T]	135	Erythrobacter sanguineus	Mutation(s): 0
UniProt
Find proteins for A0A1M7SD26 (Erythrobacter sanguineus) Explore A0A1M7SD26 Go to UniProtKB: A0A1M7SD26
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1M7SD26
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 13 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 CB [auth G] SDF format, chain CC [auth P] SDF format, chain CD [auth g] SDF format, chain ED [auth q] SDF format, chain FC [auth b] SDF format, chain FD [auth i] SDF format, chain GB [auth Q] SDF format, chain GC [auth a] SDF format, chain GD [auth L] SDF format, chain HC [auth p] SDF format, chain HD [auth L] SDF format, chain JC [auth o] SDF format, chain KA [auth A] SDF format, chain KB [auth I] SDF format, chain KC [auth n] SDF format, chain LC [auth s] SDF format, chain MB [auth J] SDF format, chain NA [auth B] SDF format, chain PB [auth K] SDF format, chain PC [auth r] SDF format, chain QA [auth C] SDF format, chain QC [auth k] SDF format, chain RB [auth R] SDF format, chain SC [auth j] SDF format, chain TC [auth c] SDF format, chain UA [auth D] SDF format, chain UB [auth S] SDF format, chain UD [auth M] SDF format, chain VC [auth d] SDF format, chain WB [auth N] SDF format, chain WD [auth M] SDF format, chain XA [auth E] SDF format, chain XC [auth e] SDF format, chain ZA [auth F] SDF format, chain ZB [auth O] SDF format, chain ZC [auth f] MOL2 format, chain CB [auth G] MOL2 format, chain CC [auth P] MOL2 format, chain CD [auth g] MOL2 format, chain ED [auth q] MOL2 format, chain FC [auth b] MOL2 format, chain FD [auth i] MOL2 format, chain GB [auth Q] MOL2 format, chain GC [auth a] MOL2 format, chain GD [auth L] MOL2 format, chain HC [auth p] MOL2 format, chain HD [auth L] MOL2 format, chain JC [auth o] MOL2 format, chain KA [auth A] MOL2 format, chain KB [auth I] MOL2 format, chain KC [auth n] MOL2 format, chain LC [auth s] MOL2 format, chain MB [auth J] MOL2 format, chain NA [auth B] MOL2 format, chain PB [auth K] MOL2 format, chain PC [auth r] MOL2 format, chain QA [auth C] MOL2 format, chain QC [auth k] MOL2 format, chain RB [auth R] MOL2 format, chain SC [auth j] MOL2 format, chain TC [auth c] MOL2 format, chain UA [auth D] MOL2 format, chain UB [auth S] MOL2 format, chain UD [auth M] MOL2 format, chain VC [auth d] MOL2 format, chain WB [auth N] MOL2 format, chain WD [auth M] MOL2 format, chain XA [auth E] MOL2 format, chain XC [auth e] MOL2 format, chain ZA [auth F] MOL2 format, chain ZB [auth O] MOL2 format, chain ZC [auth f] mmCIF format, chain CB [auth G] mmCIF format, chain CC [auth P] mmCIF format, chain CD [auth g] mmCIF format, chain ED [auth q] mmCIF format, chain FC [auth b] mmCIF format, chain FD [auth i] mmCIF format, chain GB [auth Q] mmCIF format, chain GC [auth a] mmCIF format, chain GD [auth L] mmCIF format, chain HC [auth p] mmCIF format, chain HD [auth L] mmCIF format, chain JC [auth o] mmCIF format, chain KA [auth A] mmCIF format, chain KB [auth I] mmCIF format, chain KC [auth n] mmCIF format, chain LC [auth s] mmCIF format, chain MB [auth J] mmCIF format, chain NA [auth B] mmCIF format, chain PB [auth K] mmCIF format, chain PC [auth r] mmCIF format, chain QA [auth C] mmCIF format, chain QC [auth k] mmCIF format, chain RB [auth R] mmCIF format, chain SC [auth j] mmCIF format, chain TC [auth c] mmCIF format, chain UA [auth D] mmCIF format, chain UB [auth S] mmCIF format, chain UD [auth M] mmCIF format, chain VC [auth d] mmCIF format, chain WB [auth N] mmCIF format, chain WD [auth M] mmCIF format, chain XA [auth E] mmCIF format, chain XC [auth e] mmCIF format, chain ZA [auth F] mmCIF format, chain ZB [auth O] mmCIF format, chain ZC [auth f]	CB [auth G] CC [auth P] CD [auth g] ED [auth q] FC [auth b] CB [auth G], CC [auth P], CD [auth g], ED [auth q], FC [auth b], FD [auth i], GB [auth Q], GC [auth a], GD [auth L], HC [auth p], HD [auth L], JC [auth o], KA [auth A], KB [auth I], KC [auth n], LC [auth s], MB [auth J], NA [auth B], PB [auth K], PC [auth r], QA [auth C], QC [auth k], RB [auth R], SC [auth j], TC [auth c], UA [auth D], UB [auth S], UD [auth M], VC [auth d], WB [auth N], WD [auth M], XA [auth E], XC [auth e], ZA [auth F], ZB [auth O], ZC [auth f]	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-AGGZHOMASA-M		Interactions Focus chain CB [auth G] Focus chain CC [auth P] Focus chain CD [auth g] Focus chain ED [auth q] Focus chain FC [auth b] Focus chain FD [auth i] Focus chain GB [auth Q] Focus chain GC [auth a] Focus chain GD [auth L] Focus chain HC [auth p] Focus chain HD [auth L] Focus chain JC [auth o] Focus chain KA [auth A] Focus chain KB [auth I] Focus chain KC [auth n] Focus chain LC [auth s] Focus chain MB [auth J] Focus chain NA [auth B] Focus chain PB [auth K] Focus chain PC [auth r] Focus chain QA [auth C] Focus chain QC [auth k] Focus chain RB [auth R] Focus chain SC [auth j] Focus chain TC [auth c] Focus chain UA [auth D] Focus chain UB [auth S] Focus chain UD [auth M] Focus chain VC [auth d] Focus chain WB [auth N] Focus chain WD [auth M] Focus chain XA [auth E] Focus chain XC [auth e] Focus chain ZA [auth F] Focus chain ZB [auth O] Focus chain ZC [auth f] Interactions & Density Focus chain CB [auth G] Focus chain CC [auth P] Focus chain CD [auth g] Focus chain ED [auth q] Focus chain FC [auth b] Focus chain FD [auth i] Focus chain GB [auth Q] Focus chain GC [auth a] Focus chain GD [auth L] Focus chain HC [auth p] Focus chain HD [auth L] Focus chain JC [auth o] Focus chain KA [auth A] Focus chain KB [auth I] Focus chain KC [auth n] Focus chain LC [auth s] Focus chain MB [auth J] Focus chain NA [auth B] Focus chain PB [auth K] Focus chain PC [auth r] Focus chain QA [auth C] Focus chain QC [auth k] Focus chain RB [auth R] Focus chain SC [auth j] Focus chain TC [auth c] Focus chain UA [auth D] Focus chain UB [auth S] Focus chain UD [auth M] Focus chain VC [auth d] Focus chain WB [auth N] Focus chain WD [auth M] Focus chain XA [auth E] Focus chain XC [auth e] Focus chain ZA [auth F] Focus chain ZB [auth O] Focus chain ZC [auth f]
BPH (Subject of Investigation/LOI) Query on BPH Download Ideal Coordinates CCD File SDF format, chain ID [auth L] SDF format, chain KD [auth L] MOL2 format, chain ID [auth L] MOL2 format, chain KD [auth L] mmCIF format, chain ID [auth L] mmCIF format, chain KD [auth L]	ID [auth L], KD [auth L]	BACTERIOPHEOPHYTIN A C₅₅ H₇₆ N₄ O₆ KWOZSBGNAHVCKG-SZQBJALDSA-N		Interactions Focus chain ID [auth L] Focus chain KD [auth L] Interactions & Density Focus chain ID [auth L] Focus chain KD [auth L]
PGV (Subject of Investigation/LOI) Query on PGV Download Ideal Coordinates CCD File SDF format, chain BB [auth F] SDF format, chain BE [auth M] SDF format, chain DE [auth T] SDF format, chain EB [auth G] SDF format, chain FE [auth T] SDF format, chain MD [auth L] SDF format, chain ND [auth L] SDF format, chain WA [auth D] MOL2 format, chain BB [auth F] MOL2 format, chain BE [auth M] MOL2 format, chain DE [auth T] MOL2 format, chain EB [auth G] MOL2 format, chain FE [auth T] MOL2 format, chain MD [auth L] MOL2 format, chain ND [auth L] MOL2 format, chain WA [auth D] mmCIF format, chain BB [auth F] mmCIF format, chain BE [auth M] mmCIF format, chain DE [auth T] mmCIF format, chain EB [auth G] mmCIF format, chain FE [auth T] mmCIF format, chain MD [auth L] mmCIF format, chain ND [auth L] mmCIF format, chain WA [auth D]	BB [auth F] BE [auth M] DE [auth T] EB [auth G] FE [auth T] BB [auth F], BE [auth M], DE [auth T], EB [auth G], FE [auth T], MD [auth L], ND [auth L], WA [auth D]	(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 BB [auth F] Focus chain BE [auth M] Focus chain DE [auth T] Focus chain EB [auth G] Focus chain FE [auth T] Focus chain MD [auth L] Focus chain ND [auth L] Focus chain WA [auth D] Interactions & Density Focus chain BB [auth F] Focus chain BE [auth M] Focus chain DE [auth T] Focus chain EB [auth G] Focus chain FE [auth T] Focus chain MD [auth L] Focus chain ND [auth L] Focus chain WA [auth D]
UQ8 (Subject of Investigation/LOI) Query on UQ8 Download Ideal Coordinates CCD File SDF format, chain JD [auth L] SDF format, chain LD [auth L] SDF format, chain VD [auth M] MOL2 format, chain JD [auth L] MOL2 format, chain LD [auth L] MOL2 format, chain VD [auth M] mmCIF format, chain JD [auth L] mmCIF format, chain LD [auth L] mmCIF format, chain VD [auth M]	JD [auth L], LD [auth L], VD [auth M]	Ubiquinone-8 C₄₉ H₇₄ O₄ ICFIZJQGJAJRSU-SGHXUWJISA-N		Interactions Focus chain JD [auth L] Focus chain LD [auth L] Focus chain VD [auth M] Interactions & Density Focus chain JD [auth L] Focus chain LD [auth L] Focus chain VD [auth M]
LHG (Subject of Investigation/LOI) Query on LHG Download Ideal Coordinates CCD File SDF format, chain EE [auth T] MOL2 format, chain EE [auth T] mmCIF format, chain EE [auth T]	EE [auth T]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C₃₈ H₇₅ O₁₀ P BIABMEZBCHDPBV-MPQUPPDSSA-N		Interactions Focus chain EE [auth T] Interactions & Density Focus chain EE [auth T]
PEF Query on PEF Download Ideal Coordinates CCD File SDF format, chain AE [auth M] MOL2 format, chain AE [auth M] mmCIF format, chain AE [auth M]	AE [auth M]	DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE C₃₇ H₇₄ N O₈ P SLKDGVPOSSLUAI-PGUFJCEWSA-N		Interactions Focus chain AE [auth M] Interactions & Density Focus chain AE [auth M]
H4X (Subject of Investigation/LOI) Query on H4X Download Ideal Coordinates CCD File SDF format, chain YD [auth M] MOL2 format, chain YD [auth M] mmCIF format, chain YD [auth M]	YD [auth M]	(6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},24~{E},26~{E})-2,31-dimethoxy-2,6,10,14,19,23,27,31-octamethyl-dotriaconta-6,8,10,12,14,16,18,20,22,24,26-undecaene C₄₂ H₆₄ O₂ LCTIOHZQWXQPIB-VYCPWLLESA-N		Interactions Focus chain YD [auth M] Interactions & Density Focus chain YD [auth M]
A1ELD (Subject of Investigation/LOI) Query on A1ELD Download Ideal Coordinates CCD File SDF format, chain AC [auth O] SDF format, chain BD [auth g] SDF format, chain DD [auth q] SDF format, chain EC [auth b] SDF format, chain IC [auth o] SDF format, chain MA [auth A] SDF format, chain MC [auth r] SDF format, chain OB [auth J] SDF format, chain PA [auth B] SDF format, chain RA [auth C] SDF format, chain RC [auth j] SDF format, chain SB [auth R] SDF format, chain TB [auth R] SDF format, chain UC [auth d] SDF format, chain WC [auth e] SDF format, chain YC [auth f] MOL2 format, chain AC [auth O] MOL2 format, chain BD [auth g] MOL2 format, chain DD [auth q] MOL2 format, chain EC [auth b] MOL2 format, chain IC [auth o] MOL2 format, chain MA [auth A] MOL2 format, chain MC [auth r] MOL2 format, chain OB [auth J] MOL2 format, chain PA [auth B] MOL2 format, chain RA [auth C] MOL2 format, chain RC [auth j] MOL2 format, chain SB [auth R] MOL2 format, chain TB [auth R] MOL2 format, chain UC [auth d] MOL2 format, chain WC [auth e] MOL2 format, chain YC [auth f] mmCIF format, chain AC [auth O] mmCIF format, chain BD [auth g] mmCIF format, chain DD [auth q] mmCIF format, chain EC [auth b] mmCIF format, chain IC [auth o] mmCIF format, chain MA [auth A] mmCIF format, chain MC [auth r] mmCIF format, chain OB [auth J] mmCIF format, chain PA [auth B] mmCIF format, chain RA [auth C] mmCIF format, chain RC [auth j] mmCIF format, chain SB [auth R] mmCIF format, chain TB [auth R] mmCIF format, chain UC [auth d] mmCIF format, chain WC [auth e] mmCIF format, chain YC [auth f]	AC [auth O] BD [auth g] DD [auth q] EC [auth b] IC [auth o] AC [auth O], BD [auth g], DD [auth q], EC [auth b], IC [auth o], MA [auth A], MC [auth r], OB [auth J], PA [auth B], RA [auth C], RC [auth j], SB [auth R], TB [auth R], UC [auth d], WC [auth e], YC [auth f]	(2~{Z},4~{E},6~{E},8~{E},10~{E},12~{E},14~{E},16~{E})-2-[(1~{Z},3~{Z},5~{E})-8-methoxy-4,8-dimethyl-nona-1,3,5-trienyl]-6,11,15-trimethyl-17-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]heptadeca-2,4,6,8,10,12,14,16-octaenal C₄₁ H₅₆ O₃ DFOYVSCLGRVGJK-PCDZQMFBSA-N		Interactions Focus chain AC [auth O] Focus chain BD [auth g] Focus chain DD [auth q] Focus chain EC [auth b] Focus chain IC [auth o] Focus chain MA [auth A] Focus chain MC [auth r] Focus chain OB [auth J] Focus chain PA [auth B] Focus chain RA [auth C] Focus chain RC [auth j] Focus chain SB [auth R] Focus chain TB [auth R] Focus chain UC [auth d] Focus chain WC [auth e] Focus chain YC [auth f] Interactions & Density Focus chain AC [auth O] Focus chain BD [auth g] Focus chain DD [auth q] Focus chain EC [auth b] Focus chain IC [auth o] Focus chain MA [auth A] Focus chain MC [auth r] Focus chain OB [auth J] Focus chain PA [auth B] Focus chain RA [auth C] Focus chain RC [auth j] Focus chain SB [auth R] Focus chain TB [auth R] Focus chain UC [auth d] Focus chain WC [auth e] Focus chain YC [auth f]
A1EL2 (Subject of Investigation/LOI) Query on A1EL2 Download Ideal Coordinates CCD File SDF format, chain AB [auth F] SDF format, chain BC [auth O] SDF format, chain DB [auth G] SDF format, chain DC [auth P] SDF format, chain HB [auth Q] SDF format, chain LA [auth A] SDF format, chain LB [auth I] SDF format, chain NB [auth J] SDF format, chain NC [auth r] SDF format, chain OA [auth B] SDF format, chain OC [auth r] SDF format, chain QB [auth K] SDF format, chain SA [auth C] SDF format, chain VA [auth D] SDF format, chain XB [auth N] SDF format, chain YA [auth E] MOL2 format, chain AB [auth F] MOL2 format, chain BC [auth O] MOL2 format, chain DB [auth G] MOL2 format, chain DC [auth P] MOL2 format, chain HB [auth Q] MOL2 format, chain LA [auth A] MOL2 format, chain LB [auth I] MOL2 format, chain NB [auth J] MOL2 format, chain NC [auth r] MOL2 format, chain OA [auth B] MOL2 format, chain OC [auth r] MOL2 format, chain QB [auth K] MOL2 format, chain SA [auth C] MOL2 format, chain VA [auth D] MOL2 format, chain XB [auth N] MOL2 format, chain YA [auth E] mmCIF format, chain AB [auth F] mmCIF format, chain BC [auth O] mmCIF format, chain DB [auth G] mmCIF format, chain DC [auth P] mmCIF format, chain HB [auth Q] mmCIF format, chain LA [auth A] mmCIF format, chain LB [auth I] mmCIF format, chain NB [auth J] mmCIF format, chain NC [auth r] mmCIF format, chain OA [auth B] mmCIF format, chain OC [auth r] mmCIF format, chain QB [auth K] mmCIF format, chain SA [auth C] mmCIF format, chain VA [auth D] mmCIF format, chain XB [auth N] mmCIF format, chain YA [auth E]	AB [auth F] BC [auth O] DB [auth G] DC [auth P] HB [auth Q] AB [auth F], BC [auth O], DB [auth G], DC [auth P], HB [auth Q], LA [auth A], LB [auth I], NB [auth J], NC [auth r], OA [auth B], OC [auth r], QB [auth K], SA [auth C], VA [auth D], XB [auth N], YA [auth E]	(1~{R},2~{R})-3,3,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-4-ene-1,2-diol C₄₀ H₅₆ O₃ PKHJWTKRKQNNJE-RJLXQHJHSA-N		Interactions Focus chain AB [auth F] Focus chain BC [auth O] Focus chain DB [auth G] Focus chain DC [auth P] Focus chain HB [auth Q] Focus chain LA [auth A] Focus chain LB [auth I] Focus chain NB [auth J] Focus chain NC [auth r] Focus chain OA [auth B] Focus chain OC [auth r] Focus chain QB [auth K] Focus chain SA [auth C] Focus chain VA [auth D] Focus chain XB [auth N] Focus chain YA [auth E] Interactions & Density Focus chain AB [auth F] Focus chain BC [auth O] Focus chain DB [auth G] Focus chain DC [auth P] Focus chain HB [auth Q] Focus chain LA [auth A] Focus chain LB [auth I] Focus chain NB [auth J] Focus chain NC [auth r] Focus chain OA [auth B] Focus chain OC [auth r] Focus chain QB [auth K] Focus chain SA [auth C] Focus chain VA [auth D] Focus chain XB [auth N] Focus chain YA [auth E]
LMT Query on LMT Download Ideal Coordinates CCD File SDF format, chain FB [auth G] SDF format, chain OD [auth L] SDF format, chain YB [auth N] MOL2 format, chain FB [auth G] MOL2 format, chain OD [auth L] MOL2 format, chain YB [auth N] mmCIF format, chain FB [auth G] mmCIF format, chain OD [auth L] mmCIF format, chain YB [auth N]	FB [auth G], OD [auth L], YB [auth N]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain FB [auth G] Focus chain OD [auth L] Focus chain YB [auth N] Interactions & Density Focus chain FB [auth G] Focus chain OD [auth L] Focus chain YB [auth N]
8K6 Query on 8K6 Download Ideal Coordinates CCD File SDF format, chain AD [auth f] SDF format, chain IB [auth Q] SDF format, chain JB [auth Q] SDF format, chain PD [auth L] SDF format, chain QD [auth L] SDF format, chain RD [auth L] SDF format, chain SD [auth L] SDF format, chain TA [auth C] SDF format, chain TD [auth H] SDF format, chain VB [auth S] SDF format, chain ZD [auth M] MOL2 format, chain AD [auth f] MOL2 format, chain IB [auth Q] MOL2 format, chain JB [auth Q] MOL2 format, chain PD [auth L] MOL2 format, chain QD [auth L] MOL2 format, chain RD [auth L] MOL2 format, chain SD [auth L] MOL2 format, chain TA [auth C] MOL2 format, chain TD [auth H] MOL2 format, chain VB [auth S] MOL2 format, chain ZD [auth M] mmCIF format, chain AD [auth f] mmCIF format, chain IB [auth Q] mmCIF format, chain JB [auth Q] mmCIF format, chain PD [auth L] mmCIF format, chain QD [auth L] mmCIF format, chain RD [auth L] mmCIF format, chain SD [auth L] mmCIF format, chain TA [auth C] mmCIF format, chain TD [auth H] mmCIF format, chain VB [auth S] mmCIF format, chain ZD [auth M]	AD [auth f] IB [auth Q] JB [auth Q] PD [auth L] QD [auth L] AD [auth f], IB [auth Q], JB [auth Q], PD [auth L], QD [auth L], RD [auth L], SD [auth L], TA [auth C], TD [auth H], VB [auth S], ZD [auth M]	Octadecane C₁₈ H₃₈ RZJRJXONCZWCBN-UHFFFAOYSA-N		Interactions Focus chain AD [auth f] Focus chain IB [auth Q] Focus chain JB [auth Q] Focus chain PD [auth L] Focus chain QD [auth L] Focus chain RD [auth L] Focus chain SD [auth L] Focus chain TA [auth C] Focus chain TD [auth H] Focus chain VB [auth S] Focus chain ZD [auth M] Interactions & Density Focus chain AD [auth f] Focus chain IB [auth Q] Focus chain JB [auth Q] Focus chain PD [auth L] Focus chain QD [auth L] Focus chain RD [auth L] Focus chain SD [auth L] Focus chain TA [auth C] Focus chain TD [auth H] Focus chain VB [auth S] Focus chain ZD [auth M]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain CE [auth M] MOL2 format, chain CE [auth M] mmCIF format, chain CE [auth M]	CE [auth M]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain CE [auth M] Interactions & Density Focus chain CE [auth M]
FE (Subject of Investigation/LOI) Query on FE Download Ideal Coordinates CCD File SDF format, chain XD [auth M] MOL2 format, chain XD [auth M] mmCIF format, chain XD [auth M]	XD [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain XD [auth M] Interactions & Density Focus chain XD [auth M]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.27 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2_4158

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-10

Deposition Author(s):

Yue, X.-Y.

Wang, G.-L.

Yu, L.-J.

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2022YFC3401800
Ministry of Science and Technology (MoST, China)	China	ZR2019ZD48
Ministry of Science and Technology (MoST, China)	China	2022SZX12