9K3Q | pdb_00009k3q

Cryo-EM structure of the Rhodospirillum rubrum RC-LH1 complex

PDB DOI: https://doi.org/10.2210/pdb9K3Q/pdb
EM Map EMD-62025: EMDB EMDataResource

Classification: PHOTOSYNTHESIS
Organism(s): Rhodospirillum rubrum
Expression System: Rhodospirillum rubrum
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD

Deposited: 2024-10-19 Released: 2024-12-04
Deposition Author(s): Liu, Z.K., Wang, P., Liu, L.N.
Funding Organization(s): Royal Society

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.02 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

Characterization of the Structure and Function of the Photosynthetic RC-LH1 Core Supercomplex From Rhodospirillum rubrum.

Christianson, B., Liu, Z., Zhang, Y., Wang, C., Gardner, A.M., Zhang, Y.Z., Wang, P., Liu, L.N.

(2025) Physiol Plant 177: e70275-e70275

PubMed: 40384483 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1111/ppl.70275
Primary Citation Related Structures:
9K3Q

PubMed Abstract:
Photosynthetic reaction center-light harvesting 1 (RC-LH1) core supercomplexes are essential for energy capture and electron transport in purple bacteria. Rhodospirillum rubrum, a model organism for bacterial photosynthesis, features an RC-LH1 architecture with a closed LH1 ring and lacks the peripheral LH2 antenna in the photosynthetic membranes. How this unique RC-LH1 supercomplex performs energy transfer and quinone transport remains unclear. Here, we characterized both the structural and functional properties of Rsp. rubrum RC-LH1 supercomplex using cryo-electron microscopy (cryo-EM), transient absorption (TA) spectroscopy, and cytochrome c ₂ oxidation assays. Cryo-EM of the RC-LH1 monomeric structure revealed a closed LH1 ring of 16 αβ-polypeptides encircling the RC, with weaker RC-LH1 interactions than other RC-LH1 structures reported. TA spectra and cytochrome c ₂ oxidation assays showed that Rsp. rubrum RC-LH1 monomer with a closed LH1 ring exhibits slower and more distributed excitation energy transfer (EET) kinetics from LH1 to RC and slower electron transport rates than Rba. sphaeroides RC-LH1 monomer with a large opening in the LH1 ring. Our findings provide insight into the unique architecture and spectroscopic properties of Rsp. rubrum RC-LH1 supercomplex. This study enhances our understanding of bacterial photosynthetic mechanisms and lays the foundation for bioengineering applications in artificial photosynthetic systems.

Organizational Affiliation

Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.

Macromolecule Content

Total Structure Weight: 300.81 kDa
Atom Count: 21,510
Modeled Residue Count: 2,212
Deposited Residue Count: 2,212
Unique protein chains: 5

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Light-harvesting protein B-870 beta chain	A [auth 1] AA [auth U] C [auth 3] CA [auth W] E [auth 5] A [auth 1], AA [auth U], C [auth 3], CA [auth W], E [auth 5], EA [auth Y], G [auth 7], GA [auth d], HA [auth m], I [auth 9], IA [auth n], P [auth I], R [auth K], V [auth O], W [auth Q], Y [auth S]	44	Rhodospirillum rubrum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P0C190 (Rhodospirillum rubrum) Explore P0C190 Go to UniProtKB: P0C190
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0C190
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-870 alpha chain	B [auth 2] BA [auth V] D [auth 4] DA [auth X] F [auth 6] B [auth 2], BA [auth V], D [auth 4], DA [auth X], F [auth 6], FA [auth Z], H [auth 8], J [auth A], K [auth D], L [auth E], M [auth F], N [auth G], Q [auth J], U [auth N], X [auth R], Z [auth T]	45	Rhodospirillum rubrum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P02947 (Rhodospirillum rubrum) Explore P02947 Go to UniProtKB: P02947
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02947
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Photoreaction center protein H	O [auth H]	255	Rhodospirillum rubrum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q7M149 (Rhodospirillum rubrum) Explore Q7M149 Go to UniProtKB: Q7M149
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7M149
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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	S [auth L]	274	Rhodospirillum rubrum	Mutation(s): 0 Gene Names: pufL Membrane Entity: Yes
UniProt
Find proteins for P10717 (Rhodospirillum rubrum) Explore P10717 Go to UniProtKB: P10717
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10717
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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	T [auth M]	259	Rhodospirillum rubrum	Mutation(s): 0 Gene Names: Rru_A2974 Membrane Entity: Yes
UniProt
Find proteins for P10718 (Rhodospirillum rubrum) Explore P10718 Go to UniProtKB: P10718
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10718
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
07D (Subject of Investigation/LOI) Query on 07D Download:Ideal Coordinates CCD File SDF format, chain AB [auth F] SDF format, chain BB [auth G] SDF format, chain BC [auth T] SDF format, chain DC [auth U] SDF format, chain EC [auth V] SDF format, chain FB [auth I] SDF format, chain GB [auth J] SDF format, chain GC [auth W] SDF format, chain JA [auth 1] SDF format, chain JC [auth Y] SDF format, chain LB [auth L] SDF format, chain MB [auth L] SDF format, chain NA [auth 3] SDF format, chain QA [auth 5] SDF format, chain QB [auth M] SDF format, chain RA [auth 6] SDF format, chain RB [auth M] SDF format, chain TA [auth 7] SDF format, chain TB [auth N] SDF format, chain VB [auth O] SDF format, chain YB [auth R] SDF format, chain ZA [auth E] SDF format, chain YA [auth D] SDF format, chain XB [auth Q] SDF format, chain XA [auth A] SDF format, chain WA [auth 9] SDF format, chain UA [auth 8] SDF format, chain QC [auth n] SDF format, chain OC [auth m] SDF format, chain OA [auth 4] SDF format, chain MC [auth d] SDF format, chain LA [auth 2] SDF format, chain KC [auth Z] SDF format, chain IB [auth K] SDF format, chain HC [auth X] SDF format, chain CB [auth H] SDF format, chain AC [auth S] MOL2 format, chain AB [auth F] MOL2 format, chain BB [auth G] MOL2 format, chain BC [auth T] MOL2 format, chain DC [auth U] MOL2 format, chain EC [auth V] MOL2 format, chain FB [auth I] MOL2 format, chain GB [auth J] MOL2 format, chain GC [auth W] MOL2 format, chain JA [auth 1] MOL2 format, chain JC [auth Y] MOL2 format, chain LB [auth L] MOL2 format, chain MB [auth L] MOL2 format, chain NA [auth 3] MOL2 format, chain QA [auth 5] MOL2 format, chain QB [auth M] MOL2 format, chain RA [auth 6] MOL2 format, chain RB [auth M] MOL2 format, chain TA [auth 7] MOL2 format, chain TB [auth N] MOL2 format, chain VB [auth O] MOL2 format, chain YB [auth R] MOL2 format, chain ZA [auth E] MOL2 format, chain YA [auth D] MOL2 format, chain XB [auth Q] MOL2 format, chain XA [auth A] MOL2 format, chain WA [auth 9] MOL2 format, chain UA [auth 8] MOL2 format, chain QC [auth n] MOL2 format, chain OC [auth m] MOL2 format, chain OA [auth 4] MOL2 format, chain MC [auth d] MOL2 format, chain LA [auth 2] MOL2 format, chain KC [auth Z] MOL2 format, chain IB [auth K] MOL2 format, chain HC [auth X] MOL2 format, chain CB [auth H] MOL2 format, chain AC [auth S] mmCIF format, chain AB [auth F] mmCIF format, chain BB [auth G] mmCIF format, chain BC [auth T] mmCIF format, chain DC [auth U] mmCIF format, chain EC [auth V] mmCIF format, chain FB [auth I] mmCIF format, chain GB [auth J] mmCIF format, chain GC [auth W] mmCIF format, chain JA [auth 1] mmCIF format, chain JC [auth Y] mmCIF format, chain LB [auth L] mmCIF format, chain MB [auth L] mmCIF format, chain NA [auth 3] mmCIF format, chain QA [auth 5] mmCIF format, chain QB [auth M] mmCIF format, chain RA [auth 6] mmCIF format, chain RB [auth M] mmCIF format, chain TA [auth 7] mmCIF format, chain TB [auth N] mmCIF format, chain VB [auth O] mmCIF format, chain YB [auth R] mmCIF format, chain ZA [auth E] mmCIF format, chain YA [auth D] mmCIF format, chain XB [auth Q] mmCIF format, chain XA [auth A] mmCIF format, chain WA [auth 9] mmCIF format, chain UA [auth 8] mmCIF format, chain QC [auth n] mmCIF format, chain OC [auth m] mmCIF format, chain OA [auth 4] mmCIF format, chain MC [auth d] mmCIF format, chain LA [auth 2] mmCIF format, chain KC [auth Z] mmCIF format, chain IB [auth K] mmCIF format, chain HC [auth X] mmCIF format, chain CB [auth H] mmCIF format, chain AC [auth S]	AB [auth F] AC [auth S] BB [auth G] BC [auth T] CB [auth H] AB [auth F], AC [auth S], BB [auth G], BC [auth T], CB [auth H], DC [auth U], EC [auth V], FB [auth I], GB [auth J], GC [auth W], HC [auth X], IB [auth K], JA [auth 1], JC [auth Y], KC [auth Z], LA [auth 2], LB [auth L], MB [auth L], MC [auth d], NA [auth 3], OA [auth 4], OC [auth m], QA [auth 5], QB [auth M], QC [auth n], RA [auth 6], RB [auth M], TA [auth 7], TB [auth N], UA [auth 8], VB [auth O], WA [auth 9], XA [auth A], XB [auth Q], YA [auth D], YB [auth R], ZA [auth E]	Trans-Geranyl BACTERIOCHLOROPHYLL A C₅₅ H₆₄ Mg N₄ O₆ ZBSZXIUSELHDGQ-POZHEDQMSA-M		Interactions Focus chain AB [auth F] Focus chain AC [auth S] Focus chain BB [auth G] Focus chain BC [auth T] Focus chain CB [auth H] Focus chain DC [auth U] Focus chain EC [auth V] Focus chain FB [auth I] Focus chain GB [auth J] Focus chain GC [auth W] Focus chain HC [auth X] Focus chain IB [auth K] Focus chain JA [auth 1] Focus chain JC [auth Y] Focus chain KC [auth Z] Focus chain LA [auth 2] Focus chain LB [auth L] Focus chain MB [auth L] Focus chain MC [auth d] Focus chain NA [auth 3] Focus chain OA [auth 4] Focus chain OC [auth m] Focus chain QA [auth 5] Focus chain QB [auth M] Focus chain QC [auth n] Focus chain RA [auth 6] Focus chain RB [auth M] Focus chain TA [auth 7] Focus chain TB [auth N] Focus chain UA [auth 8] Focus chain VB [auth O] Focus chain WA [auth 9] Focus chain XA [auth A] Focus chain XB [auth Q] Focus chain YA [auth D] Focus chain YB [auth R] Focus chain ZA [auth E] Interactions & Density Focus chain AB [auth F] Focus chain AC [auth S] Focus chain BB [auth G] Focus chain BC [auth T] Focus chain CB [auth H] Focus chain DC [auth U] Focus chain EC [auth V] Focus chain FB [auth I] Focus chain GB [auth J] Focus chain GC [auth W] Focus chain HC [auth X] Focus chain IB [auth K] Focus chain JA [auth 1] Focus chain JC [auth Y] Focus chain KC [auth Z] Focus chain LA [auth 2] Focus chain LB [auth L] Focus chain MB [auth L] Focus chain MC [auth d] Focus chain NA [auth 3] Focus chain OA [auth 4] Focus chain OC [auth m] Focus chain QA [auth 5] Focus chain QB [auth M] Focus chain QC [auth n] Focus chain RA [auth 6] Focus chain RB [auth M] Focus chain TA [auth 7] Focus chain TB [auth N] Focus chain UA [auth 8] Focus chain VB [auth O] Focus chain WA [auth 9] Focus chain XA [auth A] Focus chain XB [auth Q] Focus chain YA [auth D] Focus chain YB [auth R] Focus chain ZA [auth E]
BPH (Subject of Investigation/LOI) Query on BPH Download:Ideal Coordinates CCD File SDF format, chain JB [auth L] SDF format, chain OB [auth M] MOL2 format, chain JB [auth L] MOL2 format, chain OB [auth M] mmCIF format, chain JB [auth L] mmCIF format, chain OB [auth M]	JB [auth L], OB [auth M]	BACTERIOPHEOPHYTIN A C₅₅ H₇₆ N₄ O₆ KWOZSBGNAHVCKG-SZQBJALDSA-N		Interactions Focus chain JB [auth L] Focus chain OB [auth M] Interactions & Density Focus chain JB [auth L] Focus chain OB [auth M]
U10 (Subject of Investigation/LOI) Query on U10 Download:Ideal Coordinates CCD File SDF format, chain KB [auth L] SDF format, chain NB [auth L] SDF format, chain PB [auth M] MOL2 format, chain KB [auth L] MOL2 format, chain NB [auth L] MOL2 format, chain PB [auth M] mmCIF format, chain KB [auth L] mmCIF format, chain NB [auth L] mmCIF format, chain PB [auth M]	KB [auth L], NB [auth L], PB [auth M]	UBIQUINONE-10 C₅₉ H₉₀ O₄ ACTIUHUUMQJHFO-UPTCCGCDSA-N		Interactions Focus chain KB [auth L] Focus chain NB [auth L] Focus chain PB [auth M] Interactions & Density Focus chain KB [auth L] Focus chain NB [auth L] Focus chain PB [auth M]
CRT Query on CRT Download:Ideal Coordinates CCD File SDF format, chain CC [auth U] SDF format, chain EB [auth I] SDF format, chain FC [auth W] SDF format, chain KA [auth 1] SDF format, chain PA [auth 5] SDF format, chain PC [auth n] SDF format, chain SA [auth 7] SDF format, chain SB [auth M] SDF format, chain UB [auth O] SDF format, chain VA [auth 9] SDF format, chain WB [auth Q] SDF format, chain ZB [auth S] SDF format, chain NC [auth m] SDF format, chain MA [auth 3] SDF format, chain LC [auth d] SDF format, chain IC [auth Y] SDF format, chain HB [auth K] MOL2 format, chain CC [auth U] MOL2 format, chain EB [auth I] MOL2 format, chain FC [auth W] MOL2 format, chain KA [auth 1] MOL2 format, chain PA [auth 5] MOL2 format, chain PC [auth n] MOL2 format, chain SA [auth 7] MOL2 format, chain SB [auth M] MOL2 format, chain UB [auth O] MOL2 format, chain VA [auth 9] MOL2 format, chain WB [auth Q] MOL2 format, chain ZB [auth S] MOL2 format, chain NC [auth m] MOL2 format, chain MA [auth 3] MOL2 format, chain LC [auth d] MOL2 format, chain IC [auth Y] MOL2 format, chain HB [auth K] mmCIF format, chain CC [auth U] mmCIF format, chain EB [auth I] mmCIF format, chain FC [auth W] mmCIF format, chain KA [auth 1] mmCIF format, chain PA [auth 5] mmCIF format, chain PC [auth n] mmCIF format, chain SA [auth 7] mmCIF format, chain SB [auth M] mmCIF format, chain UB [auth O] mmCIF format, chain VA [auth 9] mmCIF format, chain WB [auth Q] mmCIF format, chain ZB [auth S] mmCIF format, chain NC [auth m] mmCIF format, chain MA [auth 3] mmCIF format, chain LC [auth d] mmCIF format, chain IC [auth Y] mmCIF format, chain HB [auth K]	CC [auth U] EB [auth I] FC [auth W] HB [auth K] IC [auth Y] CC [auth U], EB [auth I], FC [auth W], HB [auth K], IC [auth Y], KA [auth 1], LC [auth d], MA [auth 3], NC [auth m], PA [auth 5], PC [auth n], SA [auth 7], SB [auth M], UB [auth O], VA [auth 9], WB [auth Q], ZB [auth S]	SPIRILLOXANTHIN C₄₂ H₆₀ O₂ VAZQBTJCYODOSV-RISZBRKMSA-N		Interactions Focus chain CC [auth U] Focus chain EB [auth I] Focus chain FC [auth W] Focus chain HB [auth K] Focus chain IC [auth Y] Focus chain KA [auth 1] Focus chain LC [auth d] Focus chain MA [auth 3] Focus chain NC [auth m] Focus chain PA [auth 5] Focus chain PC [auth n] Focus chain SA [auth 7] Focus chain SB [auth M] Focus chain UB [auth O] Focus chain VA [auth 9] Focus chain WB [auth Q] Focus chain ZB [auth S] Interactions & Density Focus chain CC [auth U] Focus chain EB [auth I] Focus chain FC [auth W] Focus chain HB [auth K] Focus chain IC [auth Y] Focus chain KA [auth 1] Focus chain LC [auth d] Focus chain MA [auth 3] Focus chain NC [auth m] Focus chain PA [auth 5] Focus chain PC [auth n] Focus chain SA [auth 7] Focus chain SB [auth M] Focus chain UB [auth O] Focus chain VA [auth 9] Focus chain WB [auth Q] Focus chain ZB [auth S]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain DB [auth H] MOL2 format, chain DB [auth H] mmCIF format, chain DB [auth H]	DB [auth H]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain DB [auth H] Interactions & Density Focus chain DB [auth H]