9K3Q

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 PDBTMMemProtMD

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 1.0 of the entry. See complete history.

Literature

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

Liu, Z.K., Wang, P., Liu, L.N.

To be published.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C190
Sequence Annotations Expand
Reference Sequence LOADING

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02947
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Reference Sequence LOADING

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7M149
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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10717
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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10718
Sequence Annotations Expand
Reference Sequence LOADING

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 AC [auth S] SDF format, chain BB [auth G] SDF format, chain BC [auth T] SDF format, chain CB [auth H] 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 HC [auth X] SDF format, chain IB [auth K] SDF format, chain JA [auth 1] SDF format, chain JC [auth Y] SDF format, chain KC [auth Z] SDF format, chain LA [auth 2] SDF format, chain LB [auth L] SDF format, chain MB [auth L] SDF format, chain MC [auth d] SDF format, chain NA [auth 3] SDF format, chain OA [auth 4] SDF format, chain OC [auth m] SDF format, chain QA [auth 5] SDF format, chain QB [auth M] SDF format, chain QC [auth n] 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 UA [auth 8] SDF format, chain VB [auth O] SDF format, chain WA [auth 9] SDF format, chain XA [auth A] SDF format, chain XB [auth Q] SDF format, chain YA [auth D] SDF format, chain YB [auth R] SDF format, chain ZA [auth E] MOL2 format, chain AB [auth F] MOL2 format, chain AC [auth S] MOL2 format, chain BB [auth G] MOL2 format, chain BC [auth T] MOL2 format, chain CB [auth H] 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 HC [auth X] MOL2 format, chain IB [auth K] MOL2 format, chain JA [auth 1] MOL2 format, chain JC [auth Y] MOL2 format, chain KC [auth Z] MOL2 format, chain LA [auth 2] MOL2 format, chain LB [auth L] MOL2 format, chain MB [auth L] MOL2 format, chain MC [auth d] MOL2 format, chain NA [auth 3] MOL2 format, chain OA [auth 4] MOL2 format, chain OC [auth m] MOL2 format, chain QA [auth 5] MOL2 format, chain QB [auth M] MOL2 format, chain QC [auth n] 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 UA [auth 8] MOL2 format, chain VB [auth O] MOL2 format, chain WA [auth 9] MOL2 format, chain XA [auth A] MOL2 format, chain XB [auth Q] MOL2 format, chain YA [auth D] MOL2 format, chain YB [auth R] MOL2 format, chain ZA [auth E] mmCIF format, chain AB [auth F] mmCIF format, chain AC [auth S] mmCIF format, chain BB [auth G] mmCIF format, chain BC [auth T] mmCIF format, chain CB [auth H] 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 HC [auth X] mmCIF format, chain IB [auth K] mmCIF format, chain JA [auth 1] mmCIF format, chain JC [auth Y] mmCIF format, chain KC [auth Z] mmCIF format, chain LA [auth 2] mmCIF format, chain LB [auth L] mmCIF format, chain MB [auth L] mmCIF format, chain MC [auth d] mmCIF format, chain NA [auth 3] mmCIF format, chain OA [auth 4] mmCIF format, chain OC [auth m] mmCIF format, chain QA [auth 5] mmCIF format, chain QB [auth M] mmCIF format, chain QC [auth n] 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 UA [auth 8] mmCIF format, chain VB [auth O] mmCIF format, chain WA [auth 9] mmCIF format, chain XA [auth A] mmCIF format, chain XB [auth Q] mmCIF format, chain YA [auth D] mmCIF format, chain YB [auth R] mmCIF format, chain ZA [auth E]	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 HB [auth K] SDF format, chain IC [auth Y] SDF format, chain KA [auth 1] SDF format, chain LC [auth d] SDF format, chain MA [auth 3] SDF format, chain NC [auth m] 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] MOL2 format, chain CC [auth U] MOL2 format, chain EB [auth I] MOL2 format, chain FC [auth W] MOL2 format, chain HB [auth K] MOL2 format, chain IC [auth Y] MOL2 format, chain KA [auth 1] MOL2 format, chain LC [auth d] MOL2 format, chain MA [auth 3] MOL2 format, chain NC [auth m] 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] mmCIF format, chain CC [auth U] mmCIF format, chain EB [auth I] mmCIF format, chain FC [auth W] mmCIF format, chain HB [auth K] mmCIF format, chain IC [auth Y] mmCIF format, chain KA [auth 1] mmCIF format, chain LC [auth d] mmCIF format, chain MA [auth 3] mmCIF format, chain NC [auth m] 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]	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]