9EK8 | pdb_00009ek8

Light Harvesting complex 2 (LH2), B800-B850, of Rhodoblastus (Rbl.) acidophilus strain 7750

PDB DOI: https://doi.org/10.2210/pdb9EK8/pdb
EM Map EMD-48112: EMDB EMDataResource

Classification: PHOTOSYNTHESIS
Organism(s): Rhodoblastus acidophilus
Mutation(s): No

Deposited: 2024-12-01 Released: 2025-07-30
Deposition Author(s): Harris, D., Schlau-Cohen, G.S.
Funding Organization(s): Department of Energy (DOE, United States), National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.35 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

Robust light-harvesting properties upon chromatic acclimation in purple bacteria

Wang, D., Harris, D., Chuang, C., Schmidt, G.P., Feibig, O.C., Schlau-Cohen, G.S.

To be published.

Macromolecule Content

Total Structure Weight: 124.13 kDa
Atom Count: 8,847
Modeled Residue Count: 801
Deposited Residue Count: 801
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 alpha chain	A, C, E, G, I A, C, E, G, I, K, M, O, Q	48	Rhodoblastus acidophilus	Mutation(s): 0
UniProt
Find proteins for P26789 (Rhodoblastus acidophilus) Explore P26789 Go to UniProtKB: P26789
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P26789
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 beta chain	B, D, F, H, J B, D, F, H, J, L, N, P, R	41	Rhodoblastus acidophilus	Mutation(s): 0
UniProt
Find proteins for P26790 (Rhodoblastus acidophilus) Explore P26790 Go to UniProtKB: P26790
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P26790
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 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 AB [auth L] SDF format, chain CA [auth D] SDF format, chain CB [auth M] SDF format, chain DB [auth M] SDF format, chain EA [auth E] SDF format, chain FA [auth E] SDF format, chain FB [auth N] SDF format, chain IA [auth F] SDF format, chain IB [auth O] SDF format, chain JB [auth O] SDF format, chain KA [auth G] SDF format, chain LA [auth G] SDF format, chain LB [auth P] SDF format, chain OA [auth H] SDF format, chain OB [auth Q] SDF format, chain PB [auth Q] SDF format, chain RA [auth I] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain UA [auth J] SDF format, chain W [auth B] SDF format, chain WA [auth K] SDF format, chain XA [auth K] SDF format, chain Y [auth C] SDF format, chain Z [auth C] SDF format, chain SB [auth R] SDF format, chain QA [auth I] MOL2 format, chain AB [auth L] MOL2 format, chain CA [auth D] MOL2 format, chain CB [auth M] MOL2 format, chain DB [auth M] MOL2 format, chain EA [auth E] MOL2 format, chain FA [auth E] MOL2 format, chain FB [auth N] MOL2 format, chain IA [auth F] MOL2 format, chain IB [auth O] MOL2 format, chain JB [auth O] MOL2 format, chain KA [auth G] MOL2 format, chain LA [auth G] MOL2 format, chain LB [auth P] MOL2 format, chain OA [auth H] MOL2 format, chain OB [auth Q] MOL2 format, chain PB [auth Q] MOL2 format, chain RA [auth I] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain UA [auth J] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth K] MOL2 format, chain XA [auth K] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain SB [auth R] MOL2 format, chain QA [auth I] mmCIF format, chain AB [auth L] mmCIF format, chain CA [auth D] mmCIF format, chain CB [auth M] mmCIF format, chain DB [auth M] mmCIF format, chain EA [auth E] mmCIF format, chain FA [auth E] mmCIF format, chain FB [auth N] mmCIF format, chain IA [auth F] mmCIF format, chain IB [auth O] mmCIF format, chain JB [auth O] mmCIF format, chain KA [auth G] mmCIF format, chain LA [auth G] mmCIF format, chain LB [auth P] mmCIF format, chain OA [auth H] mmCIF format, chain OB [auth Q] mmCIF format, chain PB [auth Q] mmCIF format, chain RA [auth I] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain UA [auth J] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth K] mmCIF format, chain XA [auth K] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain SB [auth R] mmCIF format, chain QA [auth I]	AB [auth L] CA [auth D] CB [auth M] DB [auth M] EA [auth E] AB [auth L], CA [auth D], CB [auth M], DB [auth M], EA [auth E], FA [auth E], FB [auth N], IA [auth F], IB [auth O], JB [auth O], KA [auth G], LA [auth G], LB [auth P], OA [auth H], OB [auth Q], PB [auth Q], QA [auth I], RA [auth I], S [auth A], SB [auth R], T [auth A], UA [auth J], W [auth B], WA [auth K], XA [auth K], Y [auth C], Z [auth C]	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-AGGZHOMASA-M		Interactions Focus chain AB [auth L] Focus chain CA [auth D] Focus chain CB [auth M] Focus chain DB [auth M] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain FB [auth N] Focus chain IA [auth F] Focus chain IB [auth O] Focus chain JB [auth O] Focus chain KA [auth G] Focus chain LA [auth G] Focus chain LB [auth P] Focus chain OA [auth H] Focus chain OB [auth Q] Focus chain PB [auth Q] Focus chain QA [auth I] Focus chain RA [auth I] Focus chain S [auth A] Focus chain SB [auth R] Focus chain T [auth A] Focus chain UA [auth J] Focus chain W [auth B] Focus chain WA [auth K] Focus chain XA [auth K] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AB [auth L] Focus chain CA [auth D] Focus chain CB [auth M] Focus chain DB [auth M] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain FB [auth N] Focus chain IA [auth F] Focus chain IB [auth O] Focus chain JB [auth O] Focus chain KA [auth G] Focus chain LA [auth G] Focus chain LB [auth P] Focus chain OA [auth H] Focus chain OB [auth Q] Focus chain PB [auth Q] Focus chain QA [auth I] Focus chain RA [auth I] Focus chain S [auth A] Focus chain SB [auth R] Focus chain T [auth A] Focus chain UA [auth J] Focus chain W [auth B] Focus chain WA [auth K] Focus chain XA [auth K] Focus chain Y [auth C] Focus chain Z [auth C]
IRM (Subject of Investigation/LOI) Query on IRM Download Ideal Coordinates CCD File SDF format, chain BB [auth L] SDF format, chain DA [auth D] SDF format, chain GB [auth N] SDF format, chain HA [auth E] SDF format, chain MB [auth P] SDF format, chain PA [auth H] SDF format, chain TB [auth R] SDF format, chain VA [auth J] SDF format, chain X [auth B] MOL2 format, chain BB [auth L] MOL2 format, chain DA [auth D] MOL2 format, chain GB [auth N] MOL2 format, chain HA [auth E] MOL2 format, chain MB [auth P] MOL2 format, chain PA [auth H] MOL2 format, chain TB [auth R] MOL2 format, chain VA [auth J] MOL2 format, chain X [auth B] mmCIF format, chain BB [auth L] mmCIF format, chain DA [auth D] mmCIF format, chain GB [auth N] mmCIF format, chain HA [auth E] mmCIF format, chain MB [auth P] mmCIF format, chain PA [auth H] mmCIF format, chain TB [auth R] mmCIF format, chain VA [auth J] mmCIF format, chain X [auth B]	BB [auth L] DA [auth D] GB [auth N] HA [auth E] MB [auth P] BB [auth L], DA [auth D], GB [auth N], HA [auth E], MB [auth P], PA [auth H], TB [auth R], VA [auth J], X [auth B]	1,2-Dihydro-psi,psi-caroten-1-ol C₄₀ H₅₈ O CNYVJTJLUKKCGM-RGGGOQHISA-N		Interactions Focus chain BB [auth L] Focus chain DA [auth D] Focus chain GB [auth N] Focus chain HA [auth E] Focus chain MB [auth P] Focus chain PA [auth H] Focus chain TB [auth R] Focus chain VA [auth J] Focus chain X [auth B] Interactions & Density Focus chain BB [auth L] Focus chain DA [auth D] Focus chain GB [auth N] Focus chain HA [auth E] Focus chain MB [auth P] Focus chain PA [auth H] Focus chain TB [auth R] Focus chain VA [auth J] Focus chain X [auth B]
LMT Query on LMT Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain HB [auth N] SDF format, chain JA [auth F] SDF format, chain NB [auth P] SDF format, chain RB [auth R] SDF format, chain SA [auth I] SDF format, chain V [auth A] SDF format, chain ZA [auth L] SDF format, chain NA [auth H] MOL2 format, chain BA [auth D] MOL2 format, chain HB [auth N] MOL2 format, chain JA [auth F] MOL2 format, chain NB [auth P] MOL2 format, chain RB [auth R] MOL2 format, chain SA [auth I] MOL2 format, chain V [auth A] MOL2 format, chain ZA [auth L] MOL2 format, chain NA [auth H] mmCIF format, chain BA [auth D] mmCIF format, chain HB [auth N] mmCIF format, chain JA [auth F] mmCIF format, chain NB [auth P] mmCIF format, chain RB [auth R] mmCIF format, chain SA [auth I] mmCIF format, chain V [auth A] mmCIF format, chain ZA [auth L] mmCIF format, chain NA [auth H]	BA [auth D] HB [auth N] JA [auth F] NA [auth H] NB [auth P] BA [auth D], HB [auth N], JA [auth F], NA [auth H], NB [auth P], RB [auth R], SA [auth I], V [auth A], ZA [auth L]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain BA [auth D] Focus chain HB [auth N] Focus chain JA [auth F] Focus chain NA [auth H] Focus chain NB [auth P] Focus chain RB [auth R] Focus chain SA [auth I] Focus chain V [auth A] Focus chain ZA [auth L] Interactions & Density Focus chain BA [auth D] Focus chain HB [auth N] Focus chain JA [auth F] Focus chain NA [auth H] Focus chain NB [auth P] Focus chain RB [auth R] Focus chain SA [auth I] Focus chain V [auth A] Focus chain ZA [auth L]
LDA Query on LDA Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain GA [auth E] SDF format, chain KB [auth O] SDF format, chain MA [auth G] SDF format, chain QB [auth Q] SDF format, chain TA [auth I] SDF format, chain U [auth A] SDF format, chain YA [auth K] SDF format, chain EB [auth M] MOL2 format, chain AA [auth C] MOL2 format, chain GA [auth E] MOL2 format, chain KB [auth O] MOL2 format, chain MA [auth G] MOL2 format, chain QB [auth Q] MOL2 format, chain TA [auth I] MOL2 format, chain U [auth A] MOL2 format, chain YA [auth K] MOL2 format, chain EB [auth M] mmCIF format, chain AA [auth C] mmCIF format, chain GA [auth E] mmCIF format, chain KB [auth O] mmCIF format, chain MA [auth G] mmCIF format, chain QB [auth Q] mmCIF format, chain TA [auth I] mmCIF format, chain U [auth A] mmCIF format, chain YA [auth K] mmCIF format, chain EB [auth M]	AA [auth C] EB [auth M] GA [auth E] KB [auth O] MA [auth G] AA [auth C], EB [auth M], GA [auth E], KB [auth O], MA [auth G], QB [auth Q], TA [auth I], U [auth A], YA [auth K]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain EB [auth M] Focus chain GA [auth E] Focus chain KB [auth O] Focus chain MA [auth G] Focus chain QB [auth Q] Focus chain TA [auth I] Focus chain U [auth A] Focus chain YA [auth K] Interactions & Density Focus chain AA [auth C] Focus chain EB [auth M] Focus chain GA [auth E] Focus chain KB [auth O] Focus chain MA [auth G] Focus chain QB [auth Q] Focus chain TA [auth I] Focus chain U [auth A] Focus chain YA [auth K]