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

Validation slider image for 9EK8

This is version 1.1 of the entry. See complete history.

Literature

Robust light-harvesting properties upon low-light acclimation in purple bacteria

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

(2025) Chem 11: 102597

DOI: https://doi.org/10.1016/j.chempr.2025.102597

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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P26789
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 Z [auth C] SDF format, chain Y [auth C] SDF format, chain XA [auth K] SDF format, chain WA [auth K] SDF format, chain W [auth B] SDF format, chain UA [auth J] SDF format, chain T [auth A] SDF format, chain SB [auth R] SDF format, chain S [auth A] SDF format, chain RA [auth I] SDF format, chain QA [auth I] SDF format, chain PB [auth Q] SDF format, chain OB [auth Q] SDF format, chain OA [auth H] SDF format, chain LB [auth P] SDF format, chain LA [auth G] SDF format, chain KA [auth G] SDF format, chain JB [auth O] SDF format, chain IB [auth O] SDF format, chain IA [auth F] SDF format, chain FB [auth N] SDF format, chain FA [auth E] SDF format, chain EA [auth E] SDF format, chain DB [auth M] SDF format, chain CB [auth M] SDF format, chain CA [auth D] SDF format, chain AB [auth L] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain XA [auth K] MOL2 format, chain WA [auth K] MOL2 format, chain W [auth B] MOL2 format, chain UA [auth J] MOL2 format, chain T [auth A] MOL2 format, chain SB [auth R] MOL2 format, chain S [auth A] MOL2 format, chain RA [auth I] MOL2 format, chain QA [auth I] MOL2 format, chain PB [auth Q] MOL2 format, chain OB [auth Q] MOL2 format, chain OA [auth H] MOL2 format, chain LB [auth P] MOL2 format, chain LA [auth G] MOL2 format, chain KA [auth G] MOL2 format, chain JB [auth O] MOL2 format, chain IB [auth O] MOL2 format, chain IA [auth F] MOL2 format, chain FB [auth N] MOL2 format, chain FA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain DB [auth M] MOL2 format, chain CB [auth M] MOL2 format, chain CA [auth D] MOL2 format, chain AB [auth L] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain XA [auth K] mmCIF format, chain WA [auth K] mmCIF format, chain W [auth B] mmCIF format, chain UA [auth J] mmCIF format, chain T [auth A] mmCIF format, chain SB [auth R] mmCIF format, chain S [auth A] mmCIF format, chain RA [auth I] mmCIF format, chain QA [auth I] mmCIF format, chain PB [auth Q] mmCIF format, chain OB [auth Q] mmCIF format, chain OA [auth H] mmCIF format, chain LB [auth P] mmCIF format, chain LA [auth G] mmCIF format, chain KA [auth G] mmCIF format, chain JB [auth O] mmCIF format, chain IB [auth O] mmCIF format, chain IA [auth F] mmCIF format, chain FB [auth N] mmCIF format, chain FA [auth E] mmCIF format, chain EA [auth E] mmCIF format, chain DB [auth M] mmCIF format, chain CB [auth M] mmCIF format, chain CA [auth D] mmCIF format, chain AB [auth L]	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 X [auth B] SDF format, chain VA [auth J] SDF format, chain TB [auth R] SDF format, chain PA [auth H] SDF format, chain MB [auth P] SDF format, chain HA [auth E] SDF format, chain GB [auth N] SDF format, chain DA [auth D] SDF format, chain BB [auth L] MOL2 format, chain X [auth B] MOL2 format, chain VA [auth J] MOL2 format, chain TB [auth R] MOL2 format, chain PA [auth H] MOL2 format, chain MB [auth P] MOL2 format, chain HA [auth E] MOL2 format, chain GB [auth N] MOL2 format, chain DA [auth D] MOL2 format, chain BB [auth L] mmCIF format, chain X [auth B] mmCIF format, chain VA [auth J] mmCIF format, chain TB [auth R] mmCIF format, chain PA [auth H] mmCIF format, chain MB [auth P] mmCIF format, chain HA [auth E] mmCIF format, chain GB [auth N] mmCIF format, chain DA [auth D] mmCIF format, chain BB [auth L]	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 ZA [auth L] SDF format, chain V [auth A] SDF format, chain SA [auth I] SDF format, chain RB [auth R] SDF format, chain NB [auth P] SDF format, chain NA [auth H] SDF format, chain JA [auth F] SDF format, chain HB [auth N] SDF format, chain BA [auth D] MOL2 format, chain ZA [auth L] MOL2 format, chain V [auth A] MOL2 format, chain SA [auth I] MOL2 format, chain RB [auth R] MOL2 format, chain NB [auth P] MOL2 format, chain NA [auth H] MOL2 format, chain JA [auth F] MOL2 format, chain HB [auth N] MOL2 format, chain BA [auth D] mmCIF format, chain ZA [auth L] mmCIF format, chain V [auth A] mmCIF format, chain SA [auth I] mmCIF format, chain RB [auth R] mmCIF format, chain NB [auth P] mmCIF format, chain NA [auth H] mmCIF format, chain JA [auth F] mmCIF format, chain HB [auth N] mmCIF format, chain BA [auth D]	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 YA [auth K] SDF format, chain U [auth A] SDF format, chain TA [auth I] SDF format, chain QB [auth Q] SDF format, chain MA [auth G] SDF format, chain KB [auth O] SDF format, chain GA [auth E] SDF format, chain EB [auth M] SDF format, chain AA [auth C] MOL2 format, chain YA [auth K] MOL2 format, chain U [auth A] MOL2 format, chain TA [auth I] MOL2 format, chain QB [auth Q] MOL2 format, chain MA [auth G] MOL2 format, chain KB [auth O] MOL2 format, chain GA [auth E] MOL2 format, chain EB [auth M] MOL2 format, chain AA [auth C] mmCIF format, chain YA [auth K] mmCIF format, chain U [auth A] mmCIF format, chain TA [auth I] mmCIF format, chain QB [auth Q] mmCIF format, chain MA [auth G] mmCIF format, chain KB [auth O] mmCIF format, chain GA [auth E] mmCIF format, chain EB [auth M] mmCIF format, chain AA [auth C]	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]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CXM Query on CXM	A, C, E, G, I A, C, E, G, I, K, M, O, Q	L-PEPTIDE LINKING	C₆ H₁₁ N O₄ S		MET

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.35 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-30

Deposition Author(s):

Schlau-Cohen, G.S.

Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-SC0018097
National Science Foundation (NSF, United States)	United States	DMR-1419807

Revision History (Full details and data files)

Version 1.0: 2025-07-30
Type: Initial release
Version 1.1: 2026-02-11
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.