8JC8 | pdb_00008jc8

Cryo-EM structure of the LH1 complex from thermochromatium tepidum

PDB DOI: https://doi.org/10.2210/pdb8JC8/pdb
EM Map EMD-36151: EMDB EMDataResource

Classification: PHOTOSYNTHESIS
Organism(s): Thermochromatium tepidum
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2023-05-10 Released: 2024-11-13
Deposition Author(s): Wang, G.-L., Yan, Y.-H., Yu, L.-J.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.11 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

Molecular structure and characterization of the Thermochromatium tepidum light-harvesting 1 photocomplex produced in a foreign host.

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

(2024) Biochim Biophys Acta Bioenerg 1865: 149050-149050

PubMed: 38806091 Search on PubMed
DOI: https://doi.org/10.1016/j.bbabio.2024.149050
Primary Citation Related Structures:
8JC8, 8JC9

PubMed Abstract:
Purple phototrophic bacteria possess light-harvesting 1 and reaction center (LH1-RC) core complexes that play a key role in converting solar energy to chemical energy. High-resolution structures of LH1-RC and RC complexes have been intensively studied and have yielded critical insight into the architecture and interactions of their proteins, pigments, and cofactors. Nevertheless, a detailed picture of the structure and assembly of LH1-only complexes is lacking due to the intimate association between LH1 and the RC. To study the intrinsic properties and structure of an LH1-only complex, a genetic system was constructed to express the Thermochromatium (Tch.) tepidum LH1 complex heterologously in a modified Rhodospirillum rubrum mutant strain. The heterologously expressed Tch. tepidum LH1 complex was isolated in a pure form free of the RC and exhibited the characteristic absorption properties of Tch. tepidum. Cryo-EM structures of the LH1-only complexes revealed a closed circular ring consisting of either 14 or 15 αβ-subunits, making it the smallest completely closed LH1 complex discovered thus far. Surprisingly, the Tch. tepidum LH1-only complex displayed even higher thermostability than that of the native LH1-RC complex. These results reveal previously unsuspected plasticity of the LH1 complex, provide new insights into the structure and assembly of the LH1-RC complex, and show how molecular genetics can be exploited to study membrane proteins from phototrophic organisms whose genetic manipulation is not yet possible.

Organizational Affiliation

Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.

Macromolecule Content

Total Structure Weight: 222.82 kDa
Atom Count: 14,456
Modeled Residue Count: 1,398
Deposited Residue Count: 1,560
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LH1 beta polypeptide	A [auth 2] AA [auth Z] C [auth 4] DA [auth X] E [auth 6] A [auth 2], AA [auth Z], C [auth 4], DA [auth X], E [auth 6], G [auth 8], I [auth B], K [auth E], M [auth G], O [auth J], Q [auth N], S [auth P], U [auth R], W [auth T], Y [auth V]	47	Thermochromatium tepidum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for D2Z0P1 (Thermochromatium tepidum) Explore D2Z0P1 Go to UniProtKB: D2Z0P1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D2Z0P1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LH1 alpha polypeptide	B [auth 3] BA [auth 1] CA [auth Y] D [auth 5] F [auth 7] B [auth 3], BA [auth 1], CA [auth Y], D [auth 5], F [auth 7], H [auth A], J [auth D], L [auth F], N [auth I], P [auth K], R [auth O], T [auth Q], V [auth S], X [auth U], Z [auth W]	57	Thermochromatium tepidum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for D2Z0P2 (Thermochromatium tepidum) Explore D2Z0P2 Go to UniProtKB: D2Z0P2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D2Z0P2
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 ZA [auth B] SDF format, chain YC [auth Y] SDF format, chain YB [auth P] SDF format, chain XA [auth A] SDF format, chain WB [auth O] SDF format, chain VC [auth 1] SDF format, chain VB [auth N] SDF format, chain TA [auth 8] SDF format, chain RC [auth Z] SDF format, chain RB [auth K] SDF format, chain RA [auth 7] SDF format, chain PC [auth W] SDF format, chain PB [auth J] SDF format, chain PA [auth 6] SDF format, chain MC [auth U] SDF format, chain MA [auth 5] SDF format, chain LB [auth I] SDF format, chain KC [auth U] SDF format, chain JB [auth G] SDF format, chain JA [auth 4] SDF format, chain HC [auth T] SDF format, chain GB [auth F] SDF format, chain GA [auth 3] SDF format, chain FC [auth S] SDF format, chain FB [auth E] SDF format, chain EA [auth 2] SDF format, chain CC [auth R] SDF format, chain BB [auth D] SDF format, chain AD [auth X] SDF format, chain AC [auth Q] MOL2 format, chain ZA [auth B] MOL2 format, chain YC [auth Y] MOL2 format, chain YB [auth P] MOL2 format, chain XA [auth A] MOL2 format, chain WB [auth O] MOL2 format, chain VC [auth 1] MOL2 format, chain VB [auth N] MOL2 format, chain TA [auth 8] MOL2 format, chain RC [auth Z] MOL2 format, chain RB [auth K] MOL2 format, chain RA [auth 7] MOL2 format, chain PC [auth W] MOL2 format, chain PB [auth J] MOL2 format, chain PA [auth 6] MOL2 format, chain MC [auth U] MOL2 format, chain MA [auth 5] MOL2 format, chain LB [auth I] MOL2 format, chain KC [auth U] MOL2 format, chain JB [auth G] MOL2 format, chain JA [auth 4] MOL2 format, chain HC [auth T] MOL2 format, chain GB [auth F] MOL2 format, chain GA [auth 3] MOL2 format, chain FC [auth S] MOL2 format, chain FB [auth E] MOL2 format, chain EA [auth 2] MOL2 format, chain CC [auth R] MOL2 format, chain BB [auth D] MOL2 format, chain AD [auth X] MOL2 format, chain AC [auth Q] mmCIF format, chain ZA [auth B] mmCIF format, chain YC [auth Y] mmCIF format, chain YB [auth P] mmCIF format, chain XA [auth A] mmCIF format, chain WB [auth O] mmCIF format, chain VC [auth 1] mmCIF format, chain VB [auth N] mmCIF format, chain TA [auth 8] mmCIF format, chain RC [auth Z] mmCIF format, chain RB [auth K] mmCIF format, chain RA [auth 7] mmCIF format, chain PC [auth W] mmCIF format, chain PB [auth J] mmCIF format, chain PA [auth 6] mmCIF format, chain MC [auth U] mmCIF format, chain MA [auth 5] mmCIF format, chain LB [auth I] mmCIF format, chain KC [auth U] mmCIF format, chain JB [auth G] mmCIF format, chain JA [auth 4] mmCIF format, chain HC [auth T] mmCIF format, chain GB [auth F] mmCIF format, chain GA [auth 3] mmCIF format, chain FC [auth S] mmCIF format, chain FB [auth E] mmCIF format, chain EA [auth 2] mmCIF format, chain CC [auth R] mmCIF format, chain BB [auth D] mmCIF format, chain AD [auth X] mmCIF format, chain AC [auth Q]	AC [auth Q] AD [auth X] BB [auth D] CC [auth R] EA [auth 2] AC [auth Q], AD [auth X], BB [auth D], CC [auth R], EA [auth 2], FB [auth E], FC [auth S], GA [auth 3], GB [auth F], HC [auth T], JA [auth 4], JB [auth G], KC [auth U], LB [auth I], MA [auth 5], MC [auth U], PA [auth 6], PB [auth J], PC [auth W], RA [auth 7], RB [auth K], RC [auth Z], TA [auth 8], VB [auth N], VC [auth 1], WB [auth O], XA [auth A], YB [auth P], YC [auth Y], ZA [auth B]	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-AGGZHOMASA-M		Interactions Focus chain AC [auth Q] Focus chain AD [auth X] Focus chain BB [auth D] Focus chain CC [auth R] Focus chain EA [auth 2] Focus chain FB [auth E] Focus chain FC [auth S] Focus chain GA [auth 3] Focus chain GB [auth F] Focus chain HC [auth T] Focus chain JA [auth 4] Focus chain JB [auth G] Focus chain KC [auth U] Focus chain LB [auth I] Focus chain MA [auth 5] Focus chain MC [auth U] Focus chain PA [auth 6] Focus chain PB [auth J] Focus chain PC [auth W] Focus chain RA [auth 7] Focus chain RB [auth K] Focus chain RC [auth Z] Focus chain TA [auth 8] Focus chain VB [auth N] Focus chain VC [auth 1] Focus chain WB [auth O] Focus chain XA [auth A] Focus chain YB [auth P] Focus chain YC [auth Y] Focus chain ZA [auth B] Interactions & Density Focus chain AC [auth Q] Focus chain AD [auth X] Focus chain BB [auth D] Focus chain CC [auth R] Focus chain EA [auth 2] Focus chain FB [auth E] Focus chain FC [auth S] Focus chain GA [auth 3] Focus chain GB [auth F] Focus chain HC [auth T] Focus chain JA [auth 4] Focus chain JB [auth G] Focus chain KC [auth U] Focus chain LB [auth I] Focus chain MA [auth 5] Focus chain MC [auth U] Focus chain PA [auth 6] Focus chain PB [auth J] Focus chain PC [auth W] Focus chain RA [auth 7] Focus chain RB [auth K] Focus chain RC [auth Z] Focus chain TA [auth 8] Focus chain VB [auth N] Focus chain VC [auth 1] Focus chain WB [auth O] Focus chain XA [auth A] Focus chain YB [auth P] Focus chain YC [auth Y] Focus chain ZA [auth B]
CRT (Subject of Investigation/LOI) Query on CRT Download:Ideal Coordinates CCD File SDF format, chain AB [auth D] SDF format, chain DB [auth E] SDF format, chain EC [auth S] SDF format, chain IA [auth 3] SDF format, chain JC [auth U] SDF format, chain KB [auth I] SDF format, chain LA [auth 5] SDF format, chain NB [auth J] SDF format, chain NC [auth V] SDF format, chain QA [auth 7] SDF format, chain TB [auth K] SDF format, chain UB [auth N] SDF format, chain UC [auth 1] SDF format, chain WA [auth A] SDF format, chain WC [auth Y] MOL2 format, chain AB [auth D] MOL2 format, chain DB [auth E] MOL2 format, chain EC [auth S] MOL2 format, chain IA [auth 3] MOL2 format, chain JC [auth U] MOL2 format, chain KB [auth I] MOL2 format, chain LA [auth 5] MOL2 format, chain NB [auth J] MOL2 format, chain NC [auth V] MOL2 format, chain QA [auth 7] MOL2 format, chain TB [auth K] MOL2 format, chain UB [auth N] MOL2 format, chain UC [auth 1] MOL2 format, chain WA [auth A] MOL2 format, chain WC [auth Y] mmCIF format, chain AB [auth D] mmCIF format, chain DB [auth E] mmCIF format, chain EC [auth S] mmCIF format, chain IA [auth 3] mmCIF format, chain JC [auth U] mmCIF format, chain KB [auth I] mmCIF format, chain LA [auth 5] mmCIF format, chain NB [auth J] mmCIF format, chain NC [auth V] mmCIF format, chain QA [auth 7] mmCIF format, chain TB [auth K] mmCIF format, chain UB [auth N] mmCIF format, chain UC [auth 1] mmCIF format, chain WA [auth A] mmCIF format, chain WC [auth Y]	AB [auth D] DB [auth E] EC [auth S] IA [auth 3] JC [auth U] AB [auth D], DB [auth E], EC [auth S], IA [auth 3], JC [auth U], KB [auth I], LA [auth 5], NB [auth J], NC [auth V], QA [auth 7], TB [auth K], UB [auth N], UC [auth 1], WA [auth A], WC [auth Y]	SPIRILLOXANTHIN C₄₂ H₆₀ O₂ VAZQBTJCYODOSV-RISZBRKMSA-N		Interactions Focus chain AB [auth D] Focus chain DB [auth E] Focus chain EC [auth S] Focus chain IA [auth 3] Focus chain JC [auth U] Focus chain KB [auth I] Focus chain LA [auth 5] Focus chain NB [auth J] Focus chain NC [auth V] Focus chain QA [auth 7] Focus chain TB [auth K] Focus chain UB [auth N] Focus chain UC [auth 1] Focus chain WA [auth A] Focus chain WC [auth Y] Interactions & Density Focus chain AB [auth D] Focus chain DB [auth E] Focus chain EC [auth S] Focus chain IA [auth 3] Focus chain JC [auth U] Focus chain KB [auth I] Focus chain LA [auth 5] Focus chain NB [auth J] Focus chain NC [auth V] Focus chain QA [auth 7] Focus chain TB [auth K] Focus chain UB [auth N] Focus chain UC [auth 1] Focus chain WA [auth A] Focus chain WC [auth Y]
8K6 Query on 8K6 Download:Ideal Coordinates CCD File SDF format, chain ZC [auth X] SDF format, chain ZB [auth P] SDF format, chain VA [auth 8] SDF format, chain UA [auth 8] SDF format, chain SC [auth Z] SDF format, chain QB [auth J] SDF format, chain OC [auth V] SDF format, chain OB [auth J] SDF format, chain OA [auth 6] SDF format, chain KA [auth 4] SDF format, chain IC [auth T] SDF format, chain IB [auth G] SDF format, chain FA [auth 2] SDF format, chain EB [auth E] SDF format, chain DC [auth R] MOL2 format, chain ZC [auth X] MOL2 format, chain ZB [auth P] MOL2 format, chain VA [auth 8] MOL2 format, chain UA [auth 8] MOL2 format, chain SC [auth Z] MOL2 format, chain QB [auth J] MOL2 format, chain OC [auth V] MOL2 format, chain OB [auth J] MOL2 format, chain OA [auth 6] MOL2 format, chain KA [auth 4] MOL2 format, chain IC [auth T] MOL2 format, chain IB [auth G] MOL2 format, chain FA [auth 2] MOL2 format, chain EB [auth E] MOL2 format, chain DC [auth R] mmCIF format, chain ZC [auth X] mmCIF format, chain ZB [auth P] mmCIF format, chain VA [auth 8] mmCIF format, chain UA [auth 8] mmCIF format, chain SC [auth Z] mmCIF format, chain QB [auth J] mmCIF format, chain OC [auth V] mmCIF format, chain OB [auth J] mmCIF format, chain OA [auth 6] mmCIF format, chain KA [auth 4] mmCIF format, chain IC [auth T] mmCIF format, chain IB [auth G] mmCIF format, chain FA [auth 2] mmCIF format, chain EB [auth E] mmCIF format, chain DC [auth R]	DC [auth R] EB [auth E] FA [auth 2] IB [auth G] IC [auth T] DC [auth R], EB [auth E], FA [auth 2], IB [auth G], IC [auth T], KA [auth 4], OA [auth 6], OB [auth J], OC [auth V], QB [auth J], SC [auth Z], UA [auth 8], VA [auth 8], ZB [auth P], ZC [auth X]	Octadecane C₁₈ H₃₈ RZJRJXONCZWCBN-UHFFFAOYSA-N		Interactions Focus chain DC [auth R] Focus chain EB [auth E] Focus chain FA [auth 2] Focus chain IB [auth G] Focus chain IC [auth T] Focus chain KA [auth 4] Focus chain OA [auth 6] Focus chain OB [auth J] Focus chain OC [auth V] Focus chain QB [auth J] Focus chain SC [auth Z] Focus chain UA [auth 8] Focus chain VA [auth 8] Focus chain ZB [auth P] Focus chain ZC [auth X] Interactions & Density Focus chain DC [auth R] Focus chain EB [auth E] Focus chain FA [auth 2] Focus chain IB [auth G] Focus chain IC [auth T] Focus chain KA [auth 4] Focus chain OA [auth 6] Focus chain OB [auth J] Focus chain OC [auth V] Focus chain QB [auth J] Focus chain SC [auth Z] Focus chain UA [auth 8] Focus chain VA [auth 8] Focus chain ZB [auth P] Focus chain ZC [auth X]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain YA [auth A] SDF format, chain XC [auth Y] SDF format, chain XB [auth O] SDF format, chain TC [auth 1] SDF format, chain SB [auth K] SDF format, chain SA [auth 7] SDF format, chain QC [auth W] SDF format, chain NA [auth 5] SDF format, chain MB [auth I] SDF format, chain LC [auth U] SDF format, chain HB [auth F] SDF format, chain HA [auth 3] SDF format, chain GC [auth S] SDF format, chain CB [auth D] SDF format, chain BC [auth Q] MOL2 format, chain YA [auth A] MOL2 format, chain XC [auth Y] MOL2 format, chain XB [auth O] MOL2 format, chain TC [auth 1] MOL2 format, chain SB [auth K] MOL2 format, chain SA [auth 7] MOL2 format, chain QC [auth W] MOL2 format, chain NA [auth 5] MOL2 format, chain MB [auth I] MOL2 format, chain LC [auth U] MOL2 format, chain HB [auth F] MOL2 format, chain HA [auth 3] MOL2 format, chain GC [auth S] MOL2 format, chain CB [auth D] MOL2 format, chain BC [auth Q] mmCIF format, chain YA [auth A] mmCIF format, chain XC [auth Y] mmCIF format, chain XB [auth O] mmCIF format, chain TC [auth 1] mmCIF format, chain SB [auth K] mmCIF format, chain SA [auth 7] mmCIF format, chain QC [auth W] mmCIF format, chain NA [auth 5] mmCIF format, chain MB [auth I] mmCIF format, chain LC [auth U] mmCIF format, chain HB [auth F] mmCIF format, chain HA [auth 3] mmCIF format, chain GC [auth S] mmCIF format, chain CB [auth D] mmCIF format, chain BC [auth Q]	BC [auth Q] CB [auth D] GC [auth S] HA [auth 3] HB [auth F] BC [auth Q], CB [auth D], GC [auth S], HA [auth 3], HB [auth F], LC [auth U], MB [auth I], NA [auth 5], QC [auth W], SA [auth 7], SB [auth K], TC [auth 1], XB [auth O], XC [auth Y], YA [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain BC [auth Q] Focus chain CB [auth D] Focus chain GC [auth S] Focus chain HA [auth 3] Focus chain HB [auth F] Focus chain LC [auth U] Focus chain MB [auth I] Focus chain NA [auth 5] Focus chain QC [auth W] Focus chain SA [auth 7] Focus chain SB [auth K] Focus chain TC [auth 1] Focus chain XB [auth O] Focus chain XC [auth Y] Focus chain YA [auth A] Interactions & Density Focus chain BC [auth Q] Focus chain CB [auth D] Focus chain GC [auth S] Focus chain HA [auth 3] Focus chain HB [auth F] Focus chain LC [auth U] Focus chain MB [auth I] Focus chain NA [auth 5] Focus chain QC [auth W] Focus chain SA [auth 7] Focus chain SB [auth K] Focus chain TC [auth 1] Focus chain XB [auth O] Focus chain XC [auth Y] Focus chain YA [auth A]