ISDA

Deposition Date 2021-03-28

Release Date 2022-03-02

Last Version Date 2024-11-13

Entry Detail

PDB ID:

7O0X

Keywords:

MEMBRANE PROTEIN

Title:

Cryo-EM structure (model_2b) of the RC-dLH complex from Gemmatimonas phototrophica at 2.44 A

Biological Source:

Source Organism:

Gemmatimonas phototrophica (Taxon ID: 1379270)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

2.44 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polypeptide(L)
Molecule:LHh-alpha
Chain IDs:A (auth: AA), B (auth: AB), C (auth: AC), D (auth: AD), E (auth: AE), F (auth: AF), G (auth: AG), H (auth: AH), I (auth: AI), J (auth: AJ), K (auth: AK), L (auth: AL), M (auth: AM), N (auth: AN), O (auth: AO), P (auth: AP), Q (auth: AQ), R (auth: AR), S (auth: AS), T (auth: AT), U (auth: AU), V (auth: AV), W (auth: AW), X (auth: AX)
Chain Length:54
Number of Molecules:24
Biological Source:Gemmatimonas phototrophica

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Light-harvesting protein B:885 subunit beta
Gene (Uniprot):GEMMAAP_06500
Chain IDs:Y (auth: BA), Z (auth: BB), AA (auth: BC), BA (auth: BD), CA (auth: BE), DA (auth: BF), EA (auth: BG), FA (auth: BH), GA (auth: BI), HA (auth: BJ), IA (auth: BK), JA (auth: BL), KA (auth: BM), LA (auth: BN), MA (auth: BO), NA (auth: BP), OA (auth: BQ), PA (auth: BR), QA (auth: BS), RA (auth: BT), SA (auth: BU), TA (auth: BV), UA (auth: BW), VA (auth: BX), TB (auth: ba), UB (auth: bb), VB (auth: bc), WB (auth: bd), XB (auth: be), YB (auth: bf), ZB (auth: bg), AC (auth: bh), BC (auth: bi), CC (auth: bj), DC (auth: bk), EC (auth: bl), FC (auth: bm), GC (auth: bn), HC (auth: bo), IC (auth: bp)
Chain Length:44
Number of Molecules:40
Biological Source:Gemmatimonas phototrophica

UniProt ID:A0A143BHS8 Pfam ID:PF00556

Protein Blast

Polymer Type:polypeptide(L)
Molecule:MULTIHEME_CYTC domain-containing protein
Gene (Uniprot):GEMMAAP_06480
Chain IDs:WA (auth: C)
Chain Length:354
Number of Molecules:1
Biological Source:Gemmatimonas phototrophica

UniProt ID:A0A143BHR6 Pfam ID:PF02276

Polymer Type:polypeptide(L)
Molecule:RC-S
Chain IDs:XA (auth: C1)
Chain Length:202
Number of Molecules:1
Biological Source:Gemmatimonas phototrophica

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RC-U
Gene (Uniprot):GEMMAAP_12990
Chain IDs:YA (auth: C2)
Chain Length:125
Number of Molecules:1
Biological Source:Gemmatimonas phototrophica

UniProt ID:A0A143BK87

Protein Blast

Polymer Type:polypeptide(L)
Molecule:PRCH domain-containing protein
Gene (Uniprot):GEMMAAP_06435
Chain IDs:ZA (auth: H1)
Chain Length:67
Number of Molecules:1
Biological Source:Gemmatimonas phototrophica

UniProt ID:A0A143BJ28 Pfam ID:PF03967

Polymer Type:polypeptide(L)
Molecule:RC-Hc
Chain IDs:AB (auth: H2)
Chain Length:181
Number of Molecules:1
Biological Source:Gemmatimonas phototrophica

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Photosynthetic reaction center L subunit
Gene (Uniprot):GEMMAAP_06490
Chain IDs:BB (auth: L)
Chain Length:274
Number of Molecules:1
Biological Source:Gemmatimonas phototrophica

UniProt ID:A0A143BHR2 Pfam ID:PF00124

Polymer Type:polypeptide(L)
Molecule:RC-M
Chain IDs:CB (auth: M)
Chain Length:367
Number of Molecules:1
Biological Source:Gemmatimonas phototrophica

Protein Blast

Polymer Type:polypeptide(L)
Molecule:LHC domain-containing protein
Gene (Uniprot):GEMMAAP_06495
Chain IDs:DB (auth: aa)
Chain Length:54
Number of Molecules:1
Biological Source:Gemmatimonas phototrophica

UniProt ID:A0A143BHS7 Pfam ID:PF00556

Protein Blast

Polymer Type:polypeptide(L)
Molecule:LHC domain-containing protein
Gene (Uniprot):GEMMAAP_06495
Chain IDs:EB (auth: ab), FB (auth: ac), GB (auth: ad), HB (auth: ae), IB (auth: af), JB (auth: ag), KB (auth: ah), LB (auth: ai), MB (auth: aj), NB (auth: ak), OB (auth: al), PB (auth: am), QB (auth: an), RB (auth: ao), SB (auth: ap)
Chain Length:54
Number of Molecules:15
Biological Source:Gemmatimonas phototrophica

UniProt ID:A0A143BHS7 Pfam ID:PF00556

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
FME	ZA	MET	modified residue

Ligand Molecules

0V9

BCL

BPH

CD4

CRT

HEC

LMT

MQ8

NDG

PGW

UYH

V75

V7B

V7N

Primary Citation

2.4- angstrom structure of the double-ring Gemmatimonas phototrophica photosystem.

Qian, P, Gardiner, A.T, Simova, I, Naydenova, K, Croll, T.I, Jackson, P.J, Kloz, M, Cubakova, P, Kuzma, M, Zeng, Y, Castro-Hartmann, P, van Knippenberg, B, Goldie, K.N, Kaftan, D, Hrouzek, P, Hajek, J, Agirre, J, Siebert, C.A, Bina, D, Sader, K, Stahlberg, H, Sobotka, R, Russo, C.J, Polivka, T, Hunter, C.N, Koblizek, M.Show

Sci Adv 8 eabk3139 eabk3139 (2022)

PMID: 35171663 DOI: 10.1126/sciadv.abk3139

Abstact

Phototrophic Gemmatimonadetes evolved the ability to use solar energy following horizontal transfer of photosynthesis-related genes from an ancient phototrophic proteobacterium. The electron cryo-microscopy structure of the Gemmatimonas phototrophica photosystem at 2.4 Å reveals a unique, double-ring complex. Two unique membrane-extrinsic polypeptides, RC-S and RC-U, hold the central type 2 reaction center (RC) within an inner 16-subunit light-harvesting 1 (LH1) ring, which is encircled by an outer 24-subunit antenna ring (LHh) that adds light-gathering capacity. Femtosecond kinetics reveal the flow of energy within the RC-dLH complex, from the outer LHh ring to LH1 and then to the RC. This structural and functional study shows that G. phototrophica has independently evolved its own compact, robust, and highly effective architecture for harvesting and trapping solar energy.

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Primary Citation of related structures