7O0V

Cryo-EM structure (model_2a) of the RC-dLH complex from Gemmatimonas phototrophica at 2.5 A

• PDB DOI: https://doi.org/10.2210/pdb7O0V/pdb
• EM Map EMD-12680: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Gemmatimonas phototrophica
• Expression System: Gemmatimonas phototrophica
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2021-03-27 Released: 2022-03-02 
• Deposition Author(s): Qian, P., Koblizek, M.
• Funding Organization(s): Czech Science Foundation, Biotechnology and Biological Sciences Research Council (BBSRC), European Research Council (ERC), European Regional Development Fund, Wellcome Trust, Medical Research Council (MRC, United Kingdom), Royal Society

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

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.

(2022) Sci Adv 8: eabk3139-eabk3139

• PubMed: 35171663 
• DOI: https://doi.org/10.1126/sciadv.abk3139
• Primary Citation of Related Structures:  
  7O0U, 7O0V, 7O0W, 7O0X


• PubMed Abstract: 
  

  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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Organizational Affiliation: 

Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, Netherlands.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 86-mer - A40B24C16D1E1F1G1H1I1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 86-mer - A40B24C16D2E1F1G1H1 

Local Symmetry: Cyclic - C8  (Explore in 3D)
Local Stoichiometry: Homo 40-mer - A40 Local Symmetry: Cyclic - C24  (Explore in 3D)
Local Stoichiometry: Homo 24-mer - B24 Local Symmetry: Cyclic - C16  (Explore in 3D)
Local Stoichiometry: Homo 16-mer - C16 Local Symmetry: Cyclic - C8  (Explore in 3D)
Local Stoichiometry: Hetero 56-mer - A16B24C16 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 847.42 kDa 
• Atom Count: 55,475 
• Modelled Residue Count: 4,947 
• Deposited Residue Count: 5,626 
• Unique protein chains: 12

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LHh-alpha	A [auth AA], B [auth AB], 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]	54	Gemmatimonas phototrophica	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LHh-alpha	C [auth AC], D [auth AD]	54	Gemmatimonas phototrophica	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Light-harvesting protein B:885 subunit beta	AA [auth BC], AC [auth bi], BC [auth bj], CC [auth bk], DA [auth BF], DC [auth bl], EA [auth BG], EC [auth bm], FA [auth BH], GC [auth bo], HA [auth BJ], HC [auth bp], IA [auth BK], JA [auth BL], KA [auth BM], LA [auth BN], MA [auth BO], NA [auth BP], SA [auth BU], SB [auth ba], TB [auth bb], UB [auth bc], VA [auth BX], VB [auth bd], WB [auth be], XB [auth bf], Y [auth BA], YB [auth bg], ZB [auth bh]	44	Gemmatimonas phototrophica	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A143BHS8 (Gemmatimonas phototrophica) Explore A0A143BHS8  Go to UniProtKB:  A0A143BHS8

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Light-harvesting protein B:885 subunit beta	BA [auth BD], CA [auth BE], FC [auth bn], GA [auth BI], OA [auth BQ], PA [auth BR], QA [auth BS], RA [auth BT], TA [auth BV], UA [auth BW], Z [auth BB]	43	Gemmatimonas phototrophica	Mutation(s): 0  Gene Names: GEMMAAP_06500 Membrane Entity: Yes
UniProt
Find proteins for A0A143BHS8 (Gemmatimonas phototrophica) Explore A0A143BHS8  Go to UniProtKB:  A0A143BHS8

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
MULTIHEME_CYTC domain-containing protein	WA [auth C]	354	Gemmatimonas phototrophica	Mutation(s): 0
UniProt
Find proteins for A0A143BHR6 (Gemmatimonas phototrophica) Explore A0A143BHR6  Go to UniProtKB:  A0A143BHR6
Glycosylation
Glycosylation Sites: 1

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
RC-S	XA [auth C1]	202	Gemmatimonas phototrophica	Mutation(s): 0

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
PRCH domain-containing protein	YA [auth H1]	67	Gemmatimonas phototrophica	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A143BJ28 (Gemmatimonas phototrophica) Explore A0A143BJ28  Go to UniProtKB:  A0A143BJ28

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
RC-Hc	ZA [auth H2]	181	Gemmatimonas phototrophica	Mutation(s): 0

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic reaction center L subunit	AB [auth L]	274	Gemmatimonas phototrophica	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A143BHR2 (Gemmatimonas phototrophica) Explore A0A143BHR2  Go to UniProtKB:  A0A143BHR2

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
RC-M	BB [auth M]	367	Gemmatimonas phototrophica	Mutation(s): 0
Glycosylation
Glycosylation Sites: 1

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
LHC domain-containing protein	CB [auth aa]	71	Gemmatimonas phototrophica	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A143BHS7 (Gemmatimonas phototrophica) Explore A0A143BHS7  Go to UniProtKB:  A0A143BHS7

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
LHC domain-containing protein	DB [auth ab], EB [auth ac], FB [auth ad], GB [auth ae], HB [auth af], IB [auth ag], JB [auth ah], KB [auth ai], LB [auth aj], MB [auth ak], NB [auth al], OB [auth am], PB [auth an], QB [auth ao], RB [auth ap]	71	Gemmatimonas phototrophica	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A143BHS7 (Gemmatimonas phototrophica) Explore A0A143BHS7  Go to UniProtKB:  A0A143BHS7

Oligosaccharides

Help

Entity ID: 13
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-rhamnopyranose-(1-4)-alpha-D-mannopyranose	IC [auth CG], JC [auth MG]	2		O-Glycosylation

Small Molecules

Ligands 15 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD4	BK [auth H1], DK [auth H1], DL [auth ae], GL [auth af], NL [auth aj], QK [auth M]	(2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate C65 H126 O17 P2 SDCJNZZAOLRVCP-GTOSQJSUSA-N
BCL	AD [auth AE], AE [auth AN], AF [auth AV], AL [auth ab], AO [auth bn], BF [auth AW], BL [auth ac], BN [auth bh], CD [auth AF], CE [auth AN], CJ [auth BU], CL [auth ad], CM [auth bb], DF [auth AX], DG [auth BE], ED [auth AG], EE [auth AO], EF [auth AX], EI [auth BP], EL [auth ae], EM [auth bc], FD [auth AG], FG [auth BF], FK [auth L], FL [auth af], FN [auth bi], FO [auth bo], GE [auth AP], HD [auth AH], HE [auth AP], HF [auth BA], HH [auth BK], HI [auth BQ], HJ [auth BV], HL [auth ag], IM [auth bd], IN [auth bj], JD [auth AH], JE [auth AQ], JL [auth ah], JO [auth bp], KC [auth AA], KE [auth AQ], KG [auth BG], KH [auth BL], KL [auth ai], LC [auth AA], LJ [auth BW], LN [auth bk], MD [auth AI], ME [auth AR], MF [auth BB], ND [auth AI], NE [auth AR], NI [auth BR], NK [auth L], OC [auth AB], OD [auth AJ], OH [auth BM], OL [auth aj], OM [auth be], PC [auth AB], PD [auth AJ], PE [auth AS], PJ [auth BX], PL [auth ak], QC [auth AC], QE [auth AS], QL [auth al], RC [auth AC], RE [auth AS], RG [auth BH], RI [auth BS], RL [auth am], RM [auth bf], RN [auth bl], SC [auth AC], SD [auth AK], SF [auth BC], SL [auth an], TD [auth AK], TE [auth AT], TH [auth BN], TK [auth M], UD [auth AL], UG [auth BI], UL [auth ao], VC [auth AD], VL [auth ap], WD [auth AL], WE [auth AU], WK [auth M], WM [auth bg], WN [auth bm], XC [auth AE], XD [auth AM], XE [auth AU], XI [auth BT], YD [auth AM], YE [auth AV], YK [auth aa], YL [auth ba], ZC [auth AE], ZD [auth AN], ZE [auth AV], ZF [auth BD], ZG [auth BJ], ZH [auth BO]	BACTERIOCHLOROPHYLL A C55 H74 Mg N4 O6 DSJXIQQMORJERS-AGGZHOMASA-M
BPH	MK [auth L], UK [auth M]	BACTERIOPHEOPHYTIN A C55 H76 N4 O6 KWOZSBGNAHVCKG-SZQBJALDSA-N
V7B	IL [auth ag], JK [auth L]	[(2~{S})-3-[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-5-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4-bis(oxidanyl)oxan-2-yl]oxy-2-(12-methyltridecanoyloxy)propyl] 12-methyltridecanoate C43 H80 O15 FZSILUNLAKMVHD-KBRRZRKCSA-N
UYH	LL [auth ai]	[(2~{S})-3-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-octadecanoyloxy-propyl] octadecanoate C45 H86 O10 DCLTVZLYPPIIID-KTXJEQRFSA-N
PGW	CK [auth H1]	(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate C40 H77 O10 P PAZGBAOHGQRCBP-HGWHEPCSSA-N
MQ8	EK [auth L], TL [auth ao], VK [auth M]	MENAQUINONE 8 C51 H72 O2 LXKDFTDVRVLXFY-ACMRXAIVSA-N
0V9 (Subject of Investigation/LOI)	AK [auth H1], BM [auth bb], BO [auth bn], EN [auth bi], FM [auth bc], GO [auth bo], JN [auth bj], KO [auth bp], LM [auth be], ML [auth aj], MM [auth be], MN [auth bk], NN [auth bk], QN [auth bl], TM [auth bg], UN [auth bm], VM [auth bg], XL [auth ba], YJ [auth C1], ZM [auth bh]	(19R,22S)-25-amino-22-hydroxy-22-oxido-16-oxo-17,21,23-trioxa-22lambda~5~-phosphapentacosan-19-yl (9Z)-hexadec-9-enoate C37 H72 N O8 P CZOSTDZGCCEZTJ-WMHOIYFHSA-N
HEC	SJ [auth C], TJ [auth C], UJ [auth C], VJ [auth C]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
V7N	AG [auth BE], AI [auth BP], BD [auth AE], CH [auth BK], CN [auth bi], DE [auth AO], DJ [auth BV], DM [auth bc], EO [auth bo], FF [auth BA], FI [auth BQ], GN [auth bj], HG [auth BG], HM [auth bd], IH [auth BL], IO [auth bp], JJ [auth BW], KF [auth BB], KI [auth BR], KM [auth be], KN [auth bk], NG [auth BH], NH [auth BM], OJ [auth BX], PF [auth BC], PI [auth BS], PM [auth bf], PN [auth bl], SE [auth AS], SG [auth BI], SM [auth bg], TN [auth bm], VF [auth BD], WH [auth BO], WL [auth ba], YG [auth BJ], YM [auth bh], ZI [auth BU], ZL [auth bb], ZN [auth bn]	(2~{E},4~{E},6~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{Z},24~{E},26~{E},28~{E})-23-methanoyl-31-methoxy-2,6,10,14,19,27,31-heptamethyl-dotriaconta-2,4,6,10,12,14,16,18,20,22,24,26,28-tridecaenoic acid C41 H54 O4 XLPMAXZHNMJTID-YBNWOPDJSA-N
CRT	SK [auth M]	SPIRILLOXANTHIN C42 H60 O2 VAZQBTJCYODOSV-RISZBRKMSA-N
LMT	AH [auth BJ], AJ [auth BU], AM [auth bb], AN [auth bh], BE [auth AN], BG [auth BE], BH [auth BJ], BI [auth BP], BJ [auth BU], CF [auth AX], CG [auth BE], CI [auth BP], CO [auth bn], DD [auth AF], DH [auth BK], DI [auth BP], DN [auth bi], DO [auth bo], EG [auth BF], EH [auth BK], EJ [auth BV], FE [auth AP], FH [auth BK], FJ [auth BV], GD [auth AG], GF [auth BA], GG [auth BF], GH [auth BK], GI [auth BQ], GJ [auth BV], GK [auth L], GM [auth bc], HK [auth L], HN [auth bj], HO [auth bo], ID [auth AH], IE [auth AP], IF [auth BA], IG [auth BG], II [auth BQ], IJ [auth BV], IK [auth L], JF [auth BA], JG [auth BG], JH [auth BL], JI [auth BQ], JM [auth bd], KD [auth AH], KJ [auth BW], KK [auth L], LD [auth AI], LE [auth AQ], LF [auth BB], LG [auth BG], LH [auth BL], LI [auth BR], LK [auth L], MC [auth AA], MG [auth BG], MH [auth BL], MI [auth BR], MJ [auth BW], NC [auth AA], NF [auth BB], NJ [auth BW], NM [auth be], OE [auth AS], OF [auth BB], OG [auth BH], OI [auth BR], OK [auth L], ON [auth bl], PG [auth BH], PH [auth BM], QD [auth AJ], QF [auth BC], QG [auth BH], QH [auth BM], QI [auth BS], QJ [auth BX], QM [auth bf], RD [auth AJ], RF [auth BC], RH [auth BN], RJ [auth BX], RK [auth M], SH [auth BN], SI [auth BS], SN [auth bl], TC [auth AC], TF [auth BC], TG [auth BI], TI [auth BS], UC [auth AD], UE [auth AT], UF [auth BC], UH [auth BN], UI [auth BS], UM [auth bg], VD [auth AL], VE [auth AU], VG [auth BI], VH [auth BN], VI [auth BT], VN [auth bm], WC [auth AD], WF [auth BD], WG [auth BI], WI [auth BT], XF [auth BD], XG [auth BI], XH [auth BO], XM [auth bh], XN [auth bm], YC [auth AE], YF [auth BD], YH [auth BO], YI [auth BT], YN [auth bn], ZK [auth ab]	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N
V75	WJ [auth C], XK [auth M]	(2~{S},3~{S},4~{S},5~{S})-4,5-diacetyloxy-3-oxidanyl-oxane-2-carboxylic acid C10 H14 O8 PUWANSDFPUWGOX-MAUMQABQSA-N
NDG	XJ [auth C], ZJ [auth C1]	2-acetamido-2-deoxy-alpha-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-PVFLNQBWSA-N
FE	PK [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME	A [auth AA], B [auth AB], 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]	L-PEPTIDE LINKING	C6 H11 N O3 S		MET

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-03-02 
Deposition Author(s): Qian, P., Koblizek, M.

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Funding Organization	Location	Grant Number
Czech Science Foundation	Czech Republic	19-28778X,19-28323X
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/M000265/1
European Research Council (ERC)	European Union	854126
European Regional Development Fund	Czech Republic	CZ.02.1.01/0.0/0.0/15_003/0000441
Wellcome Trust	United Kingdom	Wellcome Trust
Medical Research Council (MRC, United Kingdom)	United Kingdom	MC UP 120117
Royal Society	United Kingdom	UF160039

Revision History  

• Version 1.0: 2022-03-02
  Type: Initial release
  
• Version 1.1: 2022-03-16
  Changes: Database references