7O0X

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

• PDB DOI: https://doi.org/10.2210/pdb7O0X/pdb
• EM Map EMD-12682: EMDB EMDataResource

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


• Deposited: 2021-03-28 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

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.44 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.

---

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 87-mer - A40B24C16D1E1F1G1H1I1J1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 87-mer - A40B24C16D2E1F1G1H1I1 

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: 861.98 kDa 
• Atom Count: 56,446 
• Modelled Residue Count: 5,072 
• Deposited Residue Count: 5,762 
• Unique protein chains: 11

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LHh-alpha	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]	54	Gemmatimonas phototrophica	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light-harvesting protein B:885 subunit beta	AA [auth BC], AC [auth bh], BA [auth BD], BC [auth bi], CA [auth BE], CC [auth bj], DA [auth BF], DC [auth bk], EA [auth BG], EC [auth bl], FA [auth BH], FC [auth bm], GA [auth BI], GC [auth bn], HA [auth BJ], HC [auth bo], IA [auth BK], IC [auth bp], 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], TB [auth ba], UA [auth BW], UB [auth bb], VA [auth BX], VB [auth bc], WB [auth bd], XB [auth be], Y [auth BA], YB [auth bf], Z [auth BB], ZB [auth bg]	44	Gemmatimonas phototrophica	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A143BHS8 (Gemmatimonas phototrophica) Explore A0A143BHS8  Go to UniProtKB:  A0A143BHS8

Entity ID: 3
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

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
RC-S	XA [auth C1]	202	Gemmatimonas phototrophica	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
RC-U	YA [auth C2]	125	Gemmatimonas phototrophica	Mutation(s): 0
UniProt
Find proteins for A0A143BK87 (Gemmatimonas phototrophica) Explore A0A143BK87  Go to UniProtKB:  A0A143BK87

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
PRCH domain-containing protein	ZA [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: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
RC-Hc	AB [auth H2]	181	Gemmatimonas phototrophica	Mutation(s): 0

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic reaction center L subunit	BB [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: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
RC-M	CB [auth M]	367	Gemmatimonas phototrophica	Mutation(s): 0

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
LHC domain-containing protein	DB [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: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
LHC domain-containing protein	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]	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: 12
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-rhamnopyranose-(1-4)-alpha-D-mannopyranose	JC [auth MG], KC [auth CG]	2		O-Glycosylation

Small Molecules

Ligands 15 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD4	CL [auth ad], EK [auth H1], HL [auth af], IL [auth af], OL [auth ai], SK [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 (Subject of Investigation/LOI)	AE [auth AM], AM [auth ba], BD [auth AF], BF [auth AV], BG [auth BD], BJ [auth BT], BL [auth ac], CD [auth AF], CE [auth AN], CF [auth AV], CI [auth BO], CO [auth bn], DF [auth AW], DH [auth BJ], DL [auth ad], EE [auth AN], EL [auth ae], EM [auth bb], EN [auth bh], FD [auth AG], FE [auth AO], FF [auth AW], FG [auth BE], FO [auth bo], GD [auth AG], GE [auth AO], GF [auth AW], GH [auth BK], GI [auth BP], GJ [auth BU], GL [auth af], HD [auth AH], HF [auth AX], HK [auth L], HN [auth bi], ID [auth AH], IE [auth AP], IM [auth bc], JL [auth ag], KE [auth AP], KJ [auth BV], KO [auth bp], LC [auth AA], LE [auth AQ], LF [auth BA], LG [auth BF], LI [auth BQ], LL [auth ah], LN [auth bj], MC [auth AA], ME [auth AQ], MK [auth L], MM [auth bd], NE [auth AQ], NH [auth BL], NJ [auth BW], NL [auth ai], OC [auth AB], OD [auth AI], OE [auth AR], PD [auth AI], PG [auth BG], PI [auth BR], QC [auth AB], QD [auth AJ], QE [auth AS], QL [auth aj], QM [auth be], QN [auth bk], RD [auth AJ], RE [auth AS], RF [auth BB], RK [auth M], RL [auth ak], SC [auth AC], SG [auth BH], SH [auth BM], SL [auth al], TC [auth AC], TE [auth AS], TK [auth M], TL [auth am], UC [auth AD], UD [auth AK], UF [auth BC], UJ [auth BX], VC [auth AD], VD [auth AK], VE [auth AT], VL [auth an], VM [auth bf], VN [auth bl], WD [auth AL], WL [auth ao], XI [auth BS], XL [auth ap], YC [auth AE], YD [auth AL], YE [auth AU], YG [auth BI], YH [auth BN], YK [auth aa], YN [auth bm], ZC [auth AE], ZD [auth AM], ZE [auth AU], ZK [auth ab], ZM [auth bg]	BACTERIOCHLOROPHYLL A C55 H74 Mg N4 O6 DSJXIQQMORJERS-AGGZHOMASA-M
BPH (Subject of Investigation/LOI)	FK [auth L], UK [auth M]	BACTERIOPHEOPHYTIN A C55 H76 N4 O6 KWOZSBGNAHVCKG-SZQBJALDSA-N
V7B (Subject of Investigation/LOI)	FL [auth af], KL [auth ag]	[(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 (Subject of Investigation/LOI)	ML [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	NK [auth L], UL [auth an], VK [auth M]	MENAQUINONE 8 C51 H72 O2 LXKDFTDVRVLXFY-ACMRXAIVSA-N
0V9 (Subject of Investigation/LOI)	BM [auth ba], DK [auth H1], DN [auth bh], DO [auth bn], FM [auth bb], GN [auth bi], HM [auth bc], HO [auth bo], KN [auth bj], NN [auth bk], OK [auth L], OM [auth be], PL [auth aj], PM [auth be], PN [auth bk], TM [auth bf], TN [auth bl], XM [auth bg], XN [auth bm], ZL [auth ba]	(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 (Subject of Investigation/LOI)	VJ [auth C], WJ [auth C], XJ [auth C], YJ [auth C]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
V7N (Subject of Investigation/LOI)	AD [auth AE], AH [auth BJ], AO [auth bn], BN [auth bh], CG [auth BE], CM [auth bb], DI [auth BP], EH [auth BK], EO [auth bo], FN [auth bi], HJ [auth BV], IF [auth BA], IN [auth bj], JI [auth BQ], JM [auth bc], JO [auth bp], KH [auth BL], KM [auth bd], LD [auth AH], LJ [auth BW], MG [auth BG], NI [auth BR], NM [auth be], OF [auth BB], ON [auth bk], PH [auth BM], QG [auth BH], RJ [auth BX], SF [auth BC], SM [auth bf], SN [auth bl], TH [auth BN], TI [auth BS], WE [auth AT], WF [auth BD], WM [auth bg], WN [auth bm], YI [auth BT], YL [auth ba], ZH [auth BO]	(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	WK [auth M]	SPIRILLOXANTHIN C42 H60 O2 VAZQBTJCYODOSV-RISZBRKMSA-N
LMT	AF [auth AV], AG [auth BD], AI [auth BO], AJ [auth BT], AL [auth ac], AN [auth bh], BE [auth AN], BH [auth BJ], BI [auth BO], BO [auth bn], CH [auth BJ], CJ [auth BT], CN [auth bh], DD [auth AF], DE [auth AN], DG [auth BE], DJ [auth BU], DM [auth bb], ED [auth AG], EF [auth AW], EG [auth BE], EI [auth BP], EJ [auth BU], FH [auth BK], FI [auth BP], FJ [auth BU], GG [auth BE], GK [auth L], GM [auth bc], GO [auth bo], HE [auth AO], HG [auth BE], HH [auth BK], HI [auth BP], IG [auth BF], IH [auth BK], II [auth BP], IJ [auth BV], IK [auth L], IO [auth bp], JD [auth AH], JE [auth AP], JF [auth BA], JG [auth BF], JH [auth BK], JJ [auth BV], JK [auth L], JN [auth bj], KD [auth AH], KF [auth BA], KG [auth BF], KI [auth BQ], KK [auth L], LH [auth BL], LK [auth L], LM [auth bd], MD [auth AH], MF [auth BA], MH [auth BL], MI [auth BQ], MJ [auth BW], MN [auth bk], NC [auth AA], ND [auth AI], NF [auth BA], NG [auth BG], OG [auth BG], OH [auth BL], OI [auth BR], OJ [auth BW], PC [auth AB], PE [auth AR], PF [auth BB], PJ [auth BW], QF [auth BB], QH [auth BM], QI [auth BR], QJ [auth BW], QK [auth M], RC [auth AB], RG [auth BH], RH [auth BM], RI [auth BR], RM [auth bf], RN [auth bl], SD [auth AJ], SE [auth AS], SI [auth BR], SJ [auth BX], TD [auth AK], TF [auth BC], TG [auth BH], TJ [auth BX], UE [auth AT], UG [auth BH], UH [auth BN], UI [auth BS], UM [auth bf], UN [auth bl], VF [auth BC], VG [auth BI], VH [auth BN], VI [auth BS], WC [auth AD], WG [auth BI], WH [auth BN], WI [auth BS], XC [auth AD], XD [auth AL], XE [auth AU], XF [auth BD], XG [auth BI], XH [auth BN], YF [auth BD], YM [auth bg], ZF [auth BD], ZG [auth BI], ZI [auth BT], ZN [auth bm]	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N
V75 (Subject of Investigation/LOI)	AK [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	BK [auth C1], ZJ [auth C]	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], 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]	L-PEPTIDE LINKING	C6 H11 N O3 S		MET

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.44 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.

---

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