7O0W

Cryo-EM structure of the RC-dLH complex (model_1b) from Gemmatimonas phototrophica at 2.47 A

  • Classification: MEMBRANE PROTEIN
  • Organism(s): 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

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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


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

  • 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LHh-alpha54Gemmatimonas phototrophicaMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting protein B:885 subunit beta44Gemmatimonas phototrophicaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A143BHS8 (Gemmatimonas phototrophica)
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UniProt GroupA0A143BHS8
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
MULTIHEME_CYTC domain-containing proteinWA [auth C]354Gemmatimonas phototrophicaMutation(s): 0 
UniProt
Find proteins for A0A143BHR6 (Gemmatimonas phototrophica)
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UniProt GroupA0A143BHR6
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RC-SXA [auth C1]202Gemmatimonas phototrophicaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RC-UYA [auth C2]125Gemmatimonas phototrophicaMutation(s): 0 
UniProt
Find proteins for A0A143BK87 (Gemmatimonas phototrophica)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
PRCH domain-containing proteinZA [auth H1]67Gemmatimonas phototrophicaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A143BJ28 (Gemmatimonas phototrophica)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
RC-HcAB [auth H2]181Gemmatimonas phototrophicaMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center L subunitBB [auth L]274Gemmatimonas phototrophicaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A143BHR2 (Gemmatimonas phototrophica)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
RC-MCB [auth M]367Gemmatimonas phototrophicaMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
LHC domain-containing proteinDB [auth aa]71Gemmatimonas phototrophicaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A143BHS7 (Gemmatimonas phototrophica)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
LHC domain-containing protein71Gemmatimonas phototrophicaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for A0A143BHS7 (Gemmatimonas phototrophica)
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Oligosaccharides

Help

Entity ID: 12
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-L-rhamnopyranose-(1-4)-alpha-D-mannopyranoseJC [auth CG],
KC [auth MG]		2O-Glycosylation
Small Molecules
Ligands 15 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CD4
Query on CD4
Download Ideal Coordinates CCD File 
AL [auth M]
EL [auth M]
KK [auth H1]
LL [auth ad]
QL [auth af]
AL [auth M],
EL [auth M],
KK [auth H1],
LL [auth ad],
QL [auth af],
SL [auth af]
(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)
Query on BCL
Download Ideal Coordinates CCD File 
AJ [auth BS]
AM [auth ak]
BD [auth AE]
BE [auth AM]
BF [auth AU]
AJ [auth BS],
AM [auth ak],
BD [auth AE],
BE [auth AM],
BF [auth AU],
BI [auth BN],
BL [auth M],
BM [auth al],
CD [auth AE],
CH [auth BI],
CM [auth am],
DD [auth AE],
DE [auth AM],
DF [auth AU],
DG [auth BD],
DL [auth M],
DM [auth an],
DN [auth bg],
DO [auth bn],
EF [auth AV],
EI [auth BO],
EJ [auth BT],
FD [auth AF],
FM [auth ao],
GE [auth AN],
GF [auth AV],
GL [auth aa],
GM [auth ap],
GN [auth bh],
HD [auth AG],
HE [auth AN],
HH [auth BJ],
HL [auth ab],
HO [auth bo],
ID [auth AG],
IE [auth AO],
IF [auth AW],
IM [auth ba],
JE [auth AO],
JF [auth AW],
JG [auth BE],
JI [auth BP],
JJ [auth BU],
JN [auth bi],
KD [auth AH],
KL [auth ac],
KM [auth bb],
LC [auth AA],
LD [auth AH],
LE [auth AP],
LH [auth BK],
MC [auth AA],
ME [auth AP],
MF [auth AX],
ML [auth ad],
ND [auth AH],
NF [auth AX],
NG [auth BF],
NO [auth bp],
OD [auth AI],
OE [auth AQ],
OJ [auth BV],
OL [auth ae],
OM [auth bc],
PC [auth AB],
PE [auth AQ],
PN [auth bj],
QC [auth AB],
QE [auth AQ],
QF [auth BA],
QI [auth BQ],
QK [auth L],
QM [auth bd],
RD [auth AJ],
RH [auth BL],
RL [auth af],
SC [auth AC],
SD [auth AJ],
SE [auth AR],
SG [auth BG],
SN [auth bk],
TC [auth AC],
TE [auth AS],
TI [auth BR],
TJ [auth BW],
TK [auth L],
UD [auth AK],
UE [auth AS],
UL [auth ag],
UM [auth be],
VF [auth BB],
VH [auth BM],
VJ [auth BX],
WD [auth AK],
WL [auth ah],
XC [auth AD],
XE [auth AT],
XL [auth ai],
XN [auth bl],
YC [auth AD],
YD [auth AL],
YG [auth BH],
YM [auth bf],
ZD [auth AL],
ZE [auth AT],
ZF [auth BC],
ZL [auth aj],
ZN [auth bm]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH (Subject of Investigation/LOI)
Query on BPH
Download Ideal Coordinates CCD File 
CL [auth M],
MK [auth L]		BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
V7B (Subject of Investigation/LOI)
Query on V7B
Download Ideal Coordinates CCD File 
PL [auth af],
VL [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)
Query on UYH
Download Ideal Coordinates CCD File 
YL [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
Query on PGW
Download Ideal Coordinates CCD File 
IK [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
Query on MQ8
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EM [auth ao],
OK [auth L],
XK [auth M]		MENAQUINONE 8
C51 H72 O2
LXKDFTDVRVLXFY-ACMRXAIVSA-N
0V9 (Subject of Investigation/LOI)
Query on 0V9
Download Ideal Coordinates CCD File 
BO [auth bm]
CN [auth bg]
FO [auth bn]
HN [auth bh]
IL [auth ab]
BO [auth bm],
CN [auth bg],
FO [auth bn],
HN [auth bh],
IL [auth ab],
IO [auth bo],
JK [auth H1],
KN [auth bi],
LM [auth bb],
NL [auth ad],
ON [auth bj],
OO [auth bp],
RE [auth AQ],
RM [auth bd],
RN [auth bk],
VK [auth L],
VN [auth bl],
WM [auth be],
YK [auth M],
ZM [auth bf]
(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)
Query on HEC
Download Ideal Coordinates CCD File 
AK [auth C],
BK [auth C],
CK [auth C],
ZJ [auth C]		HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
V7N (Subject of Investigation/LOI)
Query on V7N
Download Ideal Coordinates CCD File 
AE [auth AM]
AG [auth BD]
AN [auth bg]
CI [auth BO]
CO [auth bn]
AE [auth AM],
AG [auth BD],
AN [auth bg],
CI [auth BO],
CO [auth bn],
EH [auth BJ],
EN [auth bh],
GG [auth BE],
GJ [auth BU],
GO [auth bo],
HI [auth BP],
HM [auth ba],
IN [auth bi],
JM [auth bb],
KF [auth AW],
KH [auth BK],
KJ [auth BV],
LG [auth BF],
LO [auth bp],
MM [auth bc],
MN [auth bj],
NI [auth BQ],
OC [auth AA],
OF [auth BA],
PG [auth BG],
PJ [auth BW],
PM [auth bd],
QN [auth bk],
RI [auth BR],
SH [auth BM],
TL [auth ag],
TM [auth be],
UG [auth BH],
UN [auth bl],
VC [auth AD],
WE [auth AS],
XH [auth BN],
XI [auth BS],
YN [auth bm],
ZG [auth BI]
(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
Query on CRT
Download Ideal Coordinates CCD File 
ZK [auth M]SPIRILLOXANTHIN
C42 H60 O2
VAZQBTJCYODOSV-RISZBRKMSA-N
LMT
Query on LMT
Download Ideal Coordinates CCD File 
AD [auth AE]
AF [auth AT]
AH [auth BI]
AI [auth BN]
AO [auth bm]
AD [auth AE],
AF [auth AT],
AH [auth BI],
AI [auth BN],
AO [auth bm],
BG [auth BD],
BH [auth BI],
BJ [auth BS],
BN [auth bg],
CE [auth AM],
CF [auth AU],
CG [auth BD],
CJ [auth BT],
DH [auth BI],
DI [auth BO],
DJ [auth BT],
DK [auth C],
ED [auth AE],
EE [auth AN],
EG [auth BD],
EO [auth bn],
FE [auth AN],
FF [auth AV],
FG [auth BD],
FH [auth BJ],
FI [auth BO],
FJ [auth BT],
FN [auth bh],
GD [auth AG],
GH [auth BJ],
GI [auth BO],
HF [auth AV],
HG [auth BE],
HJ [auth BU],
HK [auth C2],
IG [auth BE],
IH [auth BJ],
II [auth BP],
IJ [auth BU],
JD [auth AH],
JH [auth BJ],
JL [auth ac],
JO [auth bo],
KE [auth AP],
KG [auth BE],
KI [auth BP],
KO [auth bp],
LF [auth AX],
LI [auth BP],
LJ [auth BV],
LK [auth H2],
LN [auth bi],
MD [auth AH],
MG [auth BF],
MH [auth BK],
MI [auth BP],
MJ [auth BV],
MO [auth bp],
NC [auth AA],
NE [auth AQ],
NH [auth BK],
NJ [auth BV],
NK [auth L],
NM [auth bc],
NN [auth bj],
OG [auth BF],
OH [auth BK],
OI [auth BQ],
PD [auth AJ],
PF [auth BA],
PH [auth BL],
PI [auth BQ],
PK [auth L],
QD [auth AJ],
QG [auth BG],
QH [auth BL],
QJ [auth BW],
RC [auth AB],
RF [auth BB],
RG [auth BG],
RJ [auth BW],
RK [auth L],
SF [auth BB],
SI [auth BR],
SJ [auth BW],
SK [auth L],
SM [auth be],
TD [auth AK],
TF [auth BB],
TG [auth BG],
TH [auth BM],
TN [auth bk],
UC [auth AC],
UF [auth BB],
UH [auth BM],
UI [auth BR],
UJ [auth BW],
UK [auth L],
VD [auth AK],
VE [auth AS],
VG [auth BH],
VI [auth BR],
VM [auth be],
WC [auth AD],
WF [auth BC],
WG [auth BH],
WH [auth BM],
WI [auth BR],
WJ [auth BX],
WN [auth bl],
XD [auth AL],
XF [auth BC],
XG [auth BH],
XJ [auth BX],
XM [auth bf],
YE [auth AT],
YF [auth BC],
YH [auth BN],
YI [auth BS],
YJ [auth BX],
ZC [auth AE],
ZH [auth BN],
ZI [auth BS]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
V75 (Subject of Investigation/LOI)
Query on V75
Download Ideal Coordinates CCD File 
EK [auth C],
FL [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
Query on NDG
Download Ideal Coordinates CCD File 
FK [auth C],
GK [auth C1]		2-acetamido-2-deoxy-alpha-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
FE
Query on FE
Download Ideal Coordinates CCD File 
WK [auth M]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
A [auth AA]
B [auth AB]
C [auth AC]
D [auth AD]
E [auth AE]
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 LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Czech Science FoundationCzech Republic19-28778X,19-28323X
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M000265/1
European Research Council (ERC)European Union854126
European Regional Development FundCzech RepublicCZ.02.1.01/0.0/0.0/15_003/0000441
Wellcome TrustUnited KingdomWellcome Trust
Medical Research Council (MRC, United Kingdom)United KingdomMC UP 120117
Royal SocietyUnited KingdomUF160039

Revision History  (Full details and data files)

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