7O0V | pdb_00007o0v

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

  • 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

Experimental Data Snapshot

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

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 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
LHh-alphaC [auth AC],
D [auth AD]		54Gemmatimonas phototrophicaMutation(s): 0 
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Entity ID: 3
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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting protein B:885 subunit beta43Gemmatimonas phototrophicaMutation(s): 0 
Gene Names: GEMMAAP_06500
Membrane Entity: Yes 
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UniProt GroupA0A143BHS8
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Entity ID: 5
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
Glycosylation
Glycosylation Sites: 1
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RC-SXA [auth C1]202Gemmatimonas phototrophicaMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
PRCH domain-containing proteinYA [auth H1]67Gemmatimonas phototrophicaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A143BJ28 (Gemmatimonas phototrophica)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
RC-HcZA [auth H2]181Gemmatimonas phototrophicaMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center L subunitAB [auth L]274Gemmatimonas phototrophicaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
RC-MBB [auth M]367Gemmatimonas phototrophicaMutation(s): 0 
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Glycosylation
Glycosylation Sites: 1
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
LHC domain-containing proteinCB [auth aa]71Gemmatimonas phototrophicaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A143BHS7 (Gemmatimonas phototrophica)
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Entity ID: 12
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: 13
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-L-rhamnopyranose-(1-4)-alpha-D-mannopyranoseIC [auth CG],
JC [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 
BK [auth H1]
DK [auth H1]
DL [auth ae]
GL [auth af]
NL [auth aj]
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
Query on BCL
Download Ideal Coordinates CCD File 
AD [auth AE]
AE [auth AN]
AF [auth AV]
AL [auth ab]
AO [auth bn]
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
Query on BPH
Download Ideal Coordinates CCD File 
MK [auth L],
UK [auth M]		BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
V7B
Query on V7B
Download Ideal Coordinates CCD File 
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
Query on UYH
Download Ideal Coordinates CCD File 
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
Query on PGW
Download Ideal Coordinates CCD File 
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
Query on MQ8
Download Ideal Coordinates CCD File 
EK [auth L],
TL [auth ao],
VK [auth M]		MENAQUINONE 8
C51 H72 O2
LXKDFTDVRVLXFY-ACMRXAIVSA-N
0V9 (Subject of Investigation/LOI)
Query on 0V9
Download Ideal Coordinates CCD File 
AK [auth H1]
BM [auth bb]
BO [auth bn]
EN [auth bi]
FM [auth bc]
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
Query on HEC
Download Ideal Coordinates CCD File 
SJ [auth C],
TJ [auth C],
UJ [auth C],
VJ [auth C]		HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
V7N
Query on V7N
Download Ideal Coordinates CCD File 
AG [auth BE]
AI [auth BP]
BD [auth AE]
CH [auth BK]
CN [auth bi]
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
Query on CRT
Download Ideal Coordinates CCD File 
SK [auth M]SPIRILLOXANTHIN
C42 H60 O2
VAZQBTJCYODOSV-RISZBRKMSA-N
LMT
Query on LMT
Download Ideal Coordinates CCD File 
AH [auth BJ]
AJ [auth BU]
AM [auth bb]
AN [auth bh]
BE [auth AN]
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
Query on V75
Download Ideal Coordinates CCD File 
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
Query on NDG
Download Ideal Coordinates CCD File 
XJ [auth C],
ZJ [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 
PK [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]
E [auth AE]
F [auth AF]
G [auth AG]
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 LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 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
  • Version 1.2: 2024-11-13
    Changes: Data collection, Refinement description, Structure summary