7O0X

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

  • 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 

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
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
Glycosylation
Glycosylation Sites: 1
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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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UniProt GroupA0A143BK87
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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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UniProt GroupA0A143BJ28
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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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UniProt GroupA0A143BHR2
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
RC-MCB [auth M]367Gemmatimonas phototrophicaMutation(s): 0 
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Glycosylation
Glycosylation Sites: 1
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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 
UniProt
Find proteins for A0A143BHS7 (Gemmatimonas phototrophica)
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UniProt GroupA0A143BHS7
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Oligosaccharides

Help

Entity ID: 12
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-L-rhamnopyranose-(1-4)-alpha-D-mannopyranoseJC [auth MG],
KC [auth CG]
2O-Glycosylation
Small Molecules
Ligands 15 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CD4
Query on CD4

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CL [auth ad]
EK [auth H1]
HL [auth af]
IL [auth af]
OL [auth ai]
(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

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AE [auth AM]
AM [auth ba]
BD [auth AF]
BF [auth AV]
BG [auth BD]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH (Subject of Investigation/LOI)
Query on BPH

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FK [auth L],
UK [auth M]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
V7B (Subject of Investigation/LOI)
Query on V7B

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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)
Query on UYH

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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
Query on PGW

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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

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NK [auth L],
UL [auth an],
VK [auth M]
MENAQUINONE 8
C51 H72 O2
LXKDFTDVRVLXFY-ACMRXAIVSA-N
0V9 (Subject of Investigation/LOI)
Query on 0V9

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BM [auth ba]
DK [auth H1]
DN [auth bh]
DO [auth bn]
FM [auth bb]
(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

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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)
Query on V7N

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AD [auth AE]
AH [auth BJ]
AO [auth bn]
BN [auth bh]
CG [auth BE]
(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

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WK [auth M]SPIRILLOXANTHIN
C42 H60 O2
VAZQBTJCYODOSV-RISZBRKMSA-N
LMT
Query on LMT

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AF [auth AV]
AG [auth BD]
AI [auth BO]
AJ [auth BT]
AL [auth ac]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
V75 (Subject of Investigation/LOI)
Query on V75

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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
Query on NDG

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BK [auth C1],
ZJ [auth C]
2-acetamido-2-deoxy-alpha-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
FE
Query on FE

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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]
C [auth AC]
D [auth AD]
E [auth AE]
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.44 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



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