9H22 | pdb_00009h22

Cryo EM structure of RC-dLH complex model II from Gemmatimonas groenlandica


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Two solutions for efficient light-harvesting in phototrophic Gemmatimonadota.

Gardiner, A.T.Jin, Y.Bina, D.Joosten, M.Kaftan, D.Mujakic, I.Gardian, Z.Castro-Hartmann, P.Qian, P.Koblizek, M.

(2025) mSystems : e0109425-e0109425

  • DOI: https://doi.org/10.1128/msystems.01094-25
  • Primary Citation of Related Structures:  
    9H22

  • PubMed Abstract: 

    Phototrophic Gemmatimonadota represent a unique group of phototrophic bacteria that acquired a complete set of photosynthetic genes via horizontal gene transfer and later evolved independently. Gemmatimonas ( Gem. ) phototrophica contains photosynthetic complexes with two concentric light-harvesting antenna rings that absorb at 816 and 868 nm, allowing it to better exploit the light conditions found deeper in the water column. The closely related species Gem. groenlandica , with highly similar photosynthetic genes, harvests infrared light using a single 860 nm absorption band. The cryo-electron microscopy structure of the Gem. groenlandica photosynthetic complex reveals that the outer antenna lacks monomeric bacteriochlorophylls, resulting in a smaller optical antenna cross-section. The Gem. groenlandica spectrum is red-shifted relative to Gem. phototrophica due to the formation of a H-bond enabled by a different rotamer conformation of αTrp 31 in the outer ring. This H-bond forms with a neighboring bacteriochlorophyll and increases the intra-dimer exciton coupling, affecting the exciton localization probability within the rings and increasing exciton cooperativity between the complexes. The functional consequences of the spectral shift, caused solely by a subtle conformational change of a single residue, represent a novel mechanism in which phototrophic organisms adjust their antennae for particular light conditions and enable Gem. groenlandica to grow higher in the water column where more photons are available.IMPORTANCEThe photoheterotrophic species of the phylum Gemmatimonadota employ unique photosynthetic complexes with two concentric antenna rings around a central reaction center. In contrast to other phototrophic species, these organisms have not evolved any regulatory systems to control the expression of their photosynthetic apparatus under different light conditions. Despite the overall similarity, the complexes present in Gemmatimonas phototrophica and Gemmatimonas groenlandica have different absorption properties in the near-infrared region of the spectrum that make them more suitable for low or medium light, respectively. The main difference in absorption depends on the conformation of a single tryptophan residue that can form an H-bond with a neighboring bacteriochlorophyll. The presence or absence of this H-bond affects how the protein scaffold interacts with the bacteriochlorophylls, which in turn determines how light energy is transferred within and between the photosynthetic complexes.


  • Organizational Affiliation
    • Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czech Republic.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
reaction centre S sub unitA [auth S]204Gemmatimonas groenlandicaMutation(s): 0 
UniProt
Find proteins for A0A6M4IPJ3 (Gemmatimonas groenlandica)
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UniProt GroupA0A6M4IPJ3
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein L chainB [auth L]274Gemmatimonas groenlandicaMutation(s): 0 
UniProt
Find proteins for A0A6M4IPC7 (Gemmatimonas groenlandica)
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UniProt GroupA0A6M4IPC7
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein M chainC [auth M]392Gemmatimonas groenlandicaMutation(s): 0 
UniProt
Find proteins for A0A6M4ILR2 (Gemmatimonas groenlandica)
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UniProt GroupA0A6M4ILR2
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
reaction centre Ht su unitD [auth H]66Gemmatimonas groenlandicaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
reaction centre Hc sub unitE [auth K]180Gemmatimonas groenlandicaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center cytochrome c subunitF [auth C]373Gemmatimonas groenlandicaMutation(s): 0 
UniProt
Find proteins for A0A6M4ITL7 (Gemmatimonas groenlandica)
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UniProt GroupA0A6M4ITL7
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting protein56Gemmatimonas groenlandicaMutation(s): 0 
UniProt
Find proteins for A0A6M4IQ17 (Gemmatimonas groenlandica)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting protein44Gemmatimonas groenlandicaMutation(s): 0 
UniProt
Find proteins for A0A6M4IQ93 (Gemmatimonas groenlandica)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting protein71Gemmatimonas groenlandicaMutation(s): 0 
UniProt
Find proteins for A0A6M4INU2 (Gemmatimonas groenlandica)
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Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CD4
Query on CD4

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TC [auth M],
ZH [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

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AE [auth AF]
AF [auth BL]
AI [auth Af]
AK [auth Bp]
BH [auth BX]
AE [auth AF],
AF [auth BL],
AI [auth Af],
AK [auth Bp],
BH [auth BX],
BI [auth Bf],
CF [auth AM],
CG [auth AR],
CJ [auth Bk],
DF [auth BM],
DG [auth BS],
DH [auth Aa],
DI [auth Bf],
EE [auth BG],
EJ [auth Al],
FD [auth BA],
FF [auth BN],
FH [auth Ba],
FI [auth Ag],
FJ [auth Bl],
GE [auth AH],
GG [auth BT],
HD [auth BB],
HJ [auth Bl],
IC [auth L],
IF [auth AN],
JC [auth L],
JE [auth BH],
JF [auth AO],
JG [auth AT],
JI [auth Bg],
KD [auth AB],
KH [auth Ac],
KJ [auth Am],
LE [auth AI],
MD [auth AC],
MF [auth BO],
MG [auth AT],
MI [auth Ah],
ND [auth BC],
NH [auth Bc],
NI [auth Bh],
NJ [auth Bm],
OE [auth BI],
OF [auth BP],
OG [auth AU],
OI [auth Bh],
PG [auth AU],
PI [auth Ai],
QD [auth BD],
QE [auth BJ],
QG [auth AV],
QJ [auth An],
RE [auth AK],
RF [auth BP],
RH [auth Bd],
SG [auth BV],
SI [auth Bi],
SJ [auth Bn],
TD [auth AD],
TF [auth AP],
TH [auth Bd],
UC [auth M],
UD [auth AE],
UE [auth BK],
UF [auth AQ],
UG [auth AW],
UI [auth Aj],
UJ [auth Ao],
VC [auth M],
VI [auth Bj],
WD [auth BE],
WF [auth AQ],
WG [auth BW],
WH [auth Ae],
WJ [auth Bo],
XE [auth AL],
XF [auth BQ],
XH [auth Be],
XJ [auth Bp],
YD [auth BF],
YG [auth AX],
ZF [auth BR],
ZI [auth Ak]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH
Query on BPH

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KC [auth L],
WC [auth M]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
MQ8
Query on MQ8

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AD [auth M],
PH [auth Ad],
RC [auth L]
MENAQUINONE 8
C51 H72 O2
LXKDFTDVRVLXFY-ACMRXAIVSA-N
HEC
Query on HEC

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BD [auth C],
CD [auth C],
DD [auth C],
ED [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
V7N
Query on V7N

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AH [auth BX]
BE [auth AF]
BG [auth BR]
BJ [auth Bk]
CI [auth Bf]
AH [auth BX],
BE [auth AF],
BG [auth BR],
BJ [auth Bk],
CI [auth Bf],
EH [auth Ba],
FG [auth BS],
GI [auth Ag],
GJ [auth Bl],
HE [auth AH],
HF [auth BN],
HG [auth BT],
ID [auth BB],
IH [auth Bb],
II [auth Bg],
KE [auth AI],
KG [auth AT],
LF [auth BO],
LJ [auth Am],
ME [auth AI],
MH [auth Bc],
MJ [auth Bm],
PD [auth BC],
QF [auth BP],
QH [auth Ad],
RG [auth BV],
RI [auth Bi],
RJ [auth An],
SD [auth BD],
SF [auth AP],
SH [auth Bd],
VD [auth BE],
VG [auth BW],
WE [auth BK],
XG [auth AX],
XI [auth Bj],
YE [auth AL],
ZD [auth BF],
ZE [auth BL],
ZJ [auth Bp]
(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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XC [auth M]SPIRILLOXANTHIN
C42 H60 O2
VAZQBTJCYODOSV-RISZBRKMSA-N
PEX
Query on PEX

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BK [auth Bp]
CE [auth AG]
DJ [auth Bk]
EI [auth Bf]
GH [auth Ba]
BK [auth Bp],
CE [auth AG],
DJ [auth Bk],
EI [auth Bf],
GH [auth Ba],
IJ [auth Bl],
JH [auth Bb],
KF [auth AO],
KI [auth Bg],
LG [auth AT],
OJ [auth Bm],
TI [auth Bi],
TJ [auth Bn],
UH [auth Bd],
YH [auth Be],
YI [auth Bj],
ZC [auth M]
1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
C25 H49 N O8 P
KKOSJVWUOHEQKA-HSZRJFAPSA-M
LMT
Query on LMT

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AG [auth BR]
AJ [auth Bk]
BF [auth BL]
CH [auth BX]
DE [auth BG]
AG [auth BR],
AJ [auth Bk],
BF [auth BL],
CH [auth BX],
DE [auth BG],
EF [auth BM],
EG [auth BS],
FE [auth BG],
GD [auth BA],
GF [auth BN],
HH [auth Ba],
HI [auth Bg],
IE [auth BH],
IG [auth BT],
JD [auth BB],
JJ [auth Bl],
LC [auth L],
LD [auth AB],
LH [auth Bc],
LI [auth Bg],
MC [auth L],
NC [auth L],
NE [auth BI],
NF [auth BO],
NG [auth BU],
OC [auth L],
OD [auth BC],
OH [auth Bc],
PC [auth L],
PE [auth BI],
PF [auth BP],
PJ [auth Bm],
QC [auth L],
QI [auth Bi],
RD [auth BD],
SE [auth AK],
TE [auth BK],
TG [auth BV],
VE [auth BK],
VF [auth AQ],
VH [auth Bd],
VJ [auth Bo],
WI [auth Bj],
XD [auth BF],
YC [auth M],
YF [auth BQ],
YJ [auth Bp],
ZG [auth BX]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
FE
Query on FE

Download Ideal Coordinates CCD File 
SC [auth M]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.2.1
MODEL REFINEMENTPHENIX1.20.1-4487

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Czech Academy of SciencesCzech Republic19-28778X

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-03
    Type: Initial release
  • Version 1.1: 2025-12-17
    Changes: Data collection, Database references