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 9H19 | pdb_00009h19

Cryo-EM structure of RC-dLH complex model I from Gem. groenlandica strain TET16


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

Validation slider image for 9H19

This is version 2.0 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.

(2026) mSystems 11: e0109425-e0109425

  • DOI: https://doi.org/10.1128/msystems.01094-25
  • Primary Citation Related Structures: 
    9H19, 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.

Macromolecule Content 

  • Total Structure Weight: 791.01 kDa 
  • Atom Count: 49,808 
  • Modeled Residue Count: 4,867 
  • Deposited Residue Count: 5,722 
  • Unique protein chains: 9

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Light-harvesting protein71Gemmatimonas groenlandicaMutation(s): 0 
UniProt
Find proteins for A0A6M4INU2 (Gemmatimonas groenlandica)
Explore A0A6M4INU2 
Go to UniProtKB:  A0A6M4INU2
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UniProt GroupA0A6M4INU2
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Light-harvesting protein44Gemmatimonas groenlandicaMutation(s): 0 
UniProt
Find proteins for A0A6M4IQ93 (Gemmatimonas groenlandica)
Explore A0A6M4IQ93 
Go to UniProtKB:  A0A6M4IQ93
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UniProt GroupA0A6M4IQ93
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
reaction centre S sub unitGA [auth S]204Gemmatimonas groenlandicaMutation(s): 0 
UniProt
Find proteins for A0A6M4IPJ3 (Gemmatimonas groenlandica)
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UniProt GroupA0A6M4IPJ3
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Reaction center protein L chainHA [auth L]274Gemmatimonas groenlandicaMutation(s): 0 
UniProt
Find proteins for A0A6M4IPC7 (Gemmatimonas groenlandica)
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UniProt GroupA0A6M4IPC7
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Reaction center protein M chainIA [auth M]392Gemmatimonas groenlandicaMutation(s): 0 
UniProt
Find proteins for A0A6M4ILR2 (Gemmatimonas groenlandica)
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UniProt GroupA0A6M4ILR2
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
reaction centre Ht sub unitJA [auth H]60Gemmatimonas groenlandicaMutation(s): 0 
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
reaction centre Hc sub unitKA [auth K]179Gemmatimonas groenlandicaMutation(s): 0 
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosynthetic reaction center cytochrome c subunitLA [auth C]373Gemmatimonas groenlandicaMutation(s): 0 
UniProt
Find proteins for A0A6M4ITL7 (Gemmatimonas groenlandica)
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UniProt GroupA0A6M4ITL7
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Light-harvesting protein56Gemmatimonas groenlandicaMutation(s): 0 
UniProt
Find proteins for A0A6M4IQ17 (Gemmatimonas groenlandica)
Explore A0A6M4IQ17 
Go to UniProtKB:  A0A6M4IQ17
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UniProt GroupA0A6M4IQ17
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Reference Sequence

Small Molecules

Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CD4

Query on CD4



Download:Ideal Coordinates CCD File
JD [auth Af],
LF [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)

Query on BCL



Download:Ideal Coordinates CCD File
AE [auth Aj]
AG [auth BA]
AJ [auth BS]
BD [auth Bd]
BH [auth BG]
AE [auth Aj],
AG [auth BA],
AJ [auth BS],
BD [auth Bd],
BH [auth BG],
BI [auth AM],
BK [auth BX],
CD [auth Ae],
CF [auth Bp],
CI [auth AM],
DF [auth Bp],
DG [auth BB],
DH [auth AH],
EF [auth L],
EI [auth BN],
EJ [auth AS],
FF [auth L],
GE [auth Bj],
GG [auth AB],
GI [auth AN],
HD [auth Be],
HE [auth Ak],
HG [auth AC],
HH [auth BH],
HI [auth AO],
HJ [auth AT],
ID [auth Af],
IG [auth BC],
IH [auth AI],
IJ [auth AT],
JC [auth Aa],
JH [auth AI],
KE [auth Bk],
KI [auth BO],
KJ [auth BU],
LE [auth Al],
LG [auth BD],
LH [auth BI],
MF [auth M],
MI [auth BP],
NC [auth Ab],
ND [auth Bf],
NF [auth M],
NJ [auth AU],
OE [auth Bl],
OH [auth AJ],
OJ [auth AV],
PE [auth Am],
PG [auth AD],
PH [auth AJ],
PI [auth AP],
QC [auth Bb],
QD [auth Bg],
QI [auth AQ],
QJ [auth BV],
RC [auth Ac],
RD [auth Ah],
RG [auth AE],
RH [auth AK],
RI [auth AQ],
SE [auth Bm],
SG [auth BE],
SI [auth AQ],
SJ [auth AW],
TH [auth BK],
TJ [auth AW],
UG [auth BF],
UJ [auth AW],
VC [auth Bc],
WC [auth Ad],
WD [auth Bh],
WE [auth Bn],
WH [auth AL],
WI [auth BR],
XD [auth Ai],
XE [auth Ao],
YF [auth BA],
YG [auth AF],
ZD [auth Bi],
ZE [auth Bo],
ZG [auth AG],
ZH [auth BL],
ZI [auth AR],
ZJ [auth AX]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH

Query on BPH



Download:Ideal Coordinates CCD File
GF [auth L],
OF [auth M]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
MQ8

Query on MQ8



Download:Ideal Coordinates CCD File
IF [auth L],
QF [auth M],
YC [auth Ad]
MENAQUINONE 8
C51 H72 O2
LXKDFTDVRVLXFY-ACMRXAIVSA-N
HEC

Query on HEC



Download:Ideal Coordinates CCD File
TF [auth C],
UF [auth C],
VF [auth C],
WF [auth C]
HEME C
C34 H36 Fe N4 O4
YZTICFPLOXKSQO-RGGAHWMASA-L
V7N

Query on V7N



Download:Ideal Coordinates CCD File
AD [auth Bd]
AH [auth BG]
AK [auth BX]
BF [auth Bp]
CJ [auth BS]
AD [auth Bd],
AH [auth BG],
AK [auth BX],
BF [auth Bp],
CJ [auth BS],
EE [auth Bj],
EG [auth BB],
FD [auth Be],
FH [auth BH],
FI [auth BN],
FJ [auth BT],
IC [auth Aa],
IE [auth Bk],
JI [auth BO],
KG [auth BC],
KH [auth BI],
LD [auth Bf],
MJ [auth BU],
NE [auth Bl],
NG [auth BD],
NI [auth BP],
OD [auth Bg],
PC [auth Bb],
PJ [auth BV],
QE [auth Bm],
QH [auth BJ],
TC [auth Bc],
TD [auth Bh],
TE [auth An],
UE [auth Bn],
VH [auth BK],
VI [auth BQ],
WG [auth BF],
WJ [auth BW],
XG [auth AF],
XH [auth AL],
YD [auth Bi],
YH [auth BL],
YI [auth BR],
ZF [auth BA]
(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
PF [auth M]SPIRILLOXANTHIN
C42 H60 O2
VAZQBTJCYODOSV-RISZBRKMSA-N
PEX

Query on PEX



Download:Ideal Coordinates CCD File
CE [auth Aj]
DD [auth Be]
DJ [auth AS]
GD [auth Be]
GJ [auth AT]
CE [auth Aj],
DD [auth Be],
DJ [auth AS],
GD [auth Be],
GJ [auth AT],
JE [auth Bk],
LC [auth Ba],
NH [auth AJ],
OG [auth AD],
OI [auth AP],
PD [auth Bg],
QG [auth AE],
RE [auth Bm],
UC [auth Bc],
UD [auth Bh],
VE [auth Bn],
XF [auth AA]
1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
C25 H49 N O8 P
KKOSJVWUOHEQKA-HSZRJFAPSA-M
LMT

Query on LMT



Download:Ideal Coordinates CCD File
AF [auth Bp]
AI [auth BL]
BE [auth Aj]
BG [auth BA]
BJ [auth BS]
AF [auth Bp],
AI [auth BL],
BE [auth Aj],
BG [auth BA],
BJ [auth BS],
CG [auth BA],
CH [auth BG],
DE [auth Bj],
DI [auth BM],
ED [auth Be],
EH [auth BH],
FE [auth Bj],
FG [auth BB],
GH [auth BH],
HF [auth L],
II [auth BO],
JF [auth M],
JG [auth BC],
JJ [auth BU],
KC [auth Aa],
KD [auth Bf],
LI [auth BO],
LJ [auth BU],
MC [auth Ba],
MD [auth Bf],
ME [auth Bl],
MG [auth BD],
MH [auth BI],
OC [auth Bb],
RF [auth K],
RJ [auth AW],
SC [auth Bc],
SD [auth Bh],
SF [auth C],
SH [auth BK],
TG [auth BE],
TI [auth BQ],
UH [auth BK],
UI [auth BQ],
VD [auth Bh],
VG [auth BF],
VJ [auth BW],
XC [auth Ad],
XI [auth BR],
XJ [auth BW],
YE [auth Bo],
YJ [auth AX],
ZC [auth Bd]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
FE

Query on FE



Download:Ideal Coordinates CCD File
KF [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

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Czech Science FoundationCzech Republic19-28778X

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-29
    Type: Initial release
  • Version 1.1: 2026-05-13
    Changes: Data collection, Database references
  • Version 2.0: 2026-09-23
    Type: Remediation
    Reason: Metalloprotein remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary