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

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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.

(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 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
Entity Groups
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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)
Explore A0A6M4IPJ3 
Go to UniProtKB:  A0A6M4IPJ3
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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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Entity Groups
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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)
Explore A0A6M4ILR2 
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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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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
reaction centre Hc sub unitKA [auth K]179Gemmatimonas groenlandicaMutation(s): 0 
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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)
Explore A0A6M4ITL7 
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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
Entity Groups
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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
KD [auth Af],
MF [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 Bi]
AF [auth Bo]
AH [auth AG]
AI [auth BL]
AJ [auth BS]
AE [auth Bi],
AF [auth Bo],
AH [auth AG],
AI [auth BL],
AJ [auth BS],
BE [auth Aj],
BG [auth BA],
BK [auth BX],
CD [auth Bd],
CH [auth BG],
CI [auth AM],
DD [auth Ae],
DF [auth Bp],
DI [auth AM],
EF [auth Bp],
EG [auth BB],
EH [auth AH],
EJ [auth AS],
FF [auth L],
FI [auth BN],
GF [auth L],
HE [auth Bj],
HG [auth AB],
HI [auth AN],
HJ [auth AT],
ID [auth Be],
IE [auth Ak],
IG [auth AC],
IH [auth BH],
II [auth AO],
IJ [auth AT],
JC [auth Aa],
JD [auth Af],
JG [auth BC],
JH [auth AI],
KH [auth AI],
KJ [auth BU],
LE [auth Bk],
LI [auth BO],
MC [auth Ba],
ME [auth Al],
MG [auth BD],
MH [auth BI],
NF [auth M],
NI [auth BP],
NJ [auth AU],
OC [auth Ab],
OD [auth Bf],
OF [auth M],
OJ [auth AV],
PE [auth Bl],
PH [auth AJ],
QE [auth Am],
QG [auth AD],
QH [auth AJ],
QI [auth AP],
QJ [auth BV],
RC [auth Bb],
RD [auth Bg],
RI [auth AQ],
SC [auth Ac],
SD [auth Ah],
SG [auth AE],
SH [auth AK],
SI [auth AQ],
SJ [auth AW],
TE [auth Bm],
TG [auth BE],
TJ [auth AW],
UH [auth BK],
UJ [auth AW],
VG [auth BF],
WC [auth Bc],
WI [auth BR],
XC [auth Ad],
XD [auth Bh],
XE [auth Bn],
XH [auth AL],
YD [auth Ai],
YE [auth Ao],
ZF [auth BA],
ZG [auth AF],
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
HF [auth L],
PF [auth M]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
MQ8

Query on MQ8



Download:Ideal Coordinates CCD File
JF [auth L],
RF [auth M],
ZC [auth Ad]
MENAQUINONE 8
C51 H72 O2
LXKDFTDVRVLXFY-ACMRXAIVSA-N
HEC

Query on HEC



Download:Ideal Coordinates CCD File
UF [auth C],
VF [auth C],
WF [auth C],
XF [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
V7N

Query on V7N



Download:Ideal Coordinates CCD File
AG [auth BA]
AK [auth BX]
BD [auth Bd]
BH [auth BG]
CF [auth Bp]
AG [auth BA],
AK [auth BX],
BD [auth Bd],
BH [auth BG],
CF [auth Bp],
CJ [auth BS],
FE [auth Bj],
FG [auth BB],
FJ [auth BT],
GD [auth Be],
GH [auth BH],
GI [auth BN],
IC [auth Aa],
JE [auth Bk],
KI [auth BO],
LG [auth BC],
LH [auth BI],
MD [auth Bf],
MJ [auth BU],
OE [auth Bl],
OG [auth BD],
OI [auth BP],
PD [auth Bg],
PJ [auth BV],
QC [auth Bb],
RE [auth Bm],
RH [auth BJ],
UC [auth Bc],
UD [auth Bh],
UE [auth An],
VE [auth Bn],
VI [auth BQ],
WH [auth BK],
WJ [auth BW],
XG [auth BF],
YG [auth AF],
YH [auth AL],
YI [auth BR],
ZD [auth Bi],
ZH [auth BL]
(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
QF [auth M]SPIRILLOXANTHIN
C42 H60 O2
VAZQBTJCYODOSV-RISZBRKMSA-N
PEX

Query on PEX



Download:Ideal Coordinates CCD File
DE [auth Aj]
DJ [auth AS]
ED [auth Be]
GJ [auth AT]
HD [auth Be]
DE [auth Aj],
DJ [auth AS],
ED [auth Be],
GJ [auth AT],
HD [auth Be],
KE [auth Bk],
LC [auth Ba],
OH [auth AJ],
PG [auth AD],
PI [auth AP],
QD [auth Bg],
RG [auth AE],
SE [auth Bm],
VC [auth Bc],
VD [auth Bh],
WE [auth Bn],
YF [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
AD [auth Bd]
BF [auth Bp]
BI [auth BL]
BJ [auth BS]
CE [auth Aj]
AD [auth Bd],
BF [auth Bp],
BI [auth BL],
BJ [auth BS],
CE [auth Aj],
CG [auth BA],
DG [auth BA],
DH [auth BG],
EE [auth Bj],
EI [auth BM],
FD [auth Be],
FH [auth BH],
GE [auth Bj],
GG [auth BB],
HH [auth BH],
IF [auth L],
JI [auth BO],
JJ [auth BU],
KC [auth Aa],
KF [auth M],
KG [auth BC],
LD [auth Bf],
LJ [auth BU],
MI [auth BO],
NC [auth Ba],
ND [auth Bf],
NE [auth Bl],
NG [auth BD],
NH [auth BI],
PC [auth Bb],
RJ [auth AW],
SF [auth K],
TC [auth Bc],
TD [auth Bh],
TF [auth C],
TH [auth BK],
TI [auth BQ],
UG [auth BE],
UI [auth BQ],
VH [auth BK],
VJ [auth BW],
WD [auth Bh],
WG [auth BF],
XI [auth BR],
XJ [auth BW],
YC [auth Ad],
YJ [auth AX],
ZE [auth Bo]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
FE

Query on FE



Download:Ideal Coordinates CCD File
LF [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