Skip to main content

 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
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9H22

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: 791.71 kDa 
  • Atom Count: 49,816 
  • Modeled Residue Count: 4,868 
  • Deposited Residue Count: 5,729 
  • Unique protein chains: 9

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
reaction centre S sub unitA [auth S]204Gemmatimonas groenlandicaMutation(s): 0 
UniProt
Find proteins for A0A6M4IPJ3 (Gemmatimonas groenlandica)
Explore A0A6M4IPJ3 
Go to UniProtKB:  A0A6M4IPJ3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6M4IPJ3
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Reaction center protein L chainB [auth L]274Gemmatimonas groenlandicaMutation(s): 0 
UniProt
Find proteins for A0A6M4IPC7 (Gemmatimonas groenlandica)
Explore A0A6M4IPC7 
Go to UniProtKB:  A0A6M4IPC7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6M4IPC7
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Reaction center protein M chainC [auth M]392Gemmatimonas groenlandicaMutation(s): 0 
UniProt
Find proteins for A0A6M4ILR2 (Gemmatimonas groenlandica)
Explore A0A6M4ILR2 
Go to UniProtKB:  A0A6M4ILR2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6M4ILR2
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
reaction centre Ht su unitD [auth H]66Gemmatimonas groenlandicaMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
reaction centre Hc sub unitE [auth K]180Gemmatimonas groenlandicaMutation(s): 0 
UniProt
Find proteins for A0ACM8DFI9 (Gemmatimonas groenlandica)
Explore A0ACM8DFI9 
Go to UniProtKB:  A0ACM8DFI9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACM8DFI9
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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)
Explore A0A6M4ITL7 
Go to UniProtKB:  A0A6M4ITL7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6M4ITL7
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Light-harvesting protein56Gemmatimonas groenlandicaMutation(s): 0 
UniProt
Find proteins for A0A6M4IQ17 (Gemmatimonas groenlandica)
Explore A0A6M4IQ17 
Go to UniProtKB:  A0A6M4IQ17
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6M4IQ17
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Light-harvesting protein44Gemmatimonas groenlandicaMutation(s): 0 
UniProt
Find proteins for A0A6M4IQ93 (Gemmatimonas groenlandica)
Explore A0A6M4IQ93 
Go to UniProtKB:  A0A6M4IQ93
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6M4IQ93
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Light-harvesting protein71Gemmatimonas groenlandicaMutation(s): 0 
UniProt
Find proteins for A0A6M4INU2 (Gemmatimonas groenlandica)
Explore A0A6M4INU2 
Go to UniProtKB:  A0A6M4INU2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6M4INU2
Sequence Annotations
Expand
Reference Sequence

Small Molecules

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

Query on CD4



Download:Ideal Coordinates CCD File
AI [auth Af],
TC [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
AG [auth BQ]
AK [auth Bp]
BE [auth AF]
BF [auth BL]
BH [auth AX]
AG [auth BQ],
AK [auth Bp],
BE [auth AF],
BF [auth BL],
BH [auth AX],
BI [auth Af],
CG [auth BR],
CI [auth Bf],
CJ [auth Bk],
DF [auth AM],
EF [auth BM],
EH [auth BX],
EI [auth Bf],
EJ [auth Al],
FD [auth BA],
FE [auth BG],
FG [auth AR],
FJ [auth Bl],
GF [auth BN],
GG [auth BS],
GH [auth Aa],
GI [auth Ag],
HD [auth BB],
HE [auth AH],
HJ [auth Bl],
IC [auth L],
IH [auth Ba],
JC [auth L],
JF [auth AN],
JG [auth BT],
KD [auth AB],
KE [auth BH],
KF [auth AN],
KI [auth Bg],
KJ [auth Am],
LF [auth AN],
MD [auth AC],
ME [auth AI],
MF [auth AO],
MG [auth AT],
ND [auth BC],
NH [auth Ac],
NI [auth Ah],
NJ [auth Bm],
OI [auth Bh],
PE [auth BI],
PF [auth BO],
PG [auth AT],
PI [auth Bh],
QD [auth BD],
QI [auth Ai],
QJ [auth An],
RE [auth BJ],
RF [auth BP],
RG [auth AU],
SE [auth AK],
SG [auth AU],
SJ [auth Bn],
TD [auth AD],
TG [auth AV],
TI [auth Bi],
UC [auth M],
UD [auth AD],
UF [auth BP],
UH [auth Bd],
UJ [auth Ao],
VC [auth M],
VD [auth AE],
VE [auth BK],
VG [auth BV],
VI [auth Aj],
WF [auth AP],
WI [auth Bj],
WJ [auth Bo],
XD [auth BE],
XF [auth AQ],
XG [auth AW],
XH [auth Ae],
XJ [auth Bp],
YE [auth AL],
YH [auth Be],
ZD [auth BF],
ZF [auth AQ],
ZG [auth BW]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH

Query on BPH



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

Query on MQ8



Download:Ideal Coordinates CCD File
AD [auth M],
RC [auth L],
RH [auth Ad]
MENAQUINONE 8
C51 H72 O2
LXKDFTDVRVLXFY-ACMRXAIVSA-N
HEC

Query on HEC



Download:Ideal Coordinates CCD File
BD [auth C],
CD [auth C],
DD [auth C],
ED [auth C]
HEME C
C34 H36 Fe N4 O4
YZTICFPLOXKSQO-RGGAHWMASA-L
V7N

Query on V7N



Download:Ideal Coordinates CCD File
AE [auth BF]
AF [auth BL]
AH [auth AX]
BJ [auth Bk]
CE [auth AF]
AE [auth BF],
AF [auth BL],
AH [auth AX],
BJ [auth Bk],
CE [auth AF],
DH [auth BX],
DI [auth Bf],
EG [auth BR],
GJ [auth Bl],
HH [auth Ba],
HI [auth Ag],
ID [auth BB],
IE [auth AH],
IF [auth BN],
IG [auth BS],
JI [auth Bg],
KG [auth BT],
LE [auth AI],
LH [auth Bb],
LJ [auth Am],
MJ [auth Bm],
NE [auth AI],
NG [auth AT],
OF [auth BO],
PD [auth BC],
PH [auth Bc],
RJ [auth An],
SD [auth BD],
SH [auth Ad],
SI [auth Bi],
TF [auth BP],
TH [auth Bd],
UG [auth BV],
VF [auth AP],
WD [auth BE],
XE [auth BK],
YG [auth BW],
YI [auth Bj],
ZE [auth AL],
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



Download:Ideal Coordinates CCD File
XC [auth M]SPIRILLOXANTHIN
C42 H60 O2
VAZQBTJCYODOSV-RISZBRKMSA-N
PEX

Query on PEX



Download:Ideal Coordinates CCD File
BK [auth Bp]
DE [auth AG]
DJ [auth Bk]
FI [auth Bf]
IJ [auth Bl]
BK [auth Bp],
DE [auth AG],
DJ [auth Bk],
FI [auth Bf],
IJ [auth Bl],
JH [auth Ba],
LI [auth Bg],
MH [auth Bb],
NF [auth AO],
OG [auth AT],
OJ [auth Bm],
TJ [auth Bn],
UI [auth Bi],
VH [auth Bd],
ZC [auth M],
ZH [auth Be],
ZI [auth Bj]
1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
C25 H49 N O8 P
KKOSJVWUOHEQKA-HSZRJFAPSA-M
LMT

Query on LMT



Download:Ideal Coordinates CCD File
AJ [auth Bk]
BG [auth BQ]
CF [auth BL]
CH [auth BX]
DG [auth BR]
AJ [auth Bk],
BG [auth BQ],
CF [auth BL],
CH [auth BX],
DG [auth BR],
EE [auth BG],
FF [auth BM],
FH [auth BX],
GD [auth BA],
GE [auth BG],
HF [auth BN],
HG [auth BS],
II [auth Bg],
JD [auth BB],
JE [auth BH],
JJ [auth Bl],
KH [auth Ba],
LC [auth L],
LD [auth AB],
LG [auth BT],
MC [auth L],
MI [auth Bg],
NC [auth L],
OC [auth L],
OD [auth BC],
OE [auth BI],
OH [auth Bc],
PC [auth L],
PJ [auth Bm],
QC [auth L],
QE [auth BI],
QF [auth BO],
QG [auth BU],
QH [auth Bc],
RD [auth BD],
RI [auth Bi],
SF [auth BP],
TE [auth AK],
UE [auth BK],
VJ [auth Bo],
WE [auth BK],
WG [auth BV],
WH [auth Bd],
XI [auth Bj],
YC [auth M],
YD [auth BF],
YF [auth AQ],
YJ [auth Bp]
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

View Full Validation Report



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
  • Version 1.2: 2026-01-28
    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