9LTS | pdb_00009lts

Cryo-EM structure of the Dinoroseobacter shibae RC-LH1 supercomplex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.49 Å
  • Resolution: 2.49 Å
  • Resolution: 2.49 Å
  • Resolution: 2.49 Å
  • Resolution: 2.49 Å
  • Resolution: 2.49 Å
  • Resolution: 2.49 Å
  • Resolution: 2.49 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for aerobic anoxygenic photosynthesis in the reaction center-light-harvesting 1 (RC-LH1) supercomplex of Dinoroseobacter shibae.

Liu, Z.K.Li, J.X.Zhang, Y.Y.Lv, J.L.Li, K.Chen, X.L.Zhang, Y.Z.Liu, L.N.Wang, P.

(2025) Commun Biol 8: 1565-1565

  • DOI: https://doi.org/10.1038/s42003-025-08935-7
  • Primary Citation Related Structures: 
    9LTS, 9LTU, 9LTV

  • PubMed Abstract: 

    Aerobic anoxygenic phototrophic (AAP) bacteria are essential for oceanic carbon cycling. However, their architecture and structural adaptations of their photosynthetic systems to ensure adequate light harvesting, electron transport, and oxidative resilience in oxygen-rich environments remain poorly understood. In this study, we present a 2.4-Å cryo-EM structure of the reaction center-light-harvesting 1 (RC-LH1) supercomplex from Dinoroseobacter shibae DFL-12, a marine AAP bacterial symbiont of benthic dinoflagellates. This RC-LH1 supercomplex features a closed LH1 ring comprising 17 αβ-subunits, each containing two spheroidenones per αβ-heterodimer-a previously unreported configuration in phototrophic bacteria. The cytochrome subunit of the RC is truncated to three hemes, in contrast to the four-heme configuration found in anaerobic relatives. The structure also reveals elongated bacteriochlorophyll (BChl) spacing, which may account for its blue-shifted absorption maximum that is optimized for low-light benthic environments. Furthermore, we identify a previously unknown subunit, protein-LRC, which is hypothesized to functionally couple photochemical and respiratory electron transport. Collectively, these specific structural features allow AAP bacteria to balance anoxygenic photosynthesis and protection against oxidative damage, providing a mechanistic framework for them to thrive in oxygenated marine environments. Our study provides insights into the structural and functional variability of bacterial photosynthesis in response to oxygenated marine environments.


  • Organizational Affiliation
    • MOE Key Laboratory of Evolution and Marine Biodiversity, State Key Laboratory of Marine Food Processing and Safety Control & College of Marine Life Sciences, Ocean University of China, Qingdao, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein LRC76Dinoroseobacter shibae DFL 12 = DSM 16493Mutation(s): 0 
UniProt
Find proteins for A8LIU2 (Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12))
Explore A8LIU2 
Go to UniProtKB:  A8LIU2
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UniProt GroupA8LIU2
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Antenna pigment protein alpha chain51Dinoroseobacter shibae DFL 12 = DSM 16493Mutation(s): 0 
UniProt
Find proteins for A8LQ15 (Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12))
Explore A8LQ15 
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UniProt GroupA8LQ15
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Antenna pigment protein beta chain44Dinoroseobacter shibae DFL 12 = DSM 16493Mutation(s): 0 
UniProt
Find proteins for A8LQ14 (Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12))
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UniProt GroupA8LQ14
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center cytochrome c subunitHA [auth C]357Dinoroseobacter shibae DFL 12 = DSM 16493Mutation(s): 0 
UniProt
Find proteins for A8LQ18 (Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12))
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UniProt GroupA8LQ18
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein H chainIA [auth H]255Dinoroseobacter shibae DFL 12 = DSM 16493Mutation(s): 0 
UniProt
Find proteins for A8LQ33 (Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12))
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UniProt GroupA8LQ33
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein L chainJA [auth L]273Dinoroseobacter shibae DFL 12 = DSM 16493Mutation(s): 0 
UniProt
Find proteins for A8LQ16 (Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12))
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UniProt GroupA8LQ16
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein M chainKA [auth M]325Dinoroseobacter shibae DFL 12 = DSM 16493Mutation(s): 0 
UniProt
Find proteins for A8LQ17 (Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12))
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BCL (Subject of Investigation/LOI)
Query on BCL

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AB [auth 4]
AC [auth l]
AE [auth 0]
BB [auth w]
BD [auth 8]
AB [auth 4],
AC [auth l],
AE [auth 0],
BB [auth w],
BD [auth 8],
CC [auth g],
DB [auth x],
EB [auth u],
FC [auth h],
GB [auth v],
IB [auth s],
IC [auth e],
JD [auth L],
KB [auth t],
KC [auth f],
MB [auth q],
MC [auth c],
MD [auth L],
OA [auth 1],
OB [auth r],
PC [auth d],
PD [auth M],
QB [auth o],
QC [auth a],
RB [auth p],
RD [auth M],
TA [auth 2],
TC [auth b],
UA [auth 5],
UB [auth m],
UC [auth i],
WB [auth n],
WC [auth j],
XA [auth 6],
YA [auth 3],
YB [auth k],
YC [auth 7],
YD [auth 9]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH (Subject of Investigation/LOI)
Query on BPH

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LD [auth L],
SD [auth M],
WD [auth M]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
U10 (Subject of Investigation/LOI)
Query on U10

Download Ideal Coordinates CCD File 
KD [auth L],
NA [auth A],
ND [auth L],
QD [auth M]
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
MW9 (Subject of Investigation/LOI)
Query on MW9

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DC [auth g]
EC [auth g]
FD [auth H]
GD [auth H]
HD [auth H]
DC [auth g],
EC [auth g],
FD [auth H],
GD [auth H],
HD [auth H],
ID [auth H],
UD [auth M],
VD [auth M],
XD [auth 9]
(21R,24R,27S)-24,27,28-trihydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosphaoctacosan-21-yl (9Z)-octadec-9-enoate
C42 H81 O10 P
ZEFGRNLJASLRBZ-QIJYXWHJSA-N
HEM (Subject of Investigation/LOI)
Query on HEM

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CD [auth C],
DD [auth C],
ED [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
SPN (Subject of Investigation/LOI)
Query on SPN

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AD [auth 7]
BC [auth l]
BE [auth 0]
CB [auth w]
FB [auth u]
AD [auth 7],
BC [auth l],
BE [auth 0],
CB [auth w],
FB [auth u],
GC [auth h],
HB [auth v],
HC [auth h],
JB [auth s],
JC [auth e],
LB [auth t],
LC [auth f],
NB [auth q],
NC [auth c],
OC [auth c],
PA [auth 1],
PB [auth r],
QA [auth 1],
RA [auth 1],
RC [auth a],
SA [auth 1],
SB [auth p],
SC [auth a],
TB [auth p],
TD [auth M],
VA [auth 5],
VB [auth m],
VC [auth i],
WA [auth 5],
XB [auth n],
XC [auth j],
ZA [auth 3],
ZB [auth k],
ZC [auth 7],
ZD [auth 9]
SPEROIDENONE
C41 H70 O2
GWQAMGYOEYXWJF-YCDPMLDASA-N
FE (Subject of Investigation/LOI)
Query on FE

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.49 Å
  • Resolution: 2.49 Å
  • Resolution: 2.49 Å
  • Resolution: 2.49 Å
  • Resolution: 2.49 Å
  • Resolution: 2.49 Å
  • Resolution: 2.49 Å
  • Resolution: 2.49 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32370136

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-01
    Type: Initial release
  • Version 1.1: 2026-04-15
    Changes: Data collection, Database references