8J5P

Cryo-EM structure of native RC-LH complex from Roseiflexus castenholzii at 2,000lux


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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

Carotenoid assembly regulates quinone diffusion and the Roseiflexus castenholzii reaction center-light harvesting complex architecture.

Xin, J.Shi, Y.Zhang, X.Yuan, X.Xin, Y.He, H.Shen, J.Blankenship, R.E.Xu, X.

(2023) Elife 12

  • DOI: https://doi.org/10.7554/eLife.88951
  • Primary Citation of Related Structures:  
    8HJU, 8HJV, 8J5O, 8J5P

  • PubMed Abstract: 

    Carotenoid (Car) pigments perform central roles in photosynthesis-related light harvesting (LH), photoprotection, and assembly of functional pigment-protein complexes. However, the relationships between Car depletion in the LH, assembly of the prokaryotic reaction center (RC)-LH complex, and quinone exchange are not fully understood. Here, we analyzed native RC-LH (nRC-LH) and Car-depleted RC-LH (dRC-LH) complexes in Roseiflexus castenholzii , a chlorosome-less filamentous anoxygenic phototroph that forms the deepest branch of photosynthetic bacteria. Newly identified exterior Cars functioned with the bacteriochlorophyll B800 to block the proposed quinone channel between LHαβ subunits in the nRC-LH, forming a sealed LH ring that was disrupted by transmembrane helices from cytochrome c and subunit X to allow quinone shuttling. dRC-LH lacked subunit X, leading to an exposed LH ring with a larger opening, which together accelerated the quinone exchange rate. We also assigned amino acid sequences of subunit X and two hypothetical proteins Y and Z that functioned in forming the quinone channel and stabilizing the RC-LH interactions. This study reveals the structural basis by which Cars assembly regulates the architecture and quinone exchange of bacterial RC-LH complexes. These findings mark an important step forward in understanding the evolution and diversity of prokaryotic photosynthetic apparatus.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and The Affiliated Hospital of Hangzhou Normal University, Hangzhou, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta subunit of light-harvesting 155Roseiflexus castenholzii DSM 13941Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A7NQE9 (Roseiflexus castenholzii (strain DSM 13941 / HLO8))
Explore A7NQE9 
Go to UniProtKB:  A7NQE9
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UniProt GroupA7NQE9
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha subunit of light-harvesting 142Roseiflexus castenholzii DSM 13941Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q83XD1 (Roseiflexus castenholzii)
Explore Q83XD1 
Go to UniProtKB:  Q83XD1
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UniProt GroupQ83XD1
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
MULTIHEME_CYTC DOMAIN-CONTAINING PROTEINM [auth C]320Roseiflexus castenholzii DSM 13941Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A7NQE7 (Roseiflexus castenholzii (strain DSM 13941 / HLO8))
Explore A7NQE7 
Go to UniProtKB:  A7NQE7
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UniProt GroupA7NQE7
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein L chainV [auth L]315Roseiflexus castenholzii DSM 13941Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A7NQE8 (Roseiflexus castenholzii (strain DSM 13941 / HLO8))
Explore A7NQE8 
Go to UniProtKB:  A7NQE8
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UniProt GroupA7NQE8
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein M chainW [auth M]307Roseiflexus castenholzii DSM 13941Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A7NQE8 (Roseiflexus castenholzii (strain DSM 13941 / HLO8))
Explore A7NQE8 
Go to UniProtKB:  A7NQE8
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UniProt GroupA7NQE8
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit XHA [auth X]32Roseiflexus castenholzii DSM 13941Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit YIA [auth Y]39Roseiflexus castenholzii DSM 13941Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit ZJA [auth Z]63Roseiflexus castenholzii DSM 13941Mutation(s): 0 
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Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MQE
Query on MQE

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QC [auth L],
UC [auth M],
YC [auth M]
2-methyl-3-[(2E,6E,10E,14E,18E,22E,26E,30E,34E,38E)-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,1 4,18,22,26,30,34,38,42-undecaen-1-yl]naphthalene-1,4-dione
C66 H96 O2
YYDMANIEKFAEJC-RYZSZPJESA-N
BCL
Query on BCL

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AB [auth 6]
AC [auth G]
AD [auth O]
BD [auth O]
CB [auth 7]
AB [auth 6],
AC [auth G],
AD [auth O],
BD [auth O],
CB [auth 7],
DB [auth 8],
DC [auth H],
EB [auth 8],
EC [auth I],
ED [auth P],
FC [auth I],
HB [auth 9],
HD [auth Q],
IB [auth A],
IC [auth J],
ID [auth Q],
KA [auth 0],
KB [auth B],
KC [auth K],
KD [auth R],
LA [auth 0],
LB [auth B],
LC [auth K],
MD [auth S],
NA [auth 1],
NC [auth L],
ND [auth S],
OA [auth 2],
OC [auth L],
PA [auth 2],
PD [auth T],
RA [auth 3],
RD [auth U],
SD [auth U],
TA [auth 4],
TB [auth D],
UA [auth 4],
UB [auth D],
UD [auth V],
VB [auth E],
VD [auth W],
WA [auth 5],
WC [auth M],
XD [auth X],
YB [auth F],
ZA [auth 6],
ZB [auth G],
ZC [auth N]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPB
Query on BPB

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PC [auth L],
RC [auth L],
XC [auth M]
BACTERIOPHEOPHYTIN B
C55 H74 N4 O6
SFKCKJXMIAKQMY-GTTFDWDMSA-N
PGV
Query on PGV

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GD [auth P],
SC [auth L],
TC [auth L]
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
C40 H77 O10 P
ADYWCMPUNIVOEA-GPJPVTGXSA-N
HEM
Query on HEM

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OB [auth C],
PB [auth C],
QB [auth C],
RB [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
KGD
Query on KGD

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BB [auth 6]
BC [auth G]
CC [auth H]
CD [auth O]
DD [auth P]
BB [auth 6],
BC [auth G],
CC [auth H],
CD [auth O],
DD [auth P],
FB [auth 8],
FD [auth P],
GB [auth 9],
GC [auth I],
HC [auth I],
JB [auth A],
JC [auth J],
JD [auth Q],
LD [auth R],
MA [auth 0],
MB [auth B],
MC [auth K],
NB [auth C],
OD [auth S],
QA [auth 2],
QD [auth T],
SA [auth 3],
SB [auth C],
TD [auth U],
VA [auth 4],
WB [auth E],
WD [auth W],
XA [auth 5],
XB [auth E],
YA [auth 5]
beta,psi-caroten-4-one
C40 H54 O
BRKQDNOGSHYATK-HNNISBQLSA-N
FE
Query on FE

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2023-09-20 
  • Deposition Author(s): Xu, X., Xin, J.

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

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-20
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references