8J5P | pdb_00008j5p

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

Validation slider image for 8J5P

This is version 1.3 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 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.

Macromolecule Content 

  • Total Structure Weight: 357.68 kDa 
  • Atom Count: 23,737 
  • Modeled Residue Count: 2,331 
  • Deposited Residue Count: 2,531 
  • Unique protein chains: 8

Macromolecules

Find similar proteins by:|  3D Structure
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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7NQE9
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ83XD1
Sequence Annotations
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Reference Sequence
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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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7NQE7
Sequence Annotations
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Reference Sequence
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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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7NQE8
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Reference Sequence
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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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7NQE8
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit XHA [auth X]32Roseiflexus castenholzii DSM 13941Mutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit YIA [auth Y]39Roseiflexus castenholzii DSM 13941Mutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit ZJA [auth Z]63Roseiflexus castenholzii DSM 13941Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0AAJ6N6C1 (Roseiflexus castenholzii (strain DSM 13941 / HLO8))
Explore A0AAJ6N6C1 
Go to UniProtKB:  A0AAJ6N6C1
Entity Groups
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UniProt GroupA0AAJ6N6C1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MQE

Query on MQE



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
PC [auth L],
RC [auth L],
XC [auth M]
BACTERIOPHEOPHYTIN B
C55 H74 N4 O6
SFKCKJXMIAKQMY-GTTFDWDMSA-N
PGV

Query on PGV



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

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
  • Version 1.2: 2024-11-06
    Changes: Data collection, Structure summary
  • Version 1.3: 2025-07-02
    Changes: Data collection