8IUN

Cryo-EM structure of the CRT-LESS RC-LH core complex from roseiflexus castenholzii


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

New insights on the photocomplex of Roseiflexus castenholzii revealed from comparisons of native and carotenoid-depleted complexes.

Qi, C.H.Wang, G.L.Wang, F.F.Xin, Y.Zou, M.J.Madigan, M.T.Wang-Otomo, Z.Y.Ma, F.Yu, L.J.

(2023) J Biol Chem 299: 105057-105057

  • DOI: https://doi.org/10.1016/j.jbc.2023.105057
  • Primary Citation of Related Structures:  
    8IUG, 8IUN

  • PubMed Abstract: 

    In wild-type phototrophic organisms, carotenoids (Crts) are primarily packed into specific pigment-protein complexes along with (Bacterio)chlorophylls and play important roles in the photosynthesis. Diphenylamine (DPA) inhibits carotenogenesis but not phototrophic growth of anoxygenic phototrophs and eliminates virtually all Crts from photocomplexes. To investigate the effect of Crts on assembly of the reaction center-light-harvesting (RC-LH) complex from the filamentous anoxygenic phototroph Roseiflexus (Rfl.) castenholzii, we generated carotenoidless (Crt-less) RC-LH complexes by growing cells in the presence of DPA. Here, we present cryo-EM structures of the Rfl. castenholzii native and Crt-less RC-LH complexes with resolutions of 2.86 Å and 2.85 Å, respectively. From the high-quality map obtained, several important but previously unresolved details in the Rfl. castenholzii RC-LH structure were determined unambiguously including the assignment and likely function of three small polypeptides, and the content and spatial arrangement of Crts with bacteriochlorophyll molecules. The overall structures of Crt-containing and Crt-less complexes are similar. However, structural comparisons showed that only five Crts remain in complexes from DPA-treated cells and that the subunit X (TMx) flanked on the N-terminal helix of the Cyt-subunit is missing. Based on these results, the function of Crts in the assembly of the Rfl. castenholzii RC-LH complex and the molecular mechanism of quinone exchange is discussed. These structural details provide a fresh look at the photosynthetic apparatus of an evolutionary ancient phototroph as well as new insights into the importance of Crts for proper assembly and functioning of the RC-LH complex.


  • Organizational Affiliation

    Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Antenna complex alpha/beta subunit55Roseiflexus castenholziiMutation(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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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7NQE9
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein L chainP [auth M],
Q [auth L]
641Roseiflexus castenholziiMutation(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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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7NQE8
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha subunit of light-harvesting 142Roseiflexus castenholziiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q83XD1 (Roseiflexus castenholzii)
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Go to UniProtKB:  Q83XD1
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UniProt GroupQ83XD1
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
reaction center small polypeptideGA [auth Y]39Roseiflexus castenholziiMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
reaction center small polypeptideHA [auth h]63Roseiflexus castenholziiMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome subunit of photosynthetic reaction centerIA [auth C]320Roseiflexus castenholziiMutation(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: 7
MoleculeChains Sequence LengthOrganismDetailsImage
reaction center unknown polypeptideJA [auth Z]10Roseiflexus castenholziiMutation(s): 0 
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Small Molecules
Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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OD [auth P]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
MQE (Subject of Investigation/LOI)
Query on MQE

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EC [auth M],
SC [auth L]
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 (Subject of Investigation/LOI)
Query on BCL

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AC [auth 2]
AE [auth 3]
BC [auth M]
CB [auth I]
CE [auth 3]
AC [auth 2],
AE [auth 3],
BC [auth M],
CB [auth I],
CE [auth 3],
DB [auth I],
DE [auth 5],
EE [auth 7],
FB [auth G],
FD [auth H],
FE [auth 9],
GB [auth G],
HB [auth E],
IB [auth E],
IE [auth A],
JE [auth A],
KA [auth W],
KD [auth J],
LA [auth W],
LB [auth B],
LD [auth N],
MA [auth U],
MB [auth 0],
ME [auth D],
NA [auth U],
NB [auth 0],
ND [auth P],
PC [auth L],
PE [auth F],
QA [auth S],
QC [auth L],
QD [auth R],
RA [auth S],
RB [auth 8],
RD [auth T],
SB [auth 8],
TA [auth Q],
TD [auth V],
UA [auth Q],
UB [auth 6],
VA [auth O],
VB [auth 6],
WA [auth O],
WD [auth 1],
XB [auth 4],
YA [auth K],
ZA [auth K],
ZB [auth 2]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH (Subject of Investigation/LOI)
Query on BPH

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CC [auth M],
OC [auth L],
RC [auth L]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
PGV
Query on PGV

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AB [auth K]
BB [auth K]
EB [auth I]
EF [auth C]
FC [auth M]
AB [auth K],
BB [auth K],
EB [auth I],
EF [auth C],
FC [auth M],
JB [auth E],
KB [auth E],
MD [auth N],
OA [auth U],
PA [auth U],
PB [auth 0],
QB [auth 0],
SA [auth S],
TB [auth 8],
TC [auth L],
VE [auth h],
WB [auth 6],
XA [auth O],
XD [auth 1],
YB [auth 4],
YC [auth L],
ZC [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
LHG (Subject of Investigation/LOI)
Query on LHG

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UE [auth h]1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
PEF
Query on PEF

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AD [auth L],
ED [auth L],
IC [auth M],
WE [auth h]
DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
C37 H74 N O8 P
SLKDGVPOSSLUAI-PGUFJCEWSA-N
HEC (Subject of Investigation/LOI)
Query on HEC

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AF [auth C],
BF [auth C],
CF [auth C],
ZE [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
U4Z
Query on U4Z

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BE [auth 3],
JD [auth J],
LE [auth D],
OB [auth 0],
PD [auth R]
gamma-Carotene
C40 H56
HRQKOYFGHJYEFS-BXOLYSJBSA-N
LMT
Query on LMT

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GD [auth H],
JC [auth M],
OE [auth D],
SD [auth T],
ZD [auth 1]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
BGL
Query on BGL

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BD [auth L]
CD [auth L]
FF [auth C]
GC [auth M]
HC [auth M]
BD [auth L],
CD [auth L],
FF [auth C],
GC [auth M],
HC [auth M],
HD [auth H],
KC [auth M],
RE [auth Y],
TE [auth Y],
VC [auth L],
WC [auth L]
2-O-octyl-beta-D-glucopyranose
C14 H28 O6
BVHPDIWLWHHJPD-RKQHYHRCSA-N
MN (Subject of Investigation/LOI)
Query on MN

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DC [auth M]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA
Query on CA

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DF [auth C]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
UNL
Query on UNL

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DD [auth L]
GE [auth 9]
GF [auth C]
HE [auth 9]
HF [auth C]
DD [auth L],
GE [auth 9],
GF [auth C],
HE [auth 9],
HF [auth C],
ID [auth H],
KE [auth A],
LC [auth M],
MC [auth M],
NC [auth M],
NE [auth D],
QE [auth F],
SE [auth Y],
UC [auth L],
UD [auth V],
VD [auth V],
XC [auth L],
XE [auth h],
YD [auth 1],
YE [auth h]
Unknown ligand
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2021YFA0909600
Ministry of Science and Technology (MoST, China)China2022YFC3401800
Ministry of Science and Technology (MoST, China)China2019YFA0904600

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-06
    Type: Initial release