7VOT

The structure of dimeric photosynthetic RC-LH1 supercomplex in Class-2

  • Classification: PHOTOSYNTHESIS
  • Organism(s): Cereibacter sphaeroides 2.4.1
  • Mutation(s): No 
  • Membrane Protein: Yes  OPMmpstruc

  • Deposited: 2021-10-14 Released: 2022-04-27 
  • Deposition Author(s): Cao, P., Li, M., Liu, L.N.
  • Funding Organization(s): Chinese Academy of Sciences, National Natural Science Foundation of China (NSFC), Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structural basis for the assembly and quinone transport mechanisms of the dimeric photosynthetic RC-LH1 supercomplex.

Cao, P.Bracun, L.Yamagata, A.Christianson, B.M.Negami, T.Zou, B.Terada, T.Canniffe, D.P.Shirouzu, M.Li, M.Liu, L.N.

(2022) Nat Commun 13: 1977-1977

  • DOI: https://doi.org/10.1038/s41467-022-29563-3
  • Primary Citation of Related Structures:  
    7VA9, 7VB9, 7VNM, 7VNY, 7VOR, 7VOT, 7VOY

  • PubMed Abstract: 

    The reaction center (RC) and light-harvesting complex 1 (LH1) form a RC-LH1 core supercomplex that is vital for the primary reactions of photosynthesis in purple phototrophic bacteria. Some species possess the dimeric RC-LH1 complex with a transmembrane polypeptide PufX, representing the largest photosynthetic complex in anoxygenic phototrophs. However, the details of the architecture and assembly mechanism of the RC-LH1 dimer are unclear. Here we report seven cryo-electron microscopy (cryo-EM) structures of RC-LH1 supercomplexes from Rhodobacter sphaeroides. Our structures reveal that two PufX polypeptides are positioned in the center of the S-shaped RC-LH1 dimer, interlocking association between the components and mediating RC-LH1 dimerization. Moreover, we identify another transmembrane peptide, designated PufY, which is located between the RC and LH1 subunits near the LH1 opening. PufY binds a quinone molecule and prevents LH1 subunits from completely encircling the RC, creating a channel for quinone/quinol exchange. Genetic mutagenesis, cryo-EM structures, and computational simulations provide a mechanistic understanding of the assembly and electron transport pathways of the RC-LH1 dimer and elucidate the roles of individual components in ensuring the structural and functional integrity of the photosynthetic supercomplex.


  • Organizational Affiliation

    National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein L chainA [auth L],
HA [auth l]
282Cereibacter sphaeroides 2.4.1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q3J1A5 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.))
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UniProt GroupQ3J1A5
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein M chainB [auth M],
IA [auth m]
308Cereibacter sphaeroides 2.4.1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q3J1A6 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.))
Explore Q3J1A6 
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UniProt GroupQ3J1A6
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein H chainC [auth H],
JA [auth h]
260Cereibacter sphaeroides 2.4.1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q3J170 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting protein B-875 alpha chain58Cereibacter sphaeroides 2.4.1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q3J1A4 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting protein B-875 beta chain49Cereibacter sphaeroides 2.4.1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q3J1A3 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Intrinsic membrane protein PufXFA [auth X],
MB [auth x]
82Cereibacter sphaeroides 2.4.1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P13402 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Rsp_7571 Protein-Y PufYGA [auth Y],
NB [auth y]
53Cereibacter sphaeroides 2.4.1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for U5NME9 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.))
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Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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BC [auth M],
DF [auth h],
FC [auth H],
ZE [auth m]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
BCL
Query on BCL

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AD [auth J]
AG [auth k]
AH [auth z]
BH [auth b1]
CD [auth K]
AD [auth J],
AG [auth k],
AH [auth z],
BH [auth b1],
CD [auth K],
CE [auth Z],
CG [auth n],
CH [auth 4],
DE [auth 1],
DH [auth 6],
ED [auth N],
EE [auth 2],
EF [auth a],
EG [auth o],
FE [auth 7],
FH [auth b8],
GC [auth A],
GD [auth O],
GG [auth p],
GH [auth b9],
HE [auth 8],
HG [auth q],
ID [auth P],
IE [auth 9],
IH [auth b0],
JD [auth Q],
JF [auth b],
JG [auth r],
KE [auth 0],
LC [auth B],
LD [auth R],
ME [auth l],
MG [auth s],
NE [auth l],
NF [auth d],
OB [auth L],
OD [auth S],
OG [auth t],
PB [auth L],
PC [auth D],
PF [auth e],
PG [auth u],
QD [auth T],
RC [auth E],
RD [auth U],
RF [auth f],
RG [auth v],
SE [auth l],
TC [auth F],
TD [auth V],
UB [auth L],
UF [auth g],
UG [auth w],
VE [auth m],
VF [auth i],
WC [auth G],
WD [auth W],
WG [auth c],
XB [auth M],
XC [auth I],
XG [auth 5],
YD [auth C],
YF [auth j],
ZD [auth 3]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPB
Query on BPB

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OE [auth l],
QB [auth L],
WE [auth m],
YB [auth M]
BACTERIOPHEOPHYTIN B
C55 H74 N4 O6
SFKCKJXMIAKQMY-GTTFDWDMSA-N
U10
Query on U10

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AF [auth m]
CC [auth M]
PE [auth l]
QE [auth l]
RB [auth L]
AF [auth m],
CC [auth M],
PE [auth l],
QE [auth l],
RB [auth L],
SB [auth L],
XE [auth m],
ZB [auth M]
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
PC1
Query on PC1

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BF [auth h]
CF [auth h]
DC [auth H]
EC [auth H]
GF [auth a]
BF [auth h],
CF [auth h],
DC [auth H],
EC [auth H],
GF [auth a],
HF [auth a],
IC [auth A],
IF [auth a],
JC [auth A],
KC [auth A],
LF [auth d],
MF [auth d],
NC [auth D],
OC [auth D],
RE [auth l],
TB [auth L],
TE [auth l],
VB [auth L]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
SPO
Query on SPO

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AC [auth M]
AE [auth 3]
BD [auth J]
BE [auth 3]
BG [auth n]
AC [auth M],
AE [auth 3],
BD [auth J],
BE [auth 3],
BG [auth n],
DD [auth N],
DG [auth n],
EH [auth 6],
FD [auth N],
FF [auth a],
FG [auth o],
GE [auth 7],
HC [auth A],
HD [auth O],
HH [auth b9],
IG [auth r],
JE [auth 9],
JH [auth b0],
KD [auth R],
KF [auth b],
KG [auth r],
LE [auth 0],
LG [auth r],
MC [auth B],
MD [auth R],
ND [auth R],
NG [auth s],
OF [auth d],
PD [auth S],
QC [auth D],
QF [auth e],
QG [auth u],
SC [auth E],
SD [auth U],
SF [auth f],
SG [auth v],
TF [auth f],
TG [auth v],
UC [auth F],
UD [auth V],
VC [auth F],
VD [auth V],
VG [auth c],
WF [auth i],
XD [auth C],
XF [auth i],
YC [auth I],
YE [auth m],
YG [auth 5],
ZC [auth I],
ZF [auth j],
ZG [auth 5]
SPHEROIDENE
C41 H60 O
FJOCMTHZSURUFA-KXCOHNEYSA-N
FE2
Query on FE2

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UE [auth m],
WB [auth M]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaXDB27020106
Chinese Academy of SciencesChinaXDB37020101
National Natural Science Foundation of China (NSFC)China32011530168
Biotechnology and Biological Sciences Research Council (BBSRC)ChinaBB/R003890/1 and BB/V009729/1
National Natural Science Foundation of China (NSFC)China32070259
National Natural Science Foundation of China (NSFC)China31930064
National Natural Science Foundation of China (NSFC)China32070109

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-27
    Type: Initial release