7VB9

Rba sphaeroides PufY-KO RC-LH1 dimer type-2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.45 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 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],
T [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.))
Explore Q3J1A5 
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UniProt GroupQ3J1A5
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein M chainB [auth M],
U [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],
V [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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UniProt GroupQ3J170
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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.))
Explore Q3J1A4 
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UniProt GroupQ3J1A4
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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 PufXS [auth C],
YA [auth c]
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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Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

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ZC [auth m]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
BCL (Subject of Investigation/LOI)
Query on BCL

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AB [auth L]
AC [auth J]
BD [auth a]
BE [auth q]
BF [auth c]
AB [auth L],
AC [auth J],
BD [auth a],
BE [auth q],
BF [auth c],
CC [auth K],
DB [auth L],
DC [auth N],
DE [auth q],
EC [auth O],
ED [auth b],
EE [auth r],
FC [auth 8],
GB [auth M],
GD [auth d],
GE [auth s],
HC [auth 9],
HE [auth t],
JD [auth e],
KC [auth 0],
KE [auth v],
LD [auth f],
MB [auth A],
ME [auth w],
NC [auth C],
OB [auth B],
OD [auth g],
OE [auth x],
PB [auth D],
PC [auth l],
PD [auth i],
PE [auth y],
QD [auth i],
QE [auth z],
RB [auth E],
RE [auth 5],
SC [auth l],
SE [auth 4],
TB [auth F],
TD [auth k],
UC [auth m],
UD [auth n],
UE [auth aa],
WB [auth G],
WC [auth m],
WD [auth o],
WE [auth Q],
YD [auth p],
YE [auth ab],
ZA [auth L],
ZB [auth I]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH (Subject of Investigation/LOI)
Query on BPH

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BB [auth L],
EB [auth L],
QC [auth l],
TC [auth l]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
U10 (Subject of Investigation/LOI)
Query on U10

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CB [auth L],
HB [auth M],
RC [auth l],
XC [auth m]
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
PC1 (Subject of Investigation/LOI)
Query on PC1

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AD [auth h]
AF [auth c]
CD [auth a]
JB [auth H]
KB [auth H]
AD [auth h],
AF [auth c],
CD [auth a],
JB [auth H],
KB [auth H],
LB [auth A],
MC [auth C],
NB [auth A],
VE [auth Q]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
SPO (Subject of Investigation/LOI)
Query on SPO

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AE [auth p]
BC [auth J]
CE [auth q]
DD [auth b]
FD [auth b]
AE [auth p],
BC [auth J],
CE [auth q],
DD [auth b],
FD [auth b],
FE [auth s],
GC [auth 9],
HD [auth d],
IB [auth M],
IC [auth 9],
ID [auth d],
IE [auth t],
JC [auth 0],
JE [auth u],
KD [auth e],
LC [auth 0],
LE [auth v],
MD [auth f],
ND [auth g],
NE [auth w],
OC [auth C],
QB [auth D],
RD [auth i],
SB [auth E],
SD [auth j],
TE [auth aa],
UB [auth F],
VB [auth F],
VD [auth n],
XB [auth G],
XD [auth o],
XE [auth Q],
YB [auth G],
YC [auth m],
ZD [auth p],
ZE [auth ab]
SPHEROIDENE
C41 H60 O
FJOCMTHZSURUFA-KXCOHNEYSA-N
FE2 (Subject of Investigation/LOI)
Query on FE2

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Royal SocietyUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-04
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Data collection