7VNM

Rba sphaeroides PufY-KO RC-LH1 monomer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.86 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]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 
Go to UniProtKB:  Q3J1A5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3J1A5
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein M chainB [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]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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UniProt GroupQ3J1A3
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Intrinsic membrane protein PufXBA [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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UniProt GroupP13402
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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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PA [auth M]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
BCL (Subject of Investigation/LOI)
Query on BCL

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BC [auth U]
CB [auth E]
CC [auth U]
EA [auth L]
EB [auth F]
BC [auth U],
CB [auth E],
CC [auth U],
EA [auth L],
EB [auth F],
EC [auth W],
FB [auth F],
FC [auth C],
GC [auth 7],
HB [auth I],
IA [auth L],
IB [auth I],
IC [auth 8],
JC [auth 9],
KA [auth M],
LB [auth K],
LC [auth 9],
MA [auth M],
OB [auth N],
PB [auth O],
PC [auth 1],
QB [auth O],
QC [auth 2],
TB [auth Q],
UA [auth A],
WB [auth R],
XA [auth A],
YA [auth D],
YB [auth S],
ZB [auth S]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH (Subject of Investigation/LOI)
Query on BPH

Download Ideal Coordinates CCD File 
FA [auth L],
JA [auth L]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
U10 (Subject of Investigation/LOI)
Query on U10

Download Ideal Coordinates CCD File 
HA [auth L],
NA [auth M]
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
PC1 (Subject of Investigation/LOI)
Query on PC1

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GA [auth L]
OC [auth X]
QA [auth H]
RA [auth H]
SA [auth H]
GA [auth L],
OC [auth X],
QA [auth H],
RA [auth H],
SA [auth H],
TA [auth A],
WA [auth A]
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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AB [auth D]
AC [auth S]
BB [auth D]
DB [auth E]
DC [auth U]
AB [auth D],
AC [auth S],
BB [auth D],
DB [auth E],
DC [auth U],
GB [auth F],
HC [auth 8],
JB [auth I],
KB [auth I],
KC [auth 9],
MB [auth K],
MC [auth 0],
NB [auth K],
NC [auth 0],
OA [auth M],
RB [auth P],
SB [auth P],
UB [auth Q],
VA [auth A],
VB [auth R],
XB [auth R],
ZA [auth D]
SPHEROIDENE
C41 H60 O
FJOCMTHZSURUFA-KXCOHNEYSA-N
FE2 (Subject of Investigation/LOI)
Query on FE2

Download Ideal Coordinates CCD File 
LA [auth M]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.86 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