7PIL

Cryo-EM structure of the Rhodobacter sphaeroides RC-LH1-PufXY monomer complex at 2.5 A


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Cryo-EM structure of the monomeric Rhodobacter sphaeroides RC-LH1 core complex at 2.5 angstrom.

Qian, P.Swainsbury, D.J.K.Croll, T.I.Salisbury, J.H.Martin, E.C.Jackson, P.J.Hitchcock, A.Castro-Hartmann, P.Sader, K.Hunter, C.N.

(2021) Biochem J 478: 3775-3790

  • DOI: https://doi.org/10.1042/BCJ20210631
  • Primary Citation of Related Structures:  
    7PIL

  • PubMed Abstract: 

    Reaction centre light-harvesting 1 (RC-LH1) complexes are the essential components of bacterial photosynthesis. The membrane-intrinsic LH1 complex absorbs light and the energy migrates to an enclosed RC where a succession of electron and proton transfers conserves the energy as a quinol, which is exported to the cytochrome bc1 complex. In some RC-LH1 variants quinols can diffuse through small pores in a fully circular, 16-subunit LH1 ring, while in others missing LH1 subunits create a gap for quinol export. We used cryogenic electron microscopy to obtain a 2.5 Å resolution structure of one such RC-LH1, a monomeric complex from Rhodobacter sphaeroides. The structure shows that the RC is partly enclosed by a 14-subunit LH1 ring in which each αβ heterodimer binds two bacteriochlorophylls and, unusually for currently reported complexes, two carotenoids rather than one. Although the extra carotenoids confer an advantage in terms of photoprotection and light harvesting, they could impede passage of quinones through small, transient pores in the LH1 ring, necessitating a mechanism to create a dedicated quinone channel. The structure shows that two transmembrane proteins play a part in stabilising an open ring structure; one of these components, the PufX polypeptide, is augmented by a hitherto undescribed protein subunit we designate as protein-Y, which lies against the transmembrane regions of the thirteenth and fourteenth LH1α polypeptides. Protein-Y prevents LH1 subunits 11-14 adjacent to the RC QB site from bending inwards towards the RC and, with PufX preventing complete encirclement of the RC, this pair of polypeptides ensures unhindered quinone diffusion.


  • Organizational Affiliation

    Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, Netherlands.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting protein B-875 alpha chain55Cereibacter 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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting protein B-875 beta chain43Cereibacter 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.))
Explore Q3J1A3 
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UniProt GroupQ3J1A3
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein H chainCA [auth H]246Cereibacter 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
Reaction center protein L chainDA [auth L]281Cereibacter 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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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein M chainEA [auth M]307Cereibacter 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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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RC-YFA [auth UU]49Cereibacter 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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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Intrinsic membrane protein PufXGA [auth X]55Cereibacter 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 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CD4
Query on CD4

Download Ideal Coordinates CCD File 
XC [auth M](2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate
C65 H126 O17 P2
SDCJNZZAOLRVCP-GTOSQJSUSA-N
BCL (Subject of Investigation/LOI)
Query on BCL

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AC [auth BB]
BC
CB [auth AG]
CC [auth BD]
EC [auth BF]
AC [auth BB],
BC,
CB [auth AG],
CC [auth BD],
EC [auth BF],
FB [auth AH],
FC [auth BG],
GC [auth BH],
HA [auth AA],
HB [auth AI],
HC [auth BI],
IC [auth BJ],
KA [auth AB],
KB [auth AJ],
KC [auth BL],
LC [auth BN],
NB [auth AK],
PA [auth AC],
PB [auth AK],
RB [auth AL],
RC [auth L],
SC [auth L],
TA [auth AD],
TB [auth AM],
VA [auth AE],
VB [auth AM],
VC [auth M],
XA [auth AE],
XB [auth AN],
YC [auth M],
ZA [auth AF],
ZB [auth BA]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH (Subject of Investigation/LOI)
Query on BPH

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OC [auth L],
UC [auth M]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
U10 (Subject of Investigation/LOI)
Query on U10

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PC [auth L],
WC [auth M]
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
3PE
Query on 3PE

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LA [auth AB],
MC [auth H],
NC [auth H],
RA [auth AC]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
SPO
Query on SPO

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AB [auth AF]
BB [auth AG]
DB [auth AG]
DC [auth BE]
EB [auth AH]
AB [auth AF],
BB [auth AG],
DB [auth AG],
DC [auth BE],
EB [auth AH],
GB [auth AH],
IA [auth AA],
IB [auth AI],
JB [auth AI],
JC [auth BL],
LB [auth AJ],
MA [auth AB],
MB [auth AJ],
OA [auth AC],
OB [auth AK],
QA [auth AC],
QB [auth AK],
SA [auth AD],
SB [auth AL],
UA [auth AD],
UB [auth AM],
WA [auth AE],
WB [auth AM],
YA [auth AF],
YB [auth BA],
ZC [auth M]
SPHEROIDENE
C41 H60 O
FJOCMTHZSURUFA-KXCOHNEYSA-N
LMT
Query on LMT

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BD [auth X],
JA [auth AA],
NA [auth AB],
TC [auth M]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
UQ1
Query on UQ1

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QC [auth L]UBIQUINONE-1
C14 H18 O4
SOECUQMRSRVZQQ-UHFFFAOYSA-N
FE
Query on FE

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AD [auth M]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M000265/1,
European Research Council (ERC)United Kingdom854126
Wellcome TrustUnited Kingdom209407/Z/17/Z.

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-13
    Type: Initial release
  • Version 1.1: 2021-11-03
    Changes: Data collection, Database references