7PBW

Cryo-EM structure of light harvesting complex 2 from Rba. sphaeroides.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.10 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

Cryo-EM Structure of the Rhodobacter sphaeroides Light-Harvesting 2 Complex at 2.1 angstrom.

Qian, P.Swainsbury, D.J.K.Croll, T.I.Castro-Hartmann, P.Divitini, G.Sader, K.Hunter, C.N.

(2021) Biochemistry 60: 3302-3314

  • DOI: https://doi.org/10.1021/acs.biochem.1c00576
  • Primary Citation of Related Structures:  
    7PBW

  • PubMed Abstract: 

    Light-harvesting 2 (LH2) antenna complexes augment the collection of solar energy in many phototrophic bacteria. Despite its frequent role as a model for such complexes, there has been no three-dimensional (3D) structure available for the LH2 from the purple phototroph Rhodobacter sphaeroides . We used cryo-electron microscopy (cryo-EM) to determine the 2.1 Å resolution structure of this LH2 antenna, which is a cylindrical assembly of nine αβ heterodimer subunits, each of which binds three bacteriochlorophyll a (BChl) molecules and one carotenoid. The high resolution of this structure reveals all of the interpigment and pigment-protein interactions that promote the assembly and energy-transfer properties of this complex. Near the cytoplasmic face of the complex there is a ring of nine BChls, which absorb maximally at 800 nm and are designated as B800; each B800 is coordinated by the N-terminal carboxymethionine of LH2-α, part of a network of interactions with nearby residues on both LH2-α and LH2-β and with the carotenoid. Nine carotenoids, which are spheroidene in the strain we analyzed, snake through the complex, traversing the membrane and interacting with a ring of 18 BChls situated toward the periplasmic side of the complex. Hydrogen bonds with C-terminal aromatic residues modify the absorption of these pigments, which are red-shifted to 850 nm. Overlaps between the macrocycles of the B850 BChls ensure rapid transfer of excitation energy around this ring of pigments, which act as the donors of energy to neighboring LH2 and reaction center light-harvesting 1 (RC-LH1) complexes.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting protein B-800/850 alpha chain50Cereibacter sphaeroides 2.4.1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q3J144 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.))
Explore Q3J144 
Go to UniProtKB:  Q3J144
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3J144
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting protein B-800/850 beta chain47Cereibacter sphaeroides 2.4.1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q3J145 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.))
Explore Q3J145 
Go to UniProtKB:  Q3J145
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3J145
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BCL (Subject of Investigation/LOI)
Query on BCL

Download Ideal Coordinates CCD File 
BC [auth BE]
DA [auth AC]
DB [auth AH]
EA [auth AC]
EB [auth AH]
BC [auth BE],
DA [auth AC],
DB [auth AH],
EA [auth AC],
EB [auth AH],
FC [auth BF],
IA [auth AD],
IB [auth AI],
JA [auth AD],
JB [auth AI],
JC [auth BG],
MB [auth BA],
NC [auth BH],
OA [auth AE],
PA [auth AE],
QB [auth BB],
RC [auth BI],
S [auth AA],
T [auth AA],
TA [auth AF],
UA [auth AF],
UB [auth BC],
Y [auth AB],
YA [auth AG],
YB [auth BD],
Z [auth AB],
ZA [auth AG]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
7OT
Query on 7OT

Download Ideal Coordinates CCD File 
AA [auth AB]
AB [auth AG]
FA [auth AC]
FB [auth AH]
KA [auth AD]
AA [auth AB],
AB [auth AG],
FA [auth AC],
FB [auth AH],
KA [auth AD],
KB [auth AI],
QA [auth AE],
U [auth AA],
VA [auth AF]
SPHEROIDENE
C41 H60 O
FJOCMTHZSURUFA-AXYGSFPTSA-N
LDA
Query on LDA

Download Ideal Coordinates CCD File 
AC [auth BD]
BA [auth AB]
BB [auth AG]
CA [auth AB]
CB [auth AG]
AC [auth BD],
BA [auth AB],
BB [auth AG],
CA [auth AB],
CB [auth AG],
DC [auth BE],
EC [auth BE],
GA [auth AC],
GB [auth AH],
HA [auth AC],
HB [auth AH],
HC [auth BF],
IC [auth BF],
LA [auth AD],
LB [auth AI],
LC [auth BG],
MA [auth AD],
MC [auth BG],
NA [auth AD],
OB [auth BA],
PB [auth BA],
PC [auth BH],
QC [auth BH],
RA [auth AE],
SA [auth AE],
SB [auth BB],
TB [auth BB],
TC [auth BI],
UC [auth BI],
V [auth AA],
W [auth AA],
WA [auth AF],
WB [auth BC],
X [auth AA],
XA [auth AF],
XB [auth BC]
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
CC [auth BE]
GC [auth BF]
KC [auth BG]
NB [auth BA]
OC [auth BH]
CC [auth BE],
GC [auth BF],
KC [auth BG],
NB [auth BA],
OC [auth BH],
RB [auth BB],
SC [auth BI],
VB [auth BC],
ZB [auth BD]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CXM
Query on CXM
A [auth AA]
B [auth AB]
C [auth AC]
D [auth AD]
E [auth AE]
A [auth AA],
B [auth AB],
C [auth AC],
D [auth AD],
E [auth AE],
F [auth AF],
G [auth AG],
H [auth AH],
I [auth AI]
L-PEPTIDE LINKINGC6 H11 N O4 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.10 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

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-24
    Type: Initial release
  • Version 1.1: 2022-12-07
    Changes: Database references