6ZXA

LH2 complex from Marichromatium purpuratum


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.38 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

The 2.4 angstrom cryo-EM structure of a heptameric light-harvesting 2 complex reveals two carotenoid energy transfer pathways.

Gardiner, A.T.Naydenova, K.Castro-Hartmann, P.Nguyen-Phan, T.C.Russo, C.J.Sader, K.Hunter, C.N.Cogdell, R.J.Qian, P.

(2021) Sci Adv 7

  • DOI: https://doi.org/10.1126/sciadv.abe4650
  • Primary Citation of Related Structures:  
    6ZXA

  • PubMed Abstract: 

    We report the 2.4 Ångström resolution structure of the light-harvesting 2 (LH2) complex from Marichromatium ( Mch. ) purpuratum determined by cryogenic electron microscopy. The structure contains a heptameric ring that is unique among all known LH2 structures, explaining the unusual spectroscopic properties of this bacterial antenna complex. We identify two sets of distinct carotenoids in the structure and describe a network of energy transfer pathways from the carotenoids to bacteriochlorophyll a molecules. The geometry imposed by the heptameric ring controls the resonant coupling of the long-wavelength energy absorption band. Together, these details reveal key aspects of the assembly and oligomeric form of purple bacterial LH2 complexes that were previously inaccessible by any technique.


  • Organizational Affiliation

    Institute of Molecular, Cell and Systems Biology, Glasgow University, Glasgow G12 8QQ, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LHC domain-containing protein
A, C, E, G, I
A, C, E, G, I, K, M
70Marichromatium purpuratum 984Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for W0E6A1 (Marichromatium purpuratum 984)
Explore W0E6A1 
Go to UniProtKB:  W0E6A1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW0E6A1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting protein B:800-850 subunit beta
B, D, F, H, J
B, D, F, H, J, L, N
48Marichromatium purpuratum 984Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for W0E5B0 (Marichromatium purpuratum 984)
Explore W0E5B0 
Go to UniProtKB:  W0E5B0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW0E5B0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BCL (Subject of Investigation/LOI)
Query on BCL

Download Ideal Coordinates CCD File 
BA [auth F]
CA [auth F]
DA [auth G]
GA [auth H]
HA [auth H]
BA [auth F],
CA [auth F],
DA [auth G],
GA [auth H],
HA [auth H],
IA [auth I],
LA [auth J],
MA [auth J],
NA [auth K],
O [auth A],
PA [auth L],
Q [auth B],
QA [auth L],
R [auth B],
SA [auth M],
U [auth C],
V [auth D],
VA [auth N],
W [auth D],
WA [auth N],
Y [auth E]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
QSE (Subject of Investigation/LOI)
Query on QSE

Download Ideal Coordinates CCD File 
AA [auth F]
FA [auth H]
KA [auth J]
RA [auth M]
T [auth C]
AA [auth F],
FA [auth H],
KA [auth J],
RA [auth M],
T [auth C],
UA [auth N],
X [auth E]
all-trans okenone
C41 H54 O2
FSQZIFSGNDUYRQ-TYKRLFMMSA-N
QS2 (Subject of Investigation/LOI)
Query on QS2

Download Ideal Coordinates CCD File 
EA [auth G]
JA [auth I]
OA [auth K]
P [auth A]
S [auth B]
EA [auth G],
JA [auth I],
OA [auth K],
P [auth A],
S [auth B],
TA [auth M],
Z [auth E]
9-cis-okenone
C41 H54 O2
FSQZIFSGNDUYRQ-KKGQYTAFSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.38 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.17.1
MODEL REFINEMENTREFMAC
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-SC0001035
Medical Research Council (MRC, United Kingdom)United KingdomMC_UP_120117
Biotechnology and Biological Sciences Research Council (BBSRC)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-24
    Type: Initial release