5LCB

In situ atomic-resolution structure of the baseplate antenna complex in Chlorobaculum tepidum obtained combining solid-state NMR spectroscopy, cryo electron microscopy and polarization spectroscopy


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 26.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

  • Method: SOLID-STATE NMR
  • Conformers Calculated: 80 
  • Conformers Submitted: 
  • Selection Criteria: target function 

wwPDB Validation   3D Report Full Report


This is version 1.7 of the entry. See complete history


Literature

In situ high-resolution structure of the baseplate antenna complex in Chlorobaculum tepidum.

Nielsen, J.T.Kulminskaya, N.V.Bjerring, M.Linnanto, J.M.Ratsep, M.Pedersen, M.O.Lambrev, P.H.Dorogi, M.Garab, G.Thomsen, K.Jegerschold, C.Frigaard, N.U.Lindahl, M.Nielsen, N.C.

(2016) Nat Commun 7: 12454-12454

  • DOI: https://doi.org/10.1038/ncomms12454
  • Primary Citation of Related Structures:  
    5LCB

  • PubMed Abstract: 

    Photosynthetic antenna systems enable organisms harvesting light and transfer the energy to the photosynthetic reaction centre, where the conversion to chemical energy takes place. One of the most complex antenna systems, the chlorosome, found in the photosynthetic green sulfur bacterium Chlorobaculum (Cba.) tepidum contains a baseplate, which is a scaffolding super-structure, formed by the protein CsmA and bacteriochlorophyll a. Here we present the first high-resolution structure of the CsmA baseplate using intact fully functional, light-harvesting organelles from Cba. tepidum, following a hybrid approach combining five complementary methods: solid-state NMR spectroscopy, cryo-electron microscopy, isotropic and anisotropic circular dichroism and linear dichroism. The structure calculation was facilitated through development of new software, GASyCS for efficient geometry optimization of highly symmetric oligomeric structures. We show that the baseplate is composed of rods of repeated dimers of the strongly amphipathic CsmA with pigments sandwiched within the dimer at the hydrophobic side of the helix.


  • Organizational Affiliation

    Center for Insoluble Protein Structures (inSPIN), Aarhus C DK-8000, Denmark.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bacteriochlorophyll c-binding protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N
59Chlorobaculum tepidum TLSMutation(s): 0 
Gene Names: csmACT1942
UniProt
Find proteins for P0A314 (Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS))
Explore P0A314 
Go to UniProtKB:  P0A314
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A314
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BCL
Query on BCL

Download Ideal Coordinates CCD File 
AA [auth M]
BA [auth N]
O [auth A]
P [auth B]
Q [auth C]
AA [auth M],
BA [auth N],
O [auth A],
P [auth B],
Q [auth C],
R [auth D],
S [auth E],
T [auth F],
U [auth G],
V [auth H],
W [auth I],
X [auth J],
Y [auth K],
Z [auth L]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 26.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
  • Method: SOLID-STATE NMR
  • Conformers Calculated: 80 
  • Conformers Submitted: 
  • Selection Criteria: target function 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Danish National Research FoundationDenmarkDNRF 59
Estonia Research CouncilEstoniaIUT02-28
Estonian Science FoundationEstoniaMJD262
Hungarian Scientific Research FundHungaryOTKA-PD 104530 and OTKA-K 112688

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-27
    Type: Initial release
  • Version 1.1: 2017-08-02
    Changes: Data collection, Experimental preparation
  • Version 1.2: 2017-08-30
    Changes: Data collection
  • Version 1.3: 2018-04-25
    Changes: Data collection, Database references
  • Version 1.4: 2019-08-21
    Changes: Data collection
  • Version 1.5: 2019-11-06
    Changes: Data collection, Derived calculations
  • Version 1.6: 2023-06-14
    Changes: Database references, Other
  • Version 1.7: 2023-09-13
    Changes: Data collection