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- PDB-5lcb: In situ atomic-resolution structure of the baseplate antenna comp... -

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Entry
Database: PDB / ID: 5lcb
TitleIn situ atomic-resolution structure of the baseplate antenna complex in Chlorobaculum tepidum obtained combining solid-state NMR spectroscopy, cryo electron microscopy and polarization spectroscopy
ComponentsBacteriochlorophyll c-binding protein
Keywordsbacteriochlorophyll binding protein / photosynthesis / light-harvesting protein / binds bacteriochlorophyll a / oligomeric complex
Function / homologychlorosome envelope / Bacteriochlorophyll c-binding protein / Bacteriochlorophyll c-binding superfamily / Bacteriochlorophyll C binding protein / bacteriochlorophyll binding / photosynthesis / metal ion binding / BACTERIOCHLOROPHYLL A / Bacteriochlorophyll c-binding protein
Function and homology information
Biological speciesChlorobium tepidum (bacteria)
MethodELECTRON MICROSCOPY / SOLID-STATE NMR / single particle reconstruction / torsion angle dynamics / cryo EM / Resolution: 26.5 Å
AuthorsNielsen, J.T. / Kulminskaya, N.V. / Bjerring, M. / Linnanto, J.M. / Ratsep, M. / Pedersen, M. / Lambrev, P.H. / Dorogi, M. / Garab, G. / Thomsen, K. ...Nielsen, J.T. / Kulminskaya, N.V. / Bjerring, M. / Linnanto, J.M. / Ratsep, M. / Pedersen, M. / Lambrev, P.H. / Dorogi, M. / Garab, G. / Thomsen, K. / Jegerschold, C. / Frigaard, N.U. / Lindahl, M. / Nielsen, N.C.
Funding support Denmark, Estonia, Hungary, 4items
OrganizationGrant numberCountry
Danish National Research FoundationDNRF 59 Denmark
Estonia Research CouncilIUT02-28 Estonia
Estonian Science FoundationMJD262 Estonia
Hungarian Scientific Research FundOTKA-PD 104530 and OTKA-K 112688 Hungary
Citation
Journal: Nat Commun / Year: 2016
Title: In situ high-resolution structure of the baseplate antenna complex in Chlorobaculum tepidum.
Authors: Jakob Toudahl Nielsen / Natalia V Kulminskaya / Morten Bjerring / Juha M Linnanto / Margus Rätsep / Marie Østergaard Pedersen / Petar H Lambrev / Márta Dorogi / Győző Garab / Karen ...Authors: Jakob Toudahl Nielsen / Natalia V Kulminskaya / Morten Bjerring / Juha M Linnanto / Margus Rätsep / Marie Østergaard Pedersen / Petar H Lambrev / Márta Dorogi / Győző Garab / Karen Thomsen / Caroline Jegerschöld / Niels-Ulrik Frigaard / Martin Lindahl / Niels Chr Nielsen /
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 ...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.
#1: Journal: Angew Chem Int Ed Engl / Year: 2012
Title: In situ solid-state NMR spectroscopy of protein in heterogeneous membranes: the baseplate antenna complex of Chlorobaculum tepidum.
Authors: Natalia V Kulminskaya / Marie Ø Pedersen / Morten Bjerring / Jarl Underhaug / Mette Miller / Niels-Ulrik Frigaard / Jakob T Nielsen / Niels Chr Nielsen /
Abstract: A clever combination: an in situ solid-state NMR analysis of CsmA proteins in the heterogeneous environment of the photoreceptor of Chlorobaculum tepidum is reported. Using different combinations of ...A clever combination: an in situ solid-state NMR analysis of CsmA proteins in the heterogeneous environment of the photoreceptor of Chlorobaculum tepidum is reported. Using different combinations of 2D and 3D solid-state NMR spectra, 90 % of the CsmA resonances are assigned and provide on the basis of chemical shift data information about the structure and conformation of CsmA in the CsmA-bacteriochlorophyll a complex.
History
DepositionJun 20, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Data collection / Experimental preparation / Category: em_image_scans / em_sample_support / em_software
Item: _em_sample_support.grid_type / _em_software.name / _em_software.version
Revision 1.2Aug 30, 2017Group: Data collection / Category: em_software
Revision 1.3Apr 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.4Aug 21, 2019Group: Data collection / Category: pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.5Nov 6, 2019Group: Data collection / Derived calculations
Category: em_software / pdbx_struct_conn_angle / struct_conn
Item: _em_software.name / _em_software.version
Revision 1.6Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.7Sep 13, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Assembly

Deposited unit
A: Bacteriochlorophyll c-binding protein
B: Bacteriochlorophyll c-binding protein
C: Bacteriochlorophyll c-binding protein
D: Bacteriochlorophyll c-binding protein
E: Bacteriochlorophyll c-binding protein
F: Bacteriochlorophyll c-binding protein
G: Bacteriochlorophyll c-binding protein
H: Bacteriochlorophyll c-binding protein
I: Bacteriochlorophyll c-binding protein
J: Bacteriochlorophyll c-binding protein
K: Bacteriochlorophyll c-binding protein
L: Bacteriochlorophyll c-binding protein
M: Bacteriochlorophyll c-binding protein
N: Bacteriochlorophyll c-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,00228
Polymers86,24014
Non-polymers12,76114
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area27900 Å2
ΔGint-298 kcal/mol
Surface area80300 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 80target function
RepresentativeModel #1target function and agreement with back-calculated cd spectra

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Components

#1: Protein
Bacteriochlorophyll c-binding protein / BChl c-binding / Chlorosome protein A


Mass: 6160.034 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobium tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS) (bacteria)
Gene: csmA, CT1942 / Production host: Chlorobaculum tepidum (bacteria) / References: UniProt: P0A314
#2: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A / Bacteriochlorophyll


Mass: 911.504 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C55H74MgN4O6

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Experimental details

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Experiment

Experiment
Method
ELECTRON MICROSCOPY
SOLID-STATE NMR
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 13C-13C DARR
121isotropic13D NCACX
131isotropic13D NCOCX
141isotropic13D CANCO
151isotropic13D CONCA
161isotropic12D NCA
171isotropic12D NCO
181isotropic22D 13C-13C DARR

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Sample preparation

ComponentName: Carotenosome organelle consisting of csma proteins and bchla antenna molecules.
Type: ORGANELLE OR CELLULAR COMPONENT
Details: Cryo-EM data of the ice-embedded isolated carotenosomes reveals molecular complex structure. Captured images clearly show supramolecular organization of the protein rows, originating from ...Details: Cryo-EM data of the ice-embedded isolated carotenosomes reveals molecular complex structure. Captured images clearly show supramolecular organization of the protein rows, originating from the BChl a - CsmA baseplate
Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Chlorobaculum tepidum (bacteria) / Organelle: carotenosome
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/4
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K
DetailsType: solid
Contents: 10.0 % [U-13C; U-15N] CsmA, 10.0 % [U-13C; U-15N] BACTERIOCHLOROPHYLL A, 35.0 % [U-13C] Carotenoids, 35.0 % [U-13C] Lipids, 10.0 % n.a. Magnesium ion, solid state, lyophylized
Details: Stoichiometric amounts of CsmA, BChl a, and Mg2+. Excess of carotenoids and lipids.
Label: U15N13C / Solvent system: solid state, lyophylized
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10.0 %CsmA[U-13C; U-15N]1
10.0 %BACTERIOCHLOROPHYLL A[U-13C; U-15N]1
35.0 %Carotenoids[U-13C]1
35.0 %Lipids[U-13C]1
10.0 %Magnesium ionn.a.1
Sample conditionsDetails: solid state / Ionic strength: 0.0 M / Label: U / pH: 7.0 Not defined / Pressure: 1 atm / Temperature: 280 K

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Data collection

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Calibrated defocus min: 1700 nm / Calibrated defocus max: 4000 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 8 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Num. of real images: 270
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIBrukerAVANCE II7001equipped with a standard 4 mm triple-resonance magic-angle-spinning (MAS) probe
Bruker AVANCE IIBrukerAVANCE II5002equipped with a standard 4 mm triple-resonance magic-angle-spinning (MAS) probe

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Processing

EM software
IDNameVersionCategoryDetails
1EMAN2particle selection
2EPUimage acquisition
4CTFFIND3CTF correctiondefocus determined w ctffind3, phaseflipping w Spider
10EMAN2initial Euler assignment
11Strulfinal Euler assignmentUltramicroscopy 2001 87(4): 165-75
14SPIDERCTF correction
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 1790
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 26.5 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 1790 / Algorithm: BACK PROJECTION / Symmetry type: POINT
NMR software
NameVersionDeveloperClassification
Xplor-NIH2.33Charles Schwieters, Marius Clorerefinement
GASyCSNielsenstructure calculation
SparkyGoddardpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 5
NMR representativeSelection criteria: target function and agreement with back-calculated cd spectra
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 80 / Conformers submitted total number: 1

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