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- EMDB-11516: LH2 complex from Marichromatium purpuratum -

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Basic information

Entry
Database: EMDB / ID: EMD-11516
TitleLH2 complex from Marichromatium purpuratum
Map data
SampleLight harvesting complex 2 (LH2)
  • LHC domain-containing protein
  • Light-harvesting protein B:800-850 subunit beta
  • (ligand) x 3
Function / homology
Function and homology information


plasma membrane light-harvesting complex / bacteriochlorophyll binding / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis, light reaction / protein-chromophore linkage / integral component of membrane / plasma membrane / metal ion binding
Antenna complex, alpha/beta subunit / Antenna complex, beta subunit / Light-harvesting complex
Light-harvesting protein B:800-850 subunit beta / LHC domain-containing protein
Biological speciesMarichromatium purpuratum (bacteria) / Marichromatium purpuratum 984 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.38 Å
AuthorsGardiner AT / Naydenova K / Castro-Hartmann P / Nguyen-Phan TC / Russo CJ / Sader K / Hunter CN / Cogdell RJ / Qian P
Funding support United States, United Kingdom, 3 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0001035 United States
Medical Research Council (MRC, United Kingdom)MC_UP_120117 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Sci Adv / Year: 2021
Title: The 2.4 Å cryo-EM structure of a heptameric light-harvesting 2 complex reveals two carotenoid energy transfer pathways.
Authors: Alastair T Gardiner / Katerina Naydenova / Pablo Castro-Hartmann / Tu C Nguyen-Phan / Christopher J Russo / Kasim Sader / C Neil Hunter / Richard J Cogdell / Pu Qian /
Abstract: We report the 2.4 Ångström resolution structure of the light-harvesting 2 (LH2) complex from () determined by cryogenic electron microscopy. The structure contains a heptameric ring that is ...We report the 2.4 Ångström resolution structure of the light-harvesting 2 (LH2) complex from () 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 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.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionJul 29, 2020-
Header (metadata) releaseFeb 24, 2021-
Map releaseFeb 24, 2021-
UpdateFeb 24, 2021-
Current statusFeb 24, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6zxa
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_11516.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 512 pix.
= 330.752 Å
0.65 Å/pix.
x 512 pix.
= 330.752 Å
0.65 Å/pix.
x 512 pix.
= 330.752 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.646 Å
Density
Contour LevelBy AUTHOR: 0.0167 / Movie #1: 0.02
Minimum - Maximum-0.0776035 - 0.16197382
Average (Standard dev.)7.136608e-05 (±0.0020862208)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 330.752 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.6460.6460.646
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z330.752330.752330.752
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0780.1620.000

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Supplemental data

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Sample components

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Entire Light harvesting complex 2 (LH2)

EntireName: Light harvesting complex 2 (LH2)
Details: The LH2 complex from Mar. purpuratum forms a circular heptameter. Each subunit consists of an alpha/beta pair, in which all pigment molecules, three Bchl a and two carotenoids are bound non-covalently.
Number of components: 6

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Component #1: protein, Light harvesting complex 2 (LH2)

ProteinName: Light harvesting complex 2 (LH2)
Details: The LH2 complex from Mar. purpuratum forms a circular heptameter. Each subunit consists of an alpha/beta pair, in which all pigment molecules, three Bchl a and two carotenoids are bound non-covalently.
Recombinant expression: No
MassTheoretical: 110 kDa
SourceSpecies: Marichromatium purpuratum (bacteria) / Strain: BN5500

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Component #2: protein, LHC domain-containing protein

ProteinName: LHC domain-containing protein / Number of Copies: 7 / Recombinant expression: No
MassTheoretical: 8.015369 kDa
SourceSpecies: Marichromatium purpuratum 984 (bacteria)

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Component #3: protein, Light-harvesting protein B:800-850 subunit beta

ProteinName: Light-harvesting protein B:800-850 subunit beta / Number of Copies: 7 / Recombinant expression: No
MassTheoretical: 5.554275 kDa
SourceSpecies: Marichromatium purpuratum 984 (bacteria)

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Component #4: ligand, BACTERIOCHLOROPHYLL A

LigandName: BACTERIOCHLOROPHYLL ABacteriochlorophyll / Number of Copies: 21 / Recombinant expression: No
MassTheoretical: 0.911504 kDa

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Component #5: ligand, 9-cis-okenone

LigandName: 9-cis-okenone / Number of Copies: 7 / Recombinant expression: No
MassTheoretical: 0.578866 kDa

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Component #6: ligand, all-trans okenone

LigandName: all-trans okenone / Number of Copies: 7 / Recombinant expression: No
MassTheoretical: 0.578866 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 5.5 mg/mL
Buffer solution: The final buffer contains 0.02 % n-dodecyl-beta-D-maltopyranoside (DDM)
pH: 8
Support filmFischione 1070
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 % / Details: Blowing time, 10.0 sec..

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 43.7 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 120000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 800.0 - 2400.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: (80.0 - K)
CameraDetector: OTHER

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Image acquisition

Image acquisitionNumber of digital images: 9543

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C7 (7 fold cyclic) / Number of projections: 414511
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION / Resolution: 2.38 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: REAL
Input PDB model: 1LGH, 1LGH
Chain ID: A, B

Overall bvalue: 22.55
Output model

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