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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 dataA cryo-EM map of the light harvesting complex 2 (LH2) from a photosynthetic bacterium Marichromatium purpuratum.
Sample
  • Complex: Light harvesting complex 2 (LH2)
    • Protein or peptide: LHC domain-containing protein
    • Protein or peptide: Light-harvesting protein B:800-850 subunit beta
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: 9-cis-okenone
  • Ligand: all-trans okenone
Keywordsphotosynthesis / purple bacteria / light harvesting complex / Marichromatium purpuratum / okenone.
Function / homology
Function and homology information


light-harvesting complex / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / metal ion binding / plasma membrane
Similarity search - Function
Antenna complex, alpha subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily / Light-harvesting complex
Similarity search - Domain/homology
Light-harvesting protein B:800-850 subunit beta / Uncharacterized protein
Similarity search - Component
Biological speciesMarichromatium purpuratum (bacteria) / Marichromatium purpuratum 984 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.38 Å
AuthorsGardiner AT / Naydenova K
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.
History
DepositionJul 29, 2020-
Header (metadata) releaseFeb 24, 2021-
Map releaseFeb 24, 2021-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing 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
  • Download
  • 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

emd_11516.png

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)
AnnotationA cryo-EM map of the light harvesting complex 2 (LH2) from a photosynthetic bacterium Marichromatium purpuratum.
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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0167 / Movie #1: 0.02
Minimum - Maximum-0.0776035 - 0.16197382
Average (Standard dev.)0.00007136608 (±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)
Components
  • Complex: Light harvesting complex 2 (LH2)
    • Protein or peptide: LHC domain-containing protein
    • Protein or peptide: Light-harvesting protein B:800-850 subunit beta
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: 9-cis-okenone
  • Ligand: all-trans okenone

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Supramolecule #1: Light harvesting complex 2 (LH2)

SupramoleculeName: Light harvesting complex 2 (LH2) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
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.
Source (natural)Organism: Marichromatium purpuratum (bacteria) / Strain: BN5500
Molecular weightTheoretical: 110 KDa

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Macromolecule #1: LHC domain-containing protein

MacromoleculeName: LHC domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Marichromatium purpuratum 984 (bacteria)
Molecular weightTheoretical: 8.015369 KDa
SequenceString:
MKVPVMMADE SIATINHPED DWKIWTVINP ATWMVPFFGI LFVQMWLIHS YALSLPGYGF KDSVRVAQPA

UniProtKB: Uncharacterized protein

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Macromolecule #2: Light-harvesting protein B:800-850 subunit beta

MacromoleculeName: Light-harvesting protein B:800-850 subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Marichromatium purpuratum 984 (bacteria)
Molecular weightTheoretical: 5.554275 KDa
SequenceString:
ADPKAANLSG LTDAQAKEFH EHWKHGVWSW VMIASAVHVV TWIYQPWF

UniProtKB: Light-harvesting protein B:800-850 subunit beta

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Macromolecule #3: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 3 / Number of copies: 21 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

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Macromolecule #4: 9-cis-okenone

MacromoleculeName: 9-cis-okenone / type: ligand / ID: 4 / Number of copies: 7 / Formula: QS2
Molecular weightTheoretical: 578.866 Da
Chemical component information

ChemComp-QS2:
9-cis-okenone

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Macromolecule #5: all-trans okenone

MacromoleculeName: all-trans okenone / type: ligand / ID: 5 / Number of copies: 7 / Formula: QSE
Molecular weightTheoretical: 578.866 Da
Chemical component information

ChemComp-QSE:
all-trans okenone

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5.5 mg/mL
BufferpH: 8 / Component - Concentration: 20.0 mM/L / Component - Name: Tris.HCl
Details: The final buffer contains 0.02 % n-dodecyl-beta-D-maltopyranoside (DDM)
GridModel: Homemade / Material: GOLD / Mesh: 400 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.0067 kPa / Details: Fischione 1070
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER / Details: Blowing time, 10.0 sec..
DetailsThe sample was mono disperse with detergent beta-DDM.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 80.0 K
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 9543 / Average exposure time: 0.29 sec. / Average electron dose: 43.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 0.4 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 120000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1330154
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1lgh


Details: The model of heptameter of the LH2 of Mac. purpuratum was built up using A subunit taken from 1LGH.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C7 (7 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.38 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 414511
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.1)
Details: A best class that contains 414,511 particle were used for final 3d reconstruction.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

1lgh

chain_id: A, residue_range: 1-56, source_name: PDB, initial_model_type: experimental model

1lgh

chain_id: B, residue_range: 1-45, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 22.55
Output model

PDB-6zxa:
LH2 complex from Marichromatium purpuratum

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