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- EMDB-13307: Cryo-EM structure of light harvesting complex 2 from Rba. sphaeroides. -

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Basic information

Entry
Database: EMDB / ID: EMD-13307
TitleCryo-EM structure of light harvesting complex 2 from Rba. sphaeroides.
Map dataA light harvesting complex 2 (LH2) from photosynthetic bacterium of Rba. spheroids.
Sample
  • Complex: Light harvesting complex 2
    • Protein or peptide: Light-harvesting protein B-800/850 alpha chain
    • Protein or peptide: Light-harvesting protein B-800/850 beta chain
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: SPHEROIDENE
  • Ligand: LAURYL DIMETHYLAMINE-N-OXIDE
  • Ligand: CALCIUM ION
  • Ligand: water
KeywordsPhotosynthesis / Purple bacteria / Light harvesting complex 2 / LH2 / Membrane protein / Cryo-EM.
Function / homology
Function and homology information


organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / : / metal ion binding / plasma membrane
Similarity search - Function
Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Antenna complex, alpha/beta subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily / Antenna complex alpha/beta subunit / Light-harvesting complex
Similarity search - Domain/homology
Light-harvesting protein B-800/850 alpha chain / Light-harvesting protein B-800/850 beta chain
Similarity search - Component
Biological speciesCereibacter sphaeroides 2.4.1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsQian P / Swainsbury DJK
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M000265/1 United Kingdom
CitationJournal: Biochemistry / Year: 2021
Title: Cryo-EM Structure of the Light-Harvesting 2 Complex at 2.1 Å.
Authors: Pu Qian / David J K Swainsbury / Tristan I Croll / Pablo Castro-Hartmann / Giorgio Divitini / Kasim Sader / C Neil Hunter /
Abstract: Light-harvesting 2 (LH2) antenna complexes augment the collection of solar energy in many phototrophic bacteria. Despite its frequent role as a model for such complexes, there has been no three- ...Light-harvesting 2 (LH2) antenna complexes augment the collection of solar energy in many phototrophic bacteria. Despite its frequent role as a model for such complexes, there has been no three-dimensional (3D) structure available for the LH2 from the purple phototroph . We used cryo-electron microscopy (cryo-EM) to determine the 2.1 Å resolution structure of this LH2 antenna, which is a cylindrical assembly of nine αβ heterodimer subunits, each of which binds three bacteriochlorophyll (BChl) molecules and one carotenoid. The high resolution of this structure reveals all of the interpigment and pigment-protein interactions that promote the assembly and energy-transfer properties of this complex. Near the cytoplasmic face of the complex there is a ring of nine BChls, which absorb maximally at 800 nm and are designated as B800; each B800 is coordinated by the N-terminal carboxymethionine of LH2-α, part of a network of interactions with nearby residues on both LH2-α and LH2-β and with the carotenoid. Nine carotenoids, which are spheroidene in the strain we analyzed, snake through the complex, traversing the membrane and interacting with a ring of 18 BChls situated toward the periplasmic side of the complex. Hydrogen bonds with C-terminal aromatic residues modify the absorption of these pigments, which are red-shifted to 850 nm. Overlaps between the macrocycles of the B850 BChls ensure rapid transfer of excitation energy around this ring of pigments, which act as the donors of energy to neighboring LH2 and reaction center light-harvesting 1 (RC-LH1) complexes.
History
DepositionAug 2, 2021-
Header (metadata) releaseNov 24, 2021-
Map releaseNov 24, 2021-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0305
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0305
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7pbw
  • Surface level: 0.0305
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7pbw
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13307.png

Downloads & links

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Map

FileDownload / File: emd_13307.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA light harvesting complex 2 (LH2) from photosynthetic bacterium of Rba. spheroids.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 380 pix.
= 250.8 Å		0.66 Å/pix.
x 380 pix.
= 250.8 Å		0.66 Å/pix.
x 380 pix.
= 250.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0305 / Movie #1: 0.0305
Minimum - Maximum-0.09768547 - 0.1575623
Average (Standard dev.)0.000076245386 (±0.0035594495)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 250.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.660.660.66
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z250.800250.800250.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ260260260
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS380380380
D min/max/mean-0.0980.1580.000

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Supplemental data

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Sample components

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Entire : Light harvesting complex 2

EntireName: Light harvesting complex 2
Components
  • Complex: Light harvesting complex 2
    • Protein or peptide: Light-harvesting protein B-800/850 alpha chain
    • Protein or peptide: Light-harvesting protein B-800/850 beta chain
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: SPHEROIDENE
  • Ligand: LAURYL DIMETHYLAMINE-N-OXIDE
  • Ligand: CALCIUM ION
  • Ligand: water

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Supramolecule #1: Light harvesting complex 2

SupramoleculeName: Light harvesting complex 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Cereibacter sphaeroides 2.4.1 (bacteria)
Molecular weightTheoretical: 123.7 KDa

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Macromolecule #1: Light-harvesting protein B-800/850 alpha chain

MacromoleculeName: Light-harvesting protein B-800/850 alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Cereibacter sphaeroides 2.4.1 (bacteria)
Molecular weightTheoretical: 5.275187 KDa
SequenceString:
(CXM)TNGKIWLVV KPTVGVPLFL SAAVIASVVI HAAVLTTTTW LPAYYQGSAA

UniProtKB: Light-harvesting protein B-800/850 alpha chain

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

MacromoleculeName: Light-harvesting protein B-800/850 beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Cereibacter sphaeroides 2.4.1 (bacteria)
Molecular weightTheoretical: 4.99084 KDa
SequenceString:
LNKVWPSGLT VAEAEEVHKQ LILGTRVFGG MALIAHFLAA AATPWLG

UniProtKB: Light-harvesting protein B-800/850 beta chain

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Macromolecule #3: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 3 / Number of copies: 27 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

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Macromolecule #4: SPHEROIDENE

MacromoleculeName: SPHEROIDENE / type: ligand / ID: 4 / Number of copies: 9 / Formula: 7OT
Molecular weightTheoretical: 568.914 Da
Chemical component information

ChemComp-7OT:
SPHEROIDENE

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Macromolecule #5: LAURYL DIMETHYLAMINE-N-OXIDE

MacromoleculeName: LAURYL DIMETHYLAMINE-N-OXIDE / type: ligand / ID: 5 / Number of copies: 36 / Formula: LDA
Molecular weightTheoretical: 229.402 Da
Chemical component information

ChemComp-LDA:
LAURYL DIMETHYLAMINE-N-OXIDE / LDAO, detergent*YM

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Macromolecule #6: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 6 / Number of copies: 9 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 230 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration4.5 mg/mL
BufferpH: 7.8 / Component - Concentration: 20.0 mmol / Component - Formula: C8H18N2O4S / Component - Name: Hepes
Details: The final sample buffer: 20 mM Hepes, pH 7.8, 0.1%LDAO
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 30 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Details: easiGlow was used for glow discharge.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsSample was solubilised and purified with detergent of LDAO

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Electron microscopy

MicroscopeFEI TITAN
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 3138 / Average exposure time: 1.37 sec. / Average electron dose: 41.6 e/Å2
Details: A total doe 41.6 was fractioned into 40 frames, resulting in an electron fluency of 1.04 e/A2/frame.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 1717608
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1nkz

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C9 (9 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 835641
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 was selected.
FSC plot (resolution estimation)

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