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- EMDB-14650: PucB-LH2 complex from Rps. palustris -

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Basic information

Entry
Database: EMDB / ID: EMD-14650
TitlePucB-LH2 complex from Rps. palustris
Map dataPucB-LH2
Sample
  • Complex: PucB-LH2 from Rps. palustris
    • Protein or peptide: Light-harvesting protein
    • Protein or peptide: Light-harvesting protein
    • Protein or peptide: PucA-LH2-gamma
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: 1,2-Dihydro-psi,psi-caroten-1-ol
Keywordslight harvesting complex 2 / LH2 / Rps. palustris / photosynthesis / purple bacteria / cryo-EM / single particle analysis
Function / homology
Function and homology information


organelle inner membrane / 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, 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
Uncharacterized protein / Light-harvesting protein / Light-harvesting protein
Similarity search - Component
Biological speciesRhodopseudomonas palustris ATCC 17001 (phototrophic) / Rhodopseudomonas palustris (phototrophic)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsQian P / Cogdell RJ / Nguyen-Phan TC
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N016734/1 United Kingdom
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2022
Title: Cryo-EM structures of light-harvesting 2 complexes from reveal the molecular origin of absorption tuning.
Authors: Pu Qian / Cam T Nguyen-Phan / Alastair T Gardiner / Tristan I Croll / Aleksander W Roszak / June Southall / Philip J Jackson / Cvetelin Vasilev / Pablo Castro-Hartmann / Kasim Sader / C Neil ...Authors: Pu Qian / Cam T Nguyen-Phan / Alastair T Gardiner / Tristan I Croll / Aleksander W Roszak / June Southall / Philip J Jackson / Cvetelin Vasilev / Pablo Castro-Hartmann / Kasim Sader / C Neil Hunter / Richard J Cogdell /
Abstract: The genomes of some purple photosynthetic bacteria contain a multigene family encoding a series of α- and β-polypeptides that together form a heterogeneous antenna of light-harvesting 2 (LH2) ...The genomes of some purple photosynthetic bacteria contain a multigene family encoding a series of α- and β-polypeptides that together form a heterogeneous antenna of light-harvesting 2 (LH2) complexes. To unravel this complexity, we generated four sets of deletion mutants in , each encoding a single type of gene pair and enabling the purification of complexes designated as PucA-LH2, PucB-LH2, PucD-LH2, and PucE-LH2. The structures of all four purified LH2 complexes were determined by cryogenic electron microscopy (cryo-EM) at resolutions ranging from 2.7 to 3.6 Å. Uniquely, each of these complexes contains a hitherto unknown polypeptide, γ, that forms an extended undulating ribbon that lies in the plane of the membrane and that encloses six of the nine LH2 αβ-subunits. The γ-subunit, which is located near to the cytoplasmic side of the complex, breaks the C9 symmetry of the LH2 complex and binds six extra bacteriochlorophylls (BChls) that enhance the 800-nm absorption of each complex. The structures show that all four complexes have two complete rings of BChls, conferring absorption bands centered at 800 and 850 nm on the PucA-LH2, PucB-LH2, and PucE-LH2 complexes, but, unusually, the PucD-LH2 antenna has only a single strong near-infared (NIR) absorption peak at 803 nm. Comparison of the cryo-EM structures of these LH2 complexes reveals altered patterns of hydrogen bonds between LH2 αβ-side chains and the bacteriochlorin rings, further emphasizing the major role that H bonds play in spectral tuning of bacterial antenna complexes.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2018
Title: Real-space refinement in PHENIX for cryo-EM and crystallography
Authors: Qian P / Cogdell RJ
#2: Journal: To Be Published
Title: Cryo-EM structures of light harvesting complex 2 from Rhodopseudomonas palustris: a molecular origin of spectroscopic variation
Authors: Qian P / Cogdell RJ
History
DepositionMar 29, 2022-
Header (metadata) releaseOct 5, 2022-
Map releaseOct 5, 2022-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14650.png

Downloads & links

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Map

FileDownload / File: emd_14650.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPucB-LH2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 300 pix.
= 195. Å		0.65 Å/pix.
x 300 pix.
= 195. Å		0.65 Å/pix.
x 300 pix.
= 195. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0353
Minimum - Maximum-0.29295868 - 0.49085766
Average (Standard dev.)0.00046231394 (±0.01334908)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 195.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: PucB-LH2

Fileemd_14650_half_map_1.map
AnnotationPucB-LH2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: PucB-LH2

Fileemd_14650_half_map_2.map
AnnotationPucB-LH2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PucB-LH2 from Rps. palustris

EntireName: PucB-LH2 from Rps. palustris
Components
  • Complex: PucB-LH2 from Rps. palustris
    • Protein or peptide: Light-harvesting protein
    • Protein or peptide: Light-harvesting protein
    • Protein or peptide: PucA-LH2-gamma
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: 1,2-Dihydro-psi,psi-caroten-1-ol

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Supramolecule #1: PucB-LH2 from Rps. palustris

SupramoleculeName: PucB-LH2 from Rps. palustris / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / Details: Delt-pucBA(aced)
Source (natural)Organism: Rhodopseudomonas palustris ATCC 17001 (phototrophic)

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Macromolecule #1: Light-harvesting protein

MacromoleculeName: Light-harvesting protein / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Rhodopseudomonas palustris (phototrophic)
Molecular weightTheoretical: 6.873004 KDa
SequenceString:
(CXM)NQGRIWTVV NPGVGLPLLL GSVTVIAILV HYAVLSNTTW FPKYWNGATV AAPAAAPAPA APAAKK

UniProtKB: Light-harvesting protein

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Macromolecule #2: Light-harvesting protein

MacromoleculeName: Light-harvesting protein / type: protein_or_peptide / ID: 2 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Rhodopseudomonas palustris (phototrophic)
Molecular weightTheoretical: 5.73855 KDa
SequenceString:
MADDPNKVWP TGLTIAESEE LHKHVIDGTR IFGAIAIVAH FLAYVYSPWL H

UniProtKB: Light-harvesting protein

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Macromolecule #3: PucA-LH2-gamma

MacromoleculeName: PucA-LH2-gamma / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodopseudomonas palustris (phototrophic)
Molecular weightTheoretical: 10.848179 KDa
SequenceString:
MSEEYKGHSG HPLILKQEGE YKGYSGEPLI LKQEGEYKGY SGTPLILEQK GEYQSFSGTP LILKQEGEYR GFSGAPLILK QDGEYKSFS GYPLLLNI

UniProtKB: Uncharacterized protein

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Macromolecule #4: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 4 / Number of copies: 33 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

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Macromolecule #5: 1,2-Dihydro-psi,psi-caroten-1-ol

MacromoleculeName: 1,2-Dihydro-psi,psi-caroten-1-ol / type: ligand / ID: 5 / Number of copies: 9 / Formula: IRM
Molecular weightTheoretical: 554.888 Da
Chemical component information

ChemComp-IRM:
1,2-Dihydro-psi,psi-caroten-1-ol

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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

Concentration7.0 mg/mL
BufferpH: 8 / Component - Concentration: 20.0 mM / Component - Formula: C4H11NO3 / Component - Name: Tris.HCl / Details: 0.1% LDAO in 20 mM Tris.Cl pH 8.0
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Chamber humidity: 100%; Chamber temperature: 4 oC; Blotting time: 2.5; Blotting force: 3; Wait time: 30 sec.
Detailsprotein was purified using LDAO detergent.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 80.0 K
Specialist opticsDetails: No energy filter was applied.
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 5593 / Average exposure time: 12.21 sec. / Average electron dose: 44.1 e/Å2 / Details: Images were collected in AFIS mode.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 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: 1946434
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1lgh

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 402668
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7zdi:
PucB-LH2 complex from Rps. palustris

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