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- PDB-7ze3: PucD-LH2 complex from Rps. palustris -

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Basic information

Entry
Database: PDB / ID: 7ze3
TitlePucD-LH2 complex from Rps. palustris
Components
  • (Light-harvesting protein B-800-850 ...) x 2
  • PucA-LH2-gamma
KeywordsPHOTOSYNTHESIS / light harvesting complex 2 / LH2 / Rps. palustris / 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 / : / membrane => GO:0016020 / 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
BACTERIOCHLOROPHYLL A / Chem-ZE0 / Uncharacterized protein / Light-harvesting protein B-800-850 beta chain / Light-harvesting protein B-800-850 alpha chain
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsQian, P. / Cogdell, R.J. / Nguyen-Phan, T.C.
Funding support United Kingdom, European Union, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N016734/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/T012455/1 United Kingdom
European Research Council (ERC)854126European Union
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, R.J.
#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, R.J.
History
DepositionMar 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Light-harvesting protein B-800-850 alpha chain
B: Light-harvesting protein B-800-850 beta chain
S: PucA-LH2-gamma
C: Light-harvesting protein B-800-850 alpha chain
D: Light-harvesting protein B-800-850 beta chain
E: Light-harvesting protein B-800-850 alpha chain
F: Light-harvesting protein B-800-850 beta chain
G: Light-harvesting protein B-800-850 alpha chain
H: Light-harvesting protein B-800-850 beta chain
I: Light-harvesting protein B-800-850 alpha chain
J: Light-harvesting protein B-800-850 beta chain
K: Light-harvesting protein B-800-850 alpha chain
L: Light-harvesting protein B-800-850 beta chain
M: Light-harvesting protein B-800-850 alpha chain
N: Light-harvesting protein B-800-850 beta chain
O: Light-harvesting protein B-800-850 alpha chain
P: Light-harvesting protein B-800-850 beta chain
Q: Light-harvesting protein B-800-850 alpha chain
R: Light-harvesting protein B-800-850 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,79761
Polymers120,74119
Non-polymers35,05542
Water66737
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area103960 Å2
ΔGint-783 kcal/mol
Surface area41430 Å2

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Components

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Light-harvesting protein B-800-850 ... , 2 types, 18 molecules ACEGIKMOQBDFHJLNPR

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


Mass: 6415.696 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Rhodopseudomonas palustris (phototrophic) / References: UniProt: A0A2R4GW23
#2: Protein
Light-harvesting protein B-800-850 beta chain


Mass: 5794.656 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Rhodopseudomonas palustris (phototrophic) / References: UniProt: A0A2R4GVX2

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Protein , 1 types, 1 molecules S

#3: Protein PucA-LH2-gamma


Mass: 10848.179 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodopseudomonas palustris (phototrophic) / References: UniProt: A0A2R4GRK2

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Non-polymers , 3 types, 79 molecules

#4: Chemical...
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ZE0 / (3'E)-3',4'-didehydro-1,2-dihydro-psi,psi-caroten-1-ol


Mass: 552.872 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C40H56O / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: PucD-LH2 from Rps. palustris / Type: COMPLEX / Details: Delt-pucBA(abce) / Entity ID: #1-#3 / Source: NATURAL
Source (natural)Organism: Rhodopseudomonas palustris ATCC 17001 (phototrophic)
Buffer solutionpH: 8 / Details: 0.1% LDAO in 20 mM Tris.Cl pH 8.0
Buffer componentConc.: 20 mM / Name: Tris.HCl / Formula: C4H11NO3
SpecimenConc.: 7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: protein was purified using LDAO detergent.
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: Chamber humidity: 100%; Chamber temperature: 4 oC; Blotting time: 2.5; Blotting force: 3; Wait time: 30 sec

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Electron microscopy imaging

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 FIELD / Nominal magnification: 120000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (min): 80 K
Image recordingAverage exposure time: 12.21 sec. / Electron dose: 44.1 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8149 / Details: Images were collected in AFIS mode.
EM imaging opticsDetails: No energy filter was applied.

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refinedev_4386refinement
PHENIXdev_4386refinement
EM software
IDNameVersionCategory
1cisTEM1particle selection
2EPUimage acquisition
4CTFFIND4CTF correction
7ISOLDEmodel fitting
9PHENIXmodel refinement
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 1689764
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 809902 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 31 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003410738
ELECTRON MICROSCOPYf_angle_d0.853215071
ELECTRON MICROSCOPYf_chiral_restr0.04381516
ELECTRON MICROSCOPYf_plane_restr0.00811961
ELECTRON MICROSCOPYf_dihedral_angle_d12.63863716

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