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- PDB-8b64: Cryo-EM structure of RC-LH1-PufX photosynthetic core complex from... -

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Basic information

Entry
Database: PDB / ID: 8b64
TitleCryo-EM structure of RC-LH1-PufX photosynthetic core complex from Rba. capsulatus
Components
  • (Reaction center protein ...Photosynthetic reaction centre) x 3
  • Intrinsic membrane protein PufX
  • LH1 beta chain
  • Light-harvesting protein B-870 alpha chain
KeywordsPHOTOSYNTHESIS / PufX / core complex / RC-LH1 / Rba capsulatus / photosynthetic core
Function / homology
Function and homology information


organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / metal ion binding / plasma membrane
Similarity search - Function
Intrinsic membrane protein family, PufX / Intrinsic membrane protein PufX / Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, beta domain superfamily / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Light-harvesting protein B beta chain / Antenna complex, alpha/beta subunit ...Intrinsic membrane protein family, PufX / Intrinsic membrane protein PufX / Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, beta domain superfamily / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Light-harvesting protein B beta chain / Antenna complex, alpha/beta subunit / Light-harvesting complex / Antenna complex alpha/beta subunit / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / : / SPHEROIDENE / UBIQUINONE-10 / Light-harvesting protein B-870 alpha chain / Light-harvesting protein B-870 beta chain / Reaction center protein M chain / Reaction center protein H chain ...1,2-Distearoyl-sn-glycerophosphoethanolamine / BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / : / SPHEROIDENE / UBIQUINONE-10 / Light-harvesting protein B-870 alpha chain / Light-harvesting protein B-870 beta chain / Reaction center protein M chain / Reaction center protein H chain / Reaction center protein L chain / Intrinsic membrane protein PufX
Similarity search - Component
Biological speciesRhodobacter capsulatus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.589 Å
AuthorsBracun, L. / Yamagata, A. / Shirouzu, M. / Liu, L.N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Royal Society United Kingdom
CitationJournal: Structure / Year: 2023
Title: Cryo-EM structure of a monomeric RC-LH1-PufX supercomplex with high-carotenoid content from Rhodobacter capsulatus.
Authors: Laura Bracun / Atsushi Yamagata / Bern M Christianson / Mikako Shirouzu / Lu-Ning Liu /
Abstract: In purple photosynthetic bacteria, the photochemical reaction center (RC) and light-harvesting complex 1 (LH1) assemble to form monomeric or dimeric RC-LH1 membrane complexes, essential for bacterial ...In purple photosynthetic bacteria, the photochemical reaction center (RC) and light-harvesting complex 1 (LH1) assemble to form monomeric or dimeric RC-LH1 membrane complexes, essential for bacterial photosynthesis. Here, we report a 2.59-Å resolution cryoelectron microscopy (cryo-EM) structure of the RC-LH1 supercomplex from Rhodobacter capsulatus. We show that Rba. capsulatus RC-LH1 complexes are exclusively monomers in which the RC is surrounded by a 15-subunit LH1 ring. Incorporation of a transmembrane polypeptide PufX leads to a large opening within the LH1 ring. Each LH1 subunit associates two carotenoids and two bacteriochlorophylls, which is similar to Rba. sphaeroides RC-LH1 but more than one carotenoid per LH1 in Rba. veldkampii RC-LH1 monomer. Collectively, the unique Rba. capsulatus RC-LH1-PufX represents an intermediate structure between Rba. sphaeroides and Rba. veldkampii RC-LH1-PufX. Comparison of PufX from the three Rhodobacter species indicates the important residues involved in dimerization of RC-LH1.
History
DepositionSep 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 15, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
a: Light-harvesting protein B-870 alpha chain
e: Light-harvesting protein B-870 alpha chain
D: LH1 beta chain
b: Light-harvesting protein B-870 alpha chain
A: LH1 beta chain
E: LH1 beta chain
X: Intrinsic membrane protein PufX
L: Reaction center protein L chain
M: Reaction center protein M chain
H: Reaction center protein H chain
d: Light-harvesting protein B-870 alpha chain
B: LH1 beta chain
t: Light-harvesting protein B-870 alpha chain
S: LH1 beta chain
T: LH1 beta chain
s: Light-harvesting protein B-870 alpha chain
U: LH1 beta chain
u: Light-harvesting protein B-870 alpha chain
r: Light-harvesting protein B-870 alpha chain
O: LH1 beta chain
R: LH1 beta chain
o: Light-harvesting protein B-870 alpha chain
n: Light-harvesting protein B-870 alpha chain
K: LH1 beta chain
N: LH1 beta chain
k: Light-harvesting protein B-870 alpha chain
j: Light-harvesting protein B-870 alpha chain
I: LH1 beta chain
J: LH1 beta chain
i: Light-harvesting protein B-870 alpha chain
g: Light-harvesting protein B-870 alpha chain
F: LH1 beta chain
G: LH1 beta chain
f: Light-harvesting protein B-870 alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)341,138109
Polymers284,26234
Non-polymers56,87675
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 16 molecules aebdtsuronkjigfX

#1: Protein
Light-harvesting protein B-870 alpha chain / Antenna pigment protein alpha chain / LH-1


Mass: 6600.920 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus (bacteria) / References: UniProt: P02948
#3: Protein Intrinsic membrane protein PufX / Protein C2397


Mass: 8574.901 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus (bacteria) / References: UniProt: P26240

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Protein/peptide , 1 types, 15 molecules DAEBSTUORKNIJFG

#2: Protein/peptide
LH1 beta chain


Mass: 5470.303 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus (bacteria) / References: UniProt: P02950

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Reaction center protein ... , 3 types, 3 molecules LMH

#4: Protein Reaction center protein L chain / Photosynthetic reaction centre / Photosynthetic reaction center L subunit


Mass: 31586.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus (bacteria) / References: UniProt: P19057
#5: Protein Reaction center protein M chain / Photosynthetic reaction centre / Photosynthetic reaction center M subunit


Mass: 34462.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus (bacteria) / References: UniProt: P11847
#6: Protein Reaction center protein H chain / Photosynthetic reaction centre / Photosynthetic reaction center H subunit


Mass: 28569.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus (bacteria) / References: UniProt: P19056

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Non-polymers , 6 types, 75 molecules

#7: Chemical...
ChemComp-BCL / BACTERIOCHLOROPHYLL A / Bacteriochlorophyll


Mass: 911.504 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical...
ChemComp-SPO / SPHEROIDENE


Mass: 568.914 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C41H60O / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A / Pheophytin


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical
ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C59H90O4 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical
ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Phosphatidylethanolamine


Mass: 748.065 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#12: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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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: RC-LH1-PufX photosynthetic core complex from Rba. capsulatus
Type: COMPLEX / Entity ID: #1-#6 / Source: NATURAL
Source (natural)Organism: Rhodobacter capsulatus (bacteria) / Strain: SB1003
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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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 FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50.32 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.589 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 181054 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 27.23 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002822512
ELECTRON MICROSCOPYf_angle_d2.542330996
ELECTRON MICROSCOPYf_chiral_restr0.0353117
ELECTRON MICROSCOPYf_plane_restr0.00373847
ELECTRON MICROSCOPYf_dihedral_angle_d19.58587577

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