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- PDB-8ygd: Rhodobacter blasticus RC-LH1 dimer -

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Basic information

Entry
Database: PDB / ID: 8ygd
TitleRhodobacter blasticus RC-LH1 dimer
Components
  • (Antenna pigment protein ...) x 2
  • (Reaction center protein ...) x 2
  • 1-deoxy-D-xylulose-5-phosphate synthase
  • Photosynthetic reaction center subunit H
KeywordsPHOTOSYNTHESIS / light-harvesting complex
Function / homology
Function and homology information


plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / metal ion binding / membrane / 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, alpha/beta subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily / Antenna complex alpha/beta subunit / Light-harvesting complex ...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, alpha/beta subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily / Antenna complex alpha/beta subunit / Light-harvesting complex / 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 / PRC-barrel domain / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / 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
BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CARDIOLIPIN / : / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / SPHEROIDENE / UBIQUINONE-10 / Reaction center protein L chain / Photosynthetic reaction center subunit H / Reaction center protein M chain ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CARDIOLIPIN / : / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / SPHEROIDENE / UBIQUINONE-10 / Reaction center protein L chain / Photosynthetic reaction center subunit H / Reaction center protein M chain / 1-deoxy-D-xylulose-5-phosphate synthase / Antenna pigment protein alpha chain / Antenna pigment protein beta chain
Similarity search - Component
Biological speciesFuscovulum blasticum DSM 2131 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsLiu, L.N. / Zhang, Y.Z. / Wang, P. / Christianson, B.M. / Ugurlar, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32170127 China
CitationJournal: Sci Adv / Year: 2024
Title: Architectures of photosynthetic RC-LH1 supercomplexes from .
Authors: Peng Wang / Bern M Christianson / Deniz Ugurlar / Ruichao Mao / Yi Zhang / Ze-Kun Liu / Ying-Yue Zhang / Adrian M Gardner / Jun Gao / Yu-Zhong Zhang / Lu-Ning Liu /
Abstract: The reaction center-light-harvesting complex 1 (RC-LH1) plays an essential role in the primary reactions of bacterial photosynthesis. Here, we present high-resolution structures of native monomeric ...The reaction center-light-harvesting complex 1 (RC-LH1) plays an essential role in the primary reactions of bacterial photosynthesis. Here, we present high-resolution structures of native monomeric and dimeric RC-LH1 supercomplexes from () using cryo-electron microscopy. The RC-LH1 monomer is composed of an RC encircled by an open LH1 ring comprising 15 αβ heterodimers and a PufX transmembrane polypeptide. In the RC-LH1 dimer, two crossing PufX polypeptides mediate dimerization. Unlike counterpart, RC-LH1 dimer has a less bent conformation, lacks the PufY subunit near the LH1 opening, and includes two extra LH1 αβ subunits, forming a more enclosed S-shaped LH1 ring. Spectroscopic assays reveal that these unique structural features are accompanied by changes in the kinetics of quinone/quinol trafficking between RC-LH1 and cytochrome . Our findings reveal the assembly principles and structural variability of photosynthetic RC-LH1 supercomplexes, highlighting diverse strategies used by phototrophic bacteria to optimize light-harvesting and electron transfer in competitive environments.
History
DepositionFeb 26, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: Antenna pigment protein beta chain
1: Antenna pigment protein alpha chain
2: Antenna pigment protein beta chain
3: Antenna pigment protein alpha chain
7: Antenna pigment protein alpha chain
8: Antenna pigment protein beta chain
9: Antenna pigment protein alpha chain
A: Antenna pigment protein alpha chain
B: Antenna pigment protein beta chain
C: Antenna pigment protein beta chain
D: Antenna pigment protein alpha chain
E: Antenna pigment protein beta chain
F: Antenna pigment protein alpha chain
G: Antenna pigment protein beta chain
H: Photosynthetic reaction center subunit H
I: Antenna pigment protein alpha chain
J: Antenna pigment protein beta chain
K: Antenna pigment protein alpha chain
L: Reaction center protein L chain
M: Reaction center protein M chain
N: Antenna pigment protein beta chain
O: Antenna pigment protein alpha chain
P: Antenna pigment protein beta chain
Q: Antenna pigment protein alpha chain
R: Antenna pigment protein beta chain
S: Antenna pigment protein alpha chain
T: Antenna pigment protein beta chain
U: Antenna pigment protein alpha chain
V: Antenna pigment protein beta chain
W: Antenna pigment protein alpha chain
X: 1-deoxy-D-xylulose-5-phosphate synthase
Z: Antenna pigment protein beta chain
a: Antenna pigment protein alpha chain
b: Antenna pigment protein beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)361,518121
Polymers293,06634
Non-polymers68,45187
Water00
1
0: Antenna pigment protein beta chain
1: Antenna pigment protein alpha chain
2: Antenna pigment protein beta chain
3: Antenna pigment protein alpha chain
7: Antenna pigment protein alpha chain
8: Antenna pigment protein beta chain
9: Antenna pigment protein alpha chain
A: Antenna pigment protein alpha chain
B: Antenna pigment protein beta chain
C: Antenna pigment protein beta chain
D: Antenna pigment protein alpha chain
E: Antenna pigment protein beta chain
F: Antenna pigment protein alpha chain
G: Antenna pigment protein beta chain
H: Photosynthetic reaction center subunit H
I: Antenna pigment protein alpha chain
J: Antenna pigment protein beta chain
K: Antenna pigment protein alpha chain
L: Reaction center protein L chain
M: Reaction center protein M chain
N: Antenna pigment protein beta chain
O: Antenna pigment protein alpha chain
P: Antenna pigment protein beta chain
Q: Antenna pigment protein alpha chain
R: Antenna pigment protein beta chain
S: Antenna pigment protein alpha chain
T: Antenna pigment protein beta chain
U: Antenna pigment protein alpha chain
V: Antenna pigment protein beta chain
W: Antenna pigment protein alpha chain
X: 1-deoxy-D-xylulose-5-phosphate synthase
Z: Antenna pigment protein beta chain
a: Antenna pigment protein alpha chain
b: Antenna pigment protein beta chain
hetero molecules

0: Antenna pigment protein beta chain
1: Antenna pigment protein alpha chain
2: Antenna pigment protein beta chain
3: Antenna pigment protein alpha chain
7: Antenna pigment protein alpha chain
8: Antenna pigment protein beta chain
9: Antenna pigment protein alpha chain
A: Antenna pigment protein alpha chain
B: Antenna pigment protein beta chain
C: Antenna pigment protein beta chain
D: Antenna pigment protein alpha chain
E: Antenna pigment protein beta chain
F: Antenna pigment protein alpha chain
G: Antenna pigment protein beta chain
H: Photosynthetic reaction center subunit H
I: Antenna pigment protein alpha chain
J: Antenna pigment protein beta chain
K: Antenna pigment protein alpha chain
L: Reaction center protein L chain
M: Reaction center protein M chain
N: Antenna pigment protein beta chain
O: Antenna pigment protein alpha chain
P: Antenna pigment protein beta chain
Q: Antenna pigment protein alpha chain
R: Antenna pigment protein beta chain
S: Antenna pigment protein alpha chain
T: Antenna pigment protein beta chain
U: Antenna pigment protein alpha chain
V: Antenna pigment protein beta chain
W: Antenna pigment protein alpha chain
X: 1-deoxy-D-xylulose-5-phosphate synthase
Z: Antenna pigment protein beta chain
a: Antenna pigment protein alpha chain
b: Antenna pigment protein beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)723,035242
Polymers586,13368
Non-polymers136,902174
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1

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Components

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Antenna pigment protein ... , 2 types, 30 molecules 028BCEGJNPRTVZb1379ADFIKOQSUWa

#1: Protein/peptide
Antenna pigment protein beta chain / LH1 beta chain


Mass: 5614.452 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) Fuscovulum blasticum DSM 2131 (bacteria) / References: UniProt: A0A2T4JAH7
#2: Protein
Antenna pigment protein alpha chain / LH1 alpha chain


Mass: 7096.406 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) Fuscovulum blasticum DSM 2131 (bacteria) / References: UniProt: A0A2T4JA00

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Protein , 2 types, 2 molecules HX

#3: Protein Photosynthetic reaction center subunit H


Mass: 28320.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fuscovulum blasticum DSM 2131 (bacteria) / References: UniProt: A0A2T4J4Z7
#6: Protein 1-deoxy-D-xylulose-5-phosphate synthase / PufX


Mass: 8046.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fuscovulum blasticum DSM 2131 (bacteria) / References: UniProt: A0A2T4J9W4

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Reaction center protein ... , 2 types, 2 molecules LM

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


Mass: 31494.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fuscovulum blasticum DSM 2131 (bacteria) / References: UniProt: A0A2L1K3X9
#5: Protein Reaction center protein M chain / Photosynthetic reaction center M subunit


Mass: 34542.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fuscovulum blasticum DSM 2131 (bacteria) / References: UniProt: A0A2T4J9V9

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Non-polymers , 7 types, 87 molecules

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


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.: 29 / Source method: obtained synthetically / Formula: C41H60O / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C44H88NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#10: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#11: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A


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


Mass: 863.343 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C59H90O4 / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical ChemComp-FE2 / FE (II) ION


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
Has protein modificationN

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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: Rhodobacter blasticus RC-LH1 dimer / Type: COMPLEX / Entity ID: #1-#6 / Source: NATURAL
Source (natural)Organism: Fuscovulum blasticum DSM 2131 (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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 FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9149 / Symmetry type: POINT
RefinementHighest resolution: 2.84 Å

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