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- PDB-7voy: Rba sphaeroides PufX-KO RC-LH1 -

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Basic information

Entry
Database: PDB / ID: 7voy
TitleRba sphaeroides PufX-KO RC-LH1
Components
  • (Light-harvesting protein B-875 ...) x 2
  • (Reaction center protein ...Photosynthetic reaction centre) x 3
KeywordsPHOTOSYNTHESIS / Photosystem / Complex / Mutant
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 / 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, 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 ...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
BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / : / SPEROIDENONE / UBIQUINONE-10 / Reaction center protein H chain / Light-harvesting protein B-875 beta chain / Light-harvesting protein B-875 alpha chain / Reaction center protein L chain / Reaction center protein M chain
Similarity search - Component
Biological speciesCereibacter sphaeroides 2.4.1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsBracun, L. / Yamagata, A. / Liu, L.N. / Shirouzu, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Royal Society United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis for the assembly and quinone transport mechanisms of the dimeric photosynthetic RC-LH1 supercomplex.
Authors: Peng Cao / Laura Bracun / Atsushi Yamagata / Bern M Christianson / Tatsuki Negami / Baohua Zou / Tohru Terada / Daniel P Canniffe / Mikako Shirouzu / Mei Li / Lu-Ning Liu /
Abstract: The reaction center (RC) and light-harvesting complex 1 (LH1) form a RC-LH1 core supercomplex that is vital for the primary reactions of photosynthesis in purple phototrophic bacteria. Some species ...The reaction center (RC) and light-harvesting complex 1 (LH1) form a RC-LH1 core supercomplex that is vital for the primary reactions of photosynthesis in purple phototrophic bacteria. Some species possess the dimeric RC-LH1 complex with a transmembrane polypeptide PufX, representing the largest photosynthetic complex in anoxygenic phototrophs. However, the details of the architecture and assembly mechanism of the RC-LH1 dimer are unclear. Here we report seven cryo-electron microscopy (cryo-EM) structures of RC-LH1 supercomplexes from Rhodobacter sphaeroides. Our structures reveal that two PufX polypeptides are positioned in the center of the S-shaped RC-LH1 dimer, interlocking association between the components and mediating RC-LH1 dimerization. Moreover, we identify another transmembrane peptide, designated PufY, which is located between the RC and LH1 subunits near the LH1 opening. PufY binds a quinone molecule and prevents LH1 subunits from completely encircling the RC, creating a channel for quinone/quinol exchange. Genetic mutagenesis, cryo-EM structures, and computational simulations provide a mechanistic understanding of the assembly and electron transport pathways of the RC-LH1 dimer and elucidate the roles of individual components in ensuring the structural and functional integrity of the photosynthetic supercomplex.
History
DepositionOct 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 4, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Light-harvesting protein B-875 alpha chain
B: Light-harvesting protein B-875 beta chain
D: Light-harvesting protein B-875 alpha chain
E: Light-harvesting protein B-875 beta chain
F: Light-harvesting protein B-875 alpha chain
G: Light-harvesting protein B-875 beta chain
I: Light-harvesting protein B-875 alpha chain
J: Light-harvesting protein B-875 beta chain
K: Light-harvesting protein B-875 alpha chain
N: Light-harvesting protein B-875 beta chain
O: Light-harvesting protein B-875 alpha chain
P: Light-harvesting protein B-875 beta chain
Q: Light-harvesting protein B-875 alpha chain
R: Light-harvesting protein B-875 beta chain
S: Light-harvesting protein B-875 alpha chain
T: Light-harvesting protein B-875 beta chain
U: Light-harvesting protein B-875 alpha chain
V: Light-harvesting protein B-875 beta chain
W: Light-harvesting protein B-875 alpha chain
X: Light-harvesting protein B-875 beta chain
Y: Light-harvesting protein B-875 alpha chain
Z: Light-harvesting protein B-875 beta chain
1: Light-harvesting protein B-875 alpha chain
2: Light-harvesting protein B-875 beta chain
7: Light-harvesting protein B-875 alpha chain
8: Light-harvesting protein B-875 beta chain
9: Light-harvesting protein B-875 alpha chain
0: Light-harvesting protein B-875 beta chain
4: Light-harvesting protein B-875 alpha chain
t: Light-harvesting protein B-875 beta chain
6: Light-harvesting protein B-875 alpha chain
5: Light-harvesting protein B-875 beta chain
C: Light-harvesting protein B-875 alpha chain
3: Light-harvesting protein B-875 beta chain
L: Reaction center protein L chain
M: Reaction center protein M chain
H: Reaction center protein H chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)343,81281
Polymers305,01937
Non-polymers38,79344
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.604793502587, -0.6966699927, 0.385844192), (0.204743528029, -0.604230268927, -0.770055757619), (0.769613478935, -0.386725617698, 0.508073212891)137.098164175, 143.931672404, 2.47245985533
2given(-0.713449599817, -0.421541642167, 0.559725211546), (-0.10968285189, -0.721769618565, -0.683387364324), (0.692068884232, -0.548954699074, 0.468710356022)114.663828303, 169.052762743, 21.5137101138
3given(-0.718549485475, -0.111321563206, 0.686508664541), (-0.405299068049, -0.735136142543, -0.543422043503), (0.565171922836, -0.668716951701, 0.483113171157)85.9987932765, 181.409820539, 37.5569917747
4given(-0.393262112764, 0.471358690896, 0.789408573035), (-0.886544309325, -0.421965428826, -0.189695451917), (0.243688527155, -0.77444571236, 0.583823381118)16.9358611524, 172.462685564, 60.715793935
5given(0.211958822127, 0.746603198505, 0.630600603952), (-0.975913098844, 0.195800656012, 0.0962066869276), (-0.0516437917578, -0.635803245578, 0.77012151748)-35.4432361304, 118.868939797, 61.0641512804
6given(0.524949447982, 0.691761521467, 0.495877075979), (-0.839461961582, 0.516956355575, 0.167510422026), (-0.140469541609, -0.504204446478, 0.852083437248)-44.8626397672, 82.2928408676, 53.8766686294
7given(0.779664520257, 0.536694621167, 0.322617605631), (-0.605504575815, 0.77749438135, 0.16990201775), (-0.159647876651, -0.327813011608, 0.93115583277)-41.6019443479, 47.3431395287, 38.1879521423
8given(0.939847183866, 0.306414678156, 0.1509878008), (-0.323810629811, 0.939922543117, 0.108130888104), (-0.10878394643, -0.150517965544, 0.982603885117)-26.4454334905, 20.4544049213, 19.3171794564
9given(-0.110560107985, 0.664015749835, 0.739499524336), (-0.990180375071, -0.13764150435, -0.0244466992584), (0.0855528336568, -0.734940746082, 0.672713023809)-13.2954712201, 150.346553412, 63.5702744013
10given(0.937006479639, -0.326297733665, -0.124694210453), (0.304269526998, 0.937748934272, -0.167472359546), (0.171577714334, 0.118982037621, 0.97795928477)34.9514292616, -7.02267239323, -20.173708245
11given(0.770173755269, -0.613782751147, -0.173502510327), (0.53380164617, 0.769143340392, -0.351389135399), (0.349124890608, 0.178014764344, 0.920012257763)69.5081166883, 0.33728699195, -33.7480281331
12given(0.509869015084, -0.845173541952, -0.16035981866), (0.68259742385, 0.510929538294, -0.522505276387), (0.523540203241, 0.156948051542, 0.83742042291)103.38649002, 18.3950797826, -39.323174194
13given(0.224448661458, -0.971149536941, -0.0805690714129), (0.720961575748, 0.221111985944, -0.656752537846), (0.6556197104, 0.0893200233465, 0.749789789718)126.184223551, 43.7595201925, -38.3254379675
14given(-0.10633682865, -0.993092382504, 0.049598373822), (0.650024609086, -0.107175600789, -0.752317352038), (0.752436367047, -0.0477588777991, 0.65693120122)143.604989001, 77.4551785949, -29.5897612343
15given(-0.379820089018, -0.903567414426, 0.198248903064), (0.485946863165, -0.377246417106, -0.788378580988), (0.787141884388, -0.203103590241, 0.582371518426)146.774262823, 108.769706635, -16.2254237334
16given(-0.607777607266, 0.204004078034, 0.767456002812), (-0.68114656703, -0.630738436688, -0.371763874937), (0.408222652887, -0.748699780039, 0.522305375274)51.5940574647, 183.172162871, 51.3886763316

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Components

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Light-harvesting protein B-875 ... , 2 types, 34 molecules ADFIKOQSUWY17946CBEGJNPRTVXZ28...

#1: Protein
Light-harvesting protein B-875 alpha chain / Antenna pigment protein alpha chain / LH-1


Mass: 6816.169 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides 2.4.1 (bacteria) / Strain: 2.4.1. / References: UniProt: Q3J1A4
#2: Protein/peptide
Light-harvesting protein B-875 beta chain / Antenna pigment protein beta chain / LH-3A


Mass: 5592.361 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides 2.4.1 (bacteria) / Strain: 2.4.1. / References: UniProt: Q3J1A3

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

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


Mass: 31477.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides 2.4.1 (bacteria) / Strain: 2.4.1. / References: UniProt: Q3J1A5
#4: Protein Reaction center protein M chain / Photosynthetic reaction centre / Photosynthetic reaction center M subunit


Mass: 34529.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides 2.4.1 (bacteria) / Strain: 2.4.1. / References: UniProt: Q3J1A6
#5: Protein Reaction center protein H chain / Photosynthetic reaction centre / Photosynthetic reaction center H subunit


Mass: 28066.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides 2.4.1 (bacteria) / Strain: 2.4.1. / References: UniProt: Q3J170

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Non-polymers , 5 types, 44 molecules

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


Mass: 911.504 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#7: 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
#8: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C59H90O4 / Feature type: SUBJECT OF INVESTIGATION
#9: 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
#10: Chemical ChemComp-SPN / SPEROIDENONE


Mass: 594.993 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H70O2 / 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: Rhodobacter sphaeroides PufX-KO RC-LH1 / Type: COMPLEX / Entity ID: #1-#5 / Source: NATURAL
Source (natural)Organism: Rhodobacter sphaeroides 2.4.1 (bacteria) / Strain: PufX-KO
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid 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
Image recordingElectron dose: 46.549 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.18.2_3874refinement
PHENIX1.18.2_3874refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 66058 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 76.57 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007723118
ELECTRON MICROSCOPYf_angle_d0.923232179
ELECTRON MICROSCOPYf_chiral_restr0.04313298
ELECTRON MICROSCOPYf_plane_restr0.00543870
ELECTRON MICROSCOPYf_dihedral_angle_d21.15467359

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