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- PDB-7vy2: STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF RHODOBACTER S... -

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Basic information

Entry
Database: PDB / ID: 7vy2
TitleSTRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF RHODOBACTER SPHAEROIDES DIMER
Components
  • (Antenna pigment protein ...) x 2
  • (Photosynthetic reaction center ...) x 2
  • PufX
  • Reaction center protein M chain
  • protein-U
KeywordsPHOTOSYNTHESIS / LH1-RC COMPLEX / PURPLE BACTERIA
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 / membrane => GO:0016020 / 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, 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 ...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 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 / 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 / : / Chem-PGV / PHOSPHATIDYLETHANOLAMINE / SPHEROIDENE / UBIQUINONE-10 / Uncharacterized protein / Intrinsic membrane protein PufX ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CARDIOLIPIN / : / Chem-PGV / PHOSPHATIDYLETHANOLAMINE / SPHEROIDENE / UBIQUINONE-10 / Uncharacterized protein / Intrinsic membrane protein PufX / Reaction center protein L chain / Antenna pigment protein beta chain / Reaction center protein M chain / Photosynthetic reaction center subunit H / Antenna pigment protein alpha chain
Similarity search - Component
Biological speciesRhodobacter sphaeroides f. sp. denitrificans (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsTani, K. / Kanno, R. / Kawamura, S. / Kikuchi, R. / Nagashima, K.V.P. / Hall, M. / Takahashi, A. / Yu, L.-J. / Kimura, Y. / Madigan, M.T. ...Tani, K. / Kanno, R. / Kawamura, S. / Kikuchi, R. / Nagashima, K.V.P. / Hall, M. / Takahashi, A. / Yu, L.-J. / Kimura, Y. / Madigan, M.T. / Mizoguchi, A. / Humbel, B.M. / Wang-Otomo, Z.-Y.
Funding support Japan, 6items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21am0101118 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101116 Japan
Japan Society for the Promotion of Science (JSPS)JP16H04174 Japan
Japan Society for the Promotion of Science (JSPS)JP18H05153 Japan
Japan Society for the Promotion of Science (JSPS)20H05086 Japan
Japan Society for the Promotion of Science (JSPS)20H02856 Japan
CitationJournal: Nat Commun / Year: 2022
Title: Asymmetric structure of the native Rhodobacter sphaeroides dimeric LH1-RC complex.
Authors: Kazutoshi Tani / Ryo Kanno / Riku Kikuchi / Saki Kawamura / Kenji V P Nagashima / Malgorzata Hall / Ai Takahashi / Long-Jiang Yu / Yukihiro Kimura / Michael T Madigan / Akira Mizoguchi / ...Authors: Kazutoshi Tani / Ryo Kanno / Riku Kikuchi / Saki Kawamura / Kenji V P Nagashima / Malgorzata Hall / Ai Takahashi / Long-Jiang Yu / Yukihiro Kimura / Michael T Madigan / Akira Mizoguchi / Bruno M Humbel / Zheng-Yu Wang-Otomo /
Abstract: Rhodobacter sphaeroides is a model organism in bacterial photosynthesis, and its light-harvesting-reaction center (LH1-RC) complex contains both dimeric and monomeric forms. Here we present cryo-EM ...Rhodobacter sphaeroides is a model organism in bacterial photosynthesis, and its light-harvesting-reaction center (LH1-RC) complex contains both dimeric and monomeric forms. Here we present cryo-EM structures of the native LH1-RC dimer and an LH1-RC monomer lacking protein-U (ΔU). The native dimer reveals several asymmetric features including the arrangement of its two monomeric components, the structural integrity of protein-U, the overall organization of LH1, and rigidities of the proteins and pigments. PufX plays a critical role in connecting the two monomers in a dimer, with one PufX interacting at its N-terminus with another PufX and an LH1 β-polypeptide in the other monomer. One protein-U was only partially resolved in the dimeric structure, signaling different degrees of disorder in the two monomers. The ΔU LH1-RC monomer was half-moon-shaped and contained 11 α- and 10 β-polypeptides, indicating a critical role for protein-U in controlling the number of αβ-subunits required for dimer assembly and stabilization. These features are discussed in relation to membrane topology and an assembly model proposed for the native dimeric complex.
History
DepositionNov 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _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
L: Photosynthetic reaction center L subunit
M: Reaction center protein M chain
H: Photosynthetic reaction center subunit H
A: Antenna pigment protein alpha chain
B: 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
I: Antenna pigment protein alpha chain
J: Antenna pigment protein beta chain
K: Antenna pigment protein alpha 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
V: Antenna pigment protein alpha chain
W: Antenna pigment protein beta chain
Y: Antenna pigment protein alpha chain
Z: Antenna pigment protein beta chain
1: Antenna pigment protein alpha chain
2: Antenna pigment protein beta chain
3: Antenna pigment protein alpha chain
4: Antenna pigment protein beta chain
5: Antenna pigment protein alpha chain
6: Antenna pigment protein beta chain
7: Antenna pigment protein alpha chain
8: Antenna pigment protein beta chain
X: PufX
U: protein-U
l: Photosynthetic reaction center L subunit
m: Reaction center protein M chain
h: Photosynthetic reaction center subunit H
a: Antenna pigment protein alpha chain
b: 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
i: Antenna pigment protein alpha chain
j: Antenna pigment protein beta chain
k: Antenna pigment protein alpha 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
v: Antenna pigment protein alpha chain
w: Antenna pigment protein beta chain
y: Antenna pigment protein alpha chain
z: Antenna pigment protein beta chain
01: Antenna pigment protein alpha chain
02: Antenna pigment protein beta chain
03: Antenna pigment protein alpha chain
04: Antenna pigment protein beta chain
05: Antenna pigment protein alpha chain
06: Antenna pigment protein beta chain
07: Antenna pigment protein alpha chain
08: Antenna pigment protein beta chain
x: PufX
u: protein-U
hetero molecules


Theoretical massNumber of molelcules
Total (without water)702,955267
Polymers550,79166
Non-polymers152,164201
Water00
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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Photosynthetic reaction center ... , 2 types, 4 molecules LlHh

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


Mass: 31360.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Rhodobacter sphaeroides f. sp. denitrificans (bacteria)
References: UniProt: A0A7Z6QV46
#3: Protein Photosynthetic reaction center subunit H


Mass: 28091.350 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Rhodobacter sphaeroides f. sp. denitrificans (bacteria)
References: UniProt: A0A7Z6QV87

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Protein , 3 types, 6 molecules MmXxUu

#2: Protein Reaction center protein M chain / Photosynthetic reaction center M subunit


Mass: 34412.566 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Rhodobacter sphaeroides f. sp. denitrificans (bacteria)
References: UniProt: A0A7Z6QV86
#6: Protein PufX


Mass: 8886.395 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Rhodobacter sphaeroides f. sp. denitrificans (bacteria)
References: UniProt: A0A7Z6QV32
#7: Protein protein-U


Mass: 5555.558 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Rhodobacter sphaeroides f. sp. denitrificans (bacteria)
References: UniProt: A0A7Z6QU05

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Antenna pigment protein ... , 2 types, 56 molecules ADFIKOQSVY1357adfikoqsvy01030507BE...

#4: Protein ...
Antenna pigment protein alpha chain


Mass: 6473.780 Da / Num. of mol.: 28 / Source method: isolated from a natural source
Source: (natural) Rhodobacter sphaeroides f. sp. denitrificans (bacteria)
References: UniProt: A0A7Z6W8S0
#5: Protein/peptide ...
Antenna pigment protein beta chain


Mass: 5461.166 Da / Num. of mol.: 28 / Source method: isolated from a natural source
Source: (natural) Rhodobacter sphaeroides f. sp. denitrificans (bacteria)
References: UniProt: A0A7Z6QV72

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Sugars , 1 types, 27 molecules

#11: Sugar...
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 9 types, 174 molecules

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


Mass: 911.504 Da / Num. of mol.: 64 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical
ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H76N4O6
#10: Chemical
ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C59H90O4
#12: Chemical...
ChemComp-PGV / (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / PHOSPHATIDYLGLYCEROL / 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL


Mass: 749.007 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#13: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#14: Chemical...
ChemComp-SPO / SPHEROIDENE


Mass: 568.914 Da / Num. of mol.: 54 / Source method: obtained synthetically / Formula: C41H60O
#15: 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.: 11 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#16: Chemical
ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#17: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM

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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

Component
IDNameTypeEntity IDParent-IDSource
1Photosynthetic LH1-RC complex from the purple phototrophic bacterium Rhodobacter sphaeroides dimerCOMPLEX#1-#70NATURAL
2Rhodobacter sphaeroides Dimeric LH1-RC ComplexCOMPLEX#1-#71NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Rhodobacter sphaeroides f. sp. denitrificans (bacteria)1085IL106
32Rhodobacter sphaeroides f. sp. denitrificans (bacteria)1085IL106
Buffer solutionpH: 8
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse.
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 277 K

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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: 3000 nm / Nominal defocus min: 1000 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.275 sec. / Electron dose: 42 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFINDCTF correction
7UCSF Chimeramodel fitting
10RELION3.1final Euler assignment
11RELION3.1classification
12RELION3.13D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 164496
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 124916 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingB value: 60 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient
Atomic model buildingPDB-ID: 7F0L

7f0l


Accession code: 7F0L / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 47.43 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00747992
ELECTRON MICROSCOPYf_angle_d2.74665615
ELECTRON MICROSCOPYf_dihedral_angle_d16.64418735
ELECTRON MICROSCOPYf_chiral_restr0.0486537
ELECTRON MICROSCOPYf_plane_restr0.0057889

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