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- PDB-7pqd: Cryo-EM structure of the dimeric Rhodobacter sphaeroides RC-LH1 c... -

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Basic information

Entry
Database: PDB / ID: 7pqd
TitleCryo-EM structure of the dimeric Rhodobacter sphaeroides RC-LH1 core complex at 2.9 A: the structural basis for dimerisation
Components
  • LH1-alpha
  • LH1-beta
  • PufX
  • PufY
  • PufZ
  • RC-H
  • RC-L
  • Reaction center protein M chain
KeywordsPHOTOSYNTHESIS / light harvesting complex / Cryo-EM / purple bacteria / RC-LH1 / RC-LH1-PufXYZ / dimer / dimeric core 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 / : / metal ion binding
Similarity search - Function
Photosynthetic reaction centre, M subunit / : / 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 / Chem-CD4 / : / 3,4-DIHYDROSPHEROIDENE / Chem-SQD / UBIQUINONE-10 / UBIQUINONE-1 / Reaction center protein M chain
Similarity search - Component
Biological speciesCereibacter sphaeroides 2.4.1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsQian, P. / Hunter, C.N.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M000265/1 United Kingdom
European Research Council (ERC)845126 United Kingdom
Wellcome Trust209407/Z/17/Z United Kingdom
Citation
Journal: Biochem J / Year: 2021
Title: Cryo-EM structure of the dimeric Rhodobacter sphaeroides RC-LH1 core complex at 2.9 Å: the structural basis for dimerisation.
Authors: Pu Qian / Tristan I Croll / Andrew Hitchcock / Philip J Jackson / Jack H Salisbury / Pablo Castro-Hartmann / Kasim Sader / David J K Swainsbury / C Neil Hunter /
Abstract: The dimeric reaction centre light-harvesting 1 (RC-LH1) core complex of Rhodobacter sphaeroides converts absorbed light energy to a charge separation, and then it reduces a quinone electron and ...The dimeric reaction centre light-harvesting 1 (RC-LH1) core complex of Rhodobacter sphaeroides converts absorbed light energy to a charge separation, and then it reduces a quinone electron and proton acceptor to a quinol. The angle between the two monomers imposes a bent configuration on the dimer complex, which exerts a major influence on the curvature of the membrane vesicles, known as chromatophores, where the light-driven photosynthetic reactions take place. To investigate the dimerisation interface between two RC-LH1 monomers, we determined the cryogenic electron microscopy structure of the dimeric complex at 2.9 Å resolution. The structure shows that each monomer consists of a central RC partly enclosed by a 14-subunit LH1 ring held in an open state by PufX and protein-Y polypeptides, thus enabling quinones to enter and leave the complex. Two monomers are brought together through N-terminal interactions between PufX polypeptides on the cytoplasmic side of the complex, augmented by two novel transmembrane polypeptides, designated protein-Z, that bind to the outer faces of the two central LH1 β polypeptides. The precise fit at the dimer interface, enabled by PufX and protein-Z, by C-terminal interactions between opposing LH1 αβ subunits, and by a series of interactions with a bound sulfoquinovosyl diacylglycerol lipid, bring together each monomer creating an S-shaped array of 28 bacteriochlorophylls. The seamless join between the two sets of LH1 bacteriochlorophylls provides a path for excitation energy absorbed by one half of the complex to migrate across the dimer interface to the other half.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2018
Title: Real-space refinement in PHENIX for cryo-EM and crystallography
Authors: Qian, P. / Hunter, C.N.
History
DepositionSep 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 7, 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

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Assembly

Deposited unit
AA: LH1-alpha
AB: LH1-alpha
AC: LH1-alpha
AD: LH1-alpha
AE: LH1-alpha
AF: LH1-alpha
AG: LH1-alpha
AH: LH1-alpha
AI: LH1-alpha
AJ: LH1-alpha
AK: LH1-alpha
AL: LH1-alpha
AM: LH1-alpha
AN: LH1-alpha
BA: LH1-beta
BB: LH1-beta
BC: LH1-beta
BD: LH1-beta
BE: LH1-beta
BF: LH1-beta
BG: LH1-beta
BH: LH1-beta
BI: LH1-beta
BJ: LH1-beta
BK: LH1-beta
BL: LH1-beta
BM: LH1-beta
BN: LH1-beta
H: RC-H
L: RC-L
M: Reaction center protein M chain
UA: PufZ
UB: PufZ
UU: PufY
X: PufX
aa: LH1-alpha
ab: LH1-alpha
ac: LH1-alpha
ad: LH1-alpha
ae: LH1-alpha
af: LH1-alpha
ag: LH1-alpha
ah: LH1-alpha
ai: LH1-alpha
aj: LH1-alpha
ak: LH1-alpha
al: LH1-alpha
am: LH1-alpha
an: LH1-alpha
ba: LH1-beta
bb: LH1-beta
bc: LH1-beta
bd: LH1-beta
be: LH1-beta
bf: LH1-beta
bg: LH1-beta
bh: LH1-beta
bi: LH1-beta
bj: LH1-beta
bk: LH1-beta
bl: LH1-beta
bm: LH1-beta
bn: LH1-beta
h: RC-H
l: RC-L
m: Reaction center protein M chain
ua: PufZ
ub: PufZ
uu: PufY
x: PufX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)676,531212
Polymers569,17270
Non-polymers107,359142
Water2,594144
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, Mass analysis, size exclusion gel filtration.
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 5 types, 36 molecules AAABACADAEAFAGAHAIAJAKALAMANaaabacadaeafagahaiajakalamanHh...

#1: Protein ...
LH1-alpha


Mass: 6844.180 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides 2.4.1 (bacteria)
#3: Protein RC-H


Mass: 26544.471 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides 2.4.1 (bacteria)
#4: Protein RC-L


Mass: 31346.389 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides 2.4.1 (bacteria)
#5: Protein Reaction center protein M chain / Photosynthetic reaction center M subunit


Mass: 34398.543 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides 2.4.1 (bacteria) / References: UniProt: Q3J1A6
#8: Protein PufX


Mass: 6024.157 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides 2.4.1 (bacteria)

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Protein/peptide , 3 types, 34 molecules BABBBCBDBEBFBGBHBIBJBKBLBMBNbabbbcbdbebfbgbhbibjbkblbmbnUAUB...

#2: Protein/peptide ...
LH1-beta


Mass: 5592.361 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides 2.4.1 (bacteria)
#6: Protein/peptide
PufZ


Mass: 3517.323 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides 2.4.1 (bacteria)
#7: Protein/peptide PufY


Mass: 5126.067 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides 2.4.1 (bacteria)

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Sugars , 1 types, 2 molecules

#17: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 10 types, 284 molecules

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


Mass: 911.504 Da / Num. of mol.: 64 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical...
ChemComp-SP2 / 3,4-DIHYDROSPHEROIDENE


Mass: 570.930 Da / Num. of mol.: 54 / Source method: obtained synthetically / Formula: C41H62O
#11: Chemical
ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#12: Chemical
ChemComp-CD4 / (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate / tetramyristoyl-cardiolipin


Mass: 1241.633 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C65H126O17P2
#13: Chemical ChemComp-UQ1 / UBIQUINONE-1


Mass: 250.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H18O4
#14: Chemical
ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C59H90O4 / Feature type: SUBJECT OF INVESTIGATION
#15: Chemical
ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H76N4O6 / Feature type: SUBJECT OF INVESTIGATION
#16: Chemical ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H78O12S / Feature type: SUBJECT OF INVESTIGATION
#18: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#19: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: Light harvesting core complex / Type: COMPLEX / Entity ID: #1-#8 / Source: NATURAL
Source (natural)Organism: Cereibacter sphaeroides 2.4.1 (bacteria)
Buffer solutionpH: 7.8 / Details: 20 mM HEPES, pH 7.8, 0.03% beta-DDM
Buffer componentConc.: 20 mMol / Formula: HEPES
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: In 20 mM HEPES, pH 7.8, 0.03% beta-DDM buffer solution
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 99 % / Chamber temperature: 277 K / Details: QF R1.2/1.3 300 mesh Cu grid

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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: 2200 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 (max): 80 K
Image recordingAverage exposure time: 12.21 sec. / Electron dose: 45.36 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5058

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Processing

Software
NameVersionClassification
phenix.real_space_refinedev_4351refinement
PHENIXdev_4351refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4CTF correction
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 223786
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 58945 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT

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