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- EMDB-11080: RC-LH1(16) complex from Rhodopseudomonas palustris -

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Basic information

Entry
Database: EMDB / ID: EMD-11080
TitleRC-LH1(16) complex from Rhodopseudomonas palustris
Map data
Sample
  • Complex: Reaction center-Light harvesting complex 1
    • Protein or peptide: x 5 types
  • Ligand: x 11 types
KeywordsReaction center / Light harvesting / Protein W / Quinone / PHOTOSYNTHESIS
Function / homology
Function and homology information


organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / photosynthetic electron transport in photosystem II / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / membrane / 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, 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 ...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 / 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
Reaction center protein M chain / H subunit of photosynthetic reaction center complex / Reaction center protein L chain / Light-harvesting antenna LH1, alpha subunit / Light-harvesting antenna LH1, beta subunit
Similarity search - Component
Biological speciesRhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (phototrophic)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsSwainsbury DJK / Qian P
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M000265/1 United Kingdom
CitationJournal: Sci Adv / Year: 2021
Title: Structures of RC-LH1 complexes with open or closed quinone channels.
Authors: David J K Swainsbury / Pu Qian / Philip J Jackson / Kaitlyn M Faries / Dariusz M Niedzwiedzki / Elizabeth C Martin / David A Farmer / Lorna A Malone / Rebecca F Thompson / Neil A Ranson / ...Authors: David J K Swainsbury / Pu Qian / Philip J Jackson / Kaitlyn M Faries / Dariusz M Niedzwiedzki / Elizabeth C Martin / David A Farmer / Lorna A Malone / Rebecca F Thompson / Neil A Ranson / Daniel P Canniffe / Mark J Dickman / Dewey Holten / Christine Kirmaier / Andrew Hitchcock / C Neil Hunter /
Abstract: The reaction-center light-harvesting complex 1 (RC-LH1) is the core photosynthetic component in purple phototrophic bacteria. We present two cryo-electron microscopy structures of RC-LH1 complexes ...The reaction-center light-harvesting complex 1 (RC-LH1) is the core photosynthetic component in purple phototrophic bacteria. We present two cryo-electron microscopy structures of RC-LH1 complexes from A 2.65-Å resolution structure of the RC-LH1-W complex consists of an open 14-subunit LH1 ring surrounding the RC interrupted by protein-W, whereas the complex without protein-W at 2.80-Å resolution comprises an RC completely encircled by a closed, 16-subunit LH1 ring. Comparison of these structures provides insights into quinone dynamics within RC-LH1 complexes, including a previously unidentified conformational change upon quinone binding at the RC Q site, and the locations of accessory quinone binding sites that aid their delivery to the RC. The structurally unique protein-W prevents LH1 ring closure, creating a channel for accelerated quinone/quinol exchange.
History
DepositionMay 27, 2020-
Header (metadata) releaseJan 13, 2021-
Map releaseJan 13, 2021-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.18
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.18
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6z5r
  • Surface level: 0.18
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11080.png

Downloads & links

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Map

FileDownload / File: emd_11080.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 400 pix.
= 426. Å		1.07 Å/pix.
x 400 pix.
= 426. Å		1.07 Å/pix.
x 400 pix.
= 426. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18 / Movie #1: 0.18
Minimum - Maximum-0.24812172 - 0.90050465
Average (Standard dev.)0.0012294633 (±0.017340476)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 426.00003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0651.0651.065
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z426.000426.000426.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.2480.9010.001

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Supplemental data

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Sample components

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Entire : Reaction center-Light harvesting complex 1

EntireName: Reaction center-Light harvesting complex 1
Components
  • Complex: Reaction center-Light harvesting complex 1
    • Protein or peptide: Light-harvesting complex 1 alpha chain
    • Protein or peptide: Light-harvesting complex 1 beta chain
    • Protein or peptide: H subunit of photosynthetic reaction center complex
    • Protein or peptide: Reaction center protein L chain
    • Protein or peptide: Reaction center protein M chain
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: SPIRILLOXANTHIN
  • Ligand: (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
  • Ligand: CARDIOLIPIN
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: BACTERIOPHEOPHYTIN A
  • Ligand: UBIQUINONE-10
  • Ligand: FE (III) ION
  • Ligand: (6~{R},10~{S},14~{R},19~{R},23~{S},24~{E},27~{S},28~{E})-2,6,10,14,19,23,27,31-octamethyldotriaconta-24,28-dien-2-ol
  • Ligand: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
  • Ligand: water

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Supramolecule #1: Reaction center-Light harvesting complex 1

SupramoleculeName: Reaction center-Light harvesting complex 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Details: Reaction center-Light harvesting complex 1 from Rhodopseudomonas palustris
Source (natural)Organism: Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (phototrophic)
Location in cell: Lamellar membranes
Molecular weightTheoretical: 3.52 MDa

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Macromolecule #1: Light-harvesting complex 1 alpha chain

MacromoleculeName: Light-harvesting complex 1 alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (phototrophic)
Strain: ATCC BAA-98 / CGA009
Molecular weightTheoretical: 5.779999 KDa
SequenceString:
(FME)WRIWLLFDP RRALVLLFVF LFGLAIIIHF ILLSTSRFNW LDGPRAAK

UniProtKB: Light-harvesting antenna LH1, alpha subunit

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Macromolecule #2: Light-harvesting complex 1 beta chain

MacromoleculeName: Light-harvesting complex 1 beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (phototrophic)
Strain: ATCC BAA-98 / CGA009
Molecular weightTheoretical: 5.849797 KDa
SequenceString:
MSDGSISGLS EAEAKEFHSI FVTSFFLFIV VAVVAHILAW MWRPWLPKAT GY

UniProtKB: Light-harvesting antenna LH1, beta subunit

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Macromolecule #3: H subunit of photosynthetic reaction center complex

MacromoleculeName: H subunit of photosynthetic reaction center complex / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (phototrophic)
Strain: ATCC BAA-98 / CGA009
Molecular weightTheoretical: 27.268223 KDa
SequenceString: MQPGAYLDLA QVTLYVFWIF FAGLLFYLRR EDKREGYPLV ADAGSGTRLA KIGVPAPPDP KTYLLRGGAT KTVPSTSNDR PNVALTPAA PWPGAPFVPT GNPFADGVGP GSYAQRADVP ELGLDNLPII VPLRAAKGMF LDPRDPNPVG MPVVGCDGVV G GTVTEVWV ...String:
MQPGAYLDLA QVTLYVFWIF FAGLLFYLRR EDKREGYPLV ADAGSGTRLA KIGVPAPPDP KTYLLRGGAT KTVPSTSNDR PNVALTPAA PWPGAPFVPT GNPFADGVGP GSYAQRADVP ELGLDNLPII VPLRAAKGMF LDPRDPNPVG MPVVGCDGVV G GTVTEVWV DRAEVLARYL EVEVAKSRKR VLLPVPFALI NDPFGKVSVD AIRGDQFAGV PTTSKGDQVS KLEEDKICAY YG AGTLYAT PLRSESLV

UniProtKB: H subunit of photosynthetic reaction center complex

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Macromolecule #4: Reaction center protein L chain

MacromoleculeName: Reaction center protein L chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (phototrophic)
Strain: ATCC BAA-98 / CGA009
Molecular weightTheoretical: 30.857777 KDa
SequenceString: MAMLSFEKKY RVRGGTLIGG DLFDFWVGPF YVGIFGVMTV FFALIGIALI AWNTALGPTW NLWQISVNPP DAKYGLGFAP LAEGGIWQW VSICATGAFV TWALREVEIC RKLGIGFHVP FAFSFAIFAY VTLVVIRPVL MGSWSYGFPY GIFTHLDWVS N TGYSYGQF ...String:
MAMLSFEKKY RVRGGTLIGG DLFDFWVGPF YVGIFGVMTV FFALIGIALI AWNTALGPTW NLWQISVNPP DAKYGLGFAP LAEGGIWQW VSICATGAFV TWALREVEIC RKLGIGFHVP FAFSFAIFAY VTLVVIRPVL MGSWSYGFPY GIFTHLDWVS N TGYSYGQF HYNPAHMIAI TFFFTTCLAL ALHGGLVLSA LNPDRGEPVK SPEHENTVFR DLVGYSIGTI GIHRLGLFLA LS AVFFSAV CMIISGPVLA EGGSWPDWWN WWRNLPIWNP

UniProtKB: Reaction center protein L chain

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Macromolecule #5: Reaction center protein M chain

MacromoleculeName: Reaction center protein M chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (phototrophic)
Strain: ATCC BAA-98 / CGA009
Molecular weightTheoretical: 34.453828 KDa
SequenceString: MAQYQNIFTQ VQVEGPAYAG VPLRPGSSPR ETQTTFNYWL GKIGDAQVGP VYLGFTGVCS LLCGFVAIEI IGLNMLASVD WSPIEFLRQ FCWLALEPPK PEYGLTIPPL KEGGWWLMAG FFLTVSIALW WVRTYRRSRA LGMGTHVSWA FASAILLYLA L GFIQPLLM ...String:
MAQYQNIFTQ VQVEGPAYAG VPLRPGSSPR ETQTTFNYWL GKIGDAQVGP VYLGFTGVCS LLCGFVAIEI IGLNMLASVD WSPIEFLRQ FCWLALEPPK PEYGLTIPPL KEGGWWLMAG FFLTVSIALW WVRTYRRSRA LGMGTHVSWA FASAILLYLA L GFIQPLLM GSWSEAPPFG VFPHLDWTNN FSIKYGNLYY NPFHCLSIAF LYGSALLFAM HGATILAVSR YGGEREIEQM LD RGTALER AALFWRWTMG FNATAESIHR WAWWFAVLCP LTGAIGIILT GPVVDNWFDW GVKHGLAPPR

UniProtKB: Reaction center protein M chain

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Macromolecule #6: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 6 / Number of copies: 36 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

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Macromolecule #7: SPIRILLOXANTHIN

MacromoleculeName: SPIRILLOXANTHIN / type: ligand / ID: 7 / Number of copies: 16 / Formula: CRT
Molecular weightTheoretical: 596.925 Da
Chemical component information

ChemComp-CRT:
SPIRILLOXANTHIN

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Macromolecule #8: (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-...

MacromoleculeName: (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
type: ligand / ID: 8 / Number of copies: 24 / Formula: 6PL
Molecular weightTheoretical: 763.1 Da
Chemical component information

ChemComp-6PL:
(4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE / phospholipid*YM

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Macromolecule #9: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 9 / Number of copies: 6 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #10: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 10 / Number of copies: 12 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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Macromolecule #11: BACTERIOPHEOPHYTIN A

MacromoleculeName: BACTERIOPHEOPHYTIN A / type: ligand / ID: 11 / Number of copies: 2 / Formula: BPH
Molecular weightTheoretical: 889.215 Da
Chemical component information

ChemComp-BPH:
BACTERIOPHEOPHYTIN A

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Macromolecule #12: UBIQUINONE-10

MacromoleculeName: UBIQUINONE-10 / type: ligand / ID: 12 / Number of copies: 5 / Formula: U10
Molecular weightTheoretical: 863.343 Da
Chemical component information

ChemComp-U10:
UBIQUINONE-10

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Macromolecule #13: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 13 / Number of copies: 1 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #14: (6~{R},10~{S},14~{R},19~{R},23~{S},24~{E},27~{S},28~{E})-2,6,10,1...

MacromoleculeName: (6~{R},10~{S},14~{R},19~{R},23~{S},24~{E},27~{S},28~{E})-2,6,10,14,19,23,27,31-octamethyldotriaconta-24,28-dien-2-ol
type: ligand / ID: 14 / Number of copies: 1 / Formula: QAK
Molecular weightTheoretical: 575.047 Da
Chemical component information

ChemComp-QAK:
(6~{R},10~{S},14~{R},19~{R},23~{S},24~{E},27~{S},28~{E})-2,6,10,14,19,23,27,31-octamethyldotriaconta-24,28-dien-2-ol

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Macromolecule #15: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...

MacromoleculeName: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
type: ligand / ID: 15 / Number of copies: 2 / Formula: PGT
Molecular weightTheoretical: 751.023 Da
Chemical component information

ChemComp-PGT:
(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / phospholipid*YM

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Macromolecule #16: water

MacromoleculeName: water / type: ligand / ID: 16 / Number of copies: 3 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
200.0 mMNaClNaCl
0.03 % w/vC24H46O11n-Dodecyl-beta-D-Maltopyranoside
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 60 % / Chamber temperature: 298 K / Instrument: LEICA EM GP
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 55.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 476547 / Details: Autopicked in RELION
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 260752
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: BACKBONE TRACE
Output model

PDB-6z5r:
RC-LH1(16) complex from Rhodopseudomonas palustris

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