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- EMDB-32100: STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF Allochromatiu... -

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Entry
Database: EMDB / ID: EMD-32100
TitleSTRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF Allochromatium tepidum
Map data
Sample
  • Complex: Photosynthetic LH1-RC complex from the purple phototrophic bacterium Allochromatium tepidum
    • Protein or peptide: x 9 types
  • Ligand: x 16 types
Biological speciesAllochromatium tepidum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsTani K / Kobayashi K / Hosogi N / Ji X-C / Nagashima S / Nagashima KVP / Tsukatani Y / Kanno R / Hall M / Yu L-J ...Tani K / Kobayashi K / Hosogi N / Ji X-C / Nagashima S / Nagashima KVP / Tsukatani Y / Kanno R / Hall M / Yu L-J / Ishikawa I / Okura Y / Madigan MT / Mizoguchi A / Humbel BM / Kimura Y / Wang-Otomo Z-Y
Funding support Japan, 6 items
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: J Biol Chem / Year: 2022
Title: A Ca-binding motif underlies the unusual properties of certain photosynthetic bacterial core light-harvesting complexes.
Authors: Kazutoshi Tani / Kazumi Kobayashi / Naoki Hosogi / Xuan-Cheng Ji / Sakiko Nagashima / Kenji V P Nagashima / Airi Izumida / Kazuhito Inoue / Yusuke Tsukatani / Ryo Kanno / Malgorzata Hall / ...Authors: Kazutoshi Tani / Kazumi Kobayashi / Naoki Hosogi / Xuan-Cheng Ji / Sakiko Nagashima / Kenji V P Nagashima / Airi Izumida / Kazuhito Inoue / Yusuke Tsukatani / Ryo Kanno / Malgorzata Hall / Long-Jiang Yu / Isamu Ishikawa / Yoshihiro Okura / Michael T Madigan / Akira Mizoguchi / Bruno M Humbel / Yukihiro Kimura / Zheng-Yu Wang-Otomo /
Abstract: The mildly thermophilic purple phototrophic bacterium Allochromatium tepidum provides a unique model for investigating various intermediate phenotypes observed between those of thermophilic and ...The mildly thermophilic purple phototrophic bacterium Allochromatium tepidum provides a unique model for investigating various intermediate phenotypes observed between those of thermophilic and mesophilic counterparts. The core light-harvesting (LH1) complex from A. tepidum exhibits an absorption maximum at 890 nm and mildly enhanced thermostability, both of which are Ca-dependent. However, it is unknown what structural determinants might contribute to these properties. Here, we present a cryo-EM structure of the reaction center-associated LH1 complex at 2.81 Å resolution, in which we identify multiple pigment-binding α- and β-polypeptides within an LH1 ring. Of the 16 α-polypeptides, we show that six (α1) bind Ca along with β1- or β3-polypeptides to form the Ca-binding sites. This structure differs from that of fully Ca-bound LH1 from Thermochromatium tepidum, enabling determination of the minimum structural requirements for Ca-binding. We also identified three amino acids (Trp44, Asp47, and Ile49) in the C-terminal region of the A. tepidum α1-polypeptide that ligate each Ca ion, forming a Ca-binding WxxDxI motif that is conserved in all Ca-bound LH1 α-polypeptides from other species with reported structures. The partial Ca-bound structure further explains the unusual phenotypic properties observed for this bacterium in terms of its Ca-requirements for thermostability, spectroscopy, and phototrophic growth, and supports the hypothesis that A. tepidum may represent a "transitional" species between mesophilic and thermophilic purple sulfur bacteria. The characteristic arrangement of multiple αβ-polypeptides also suggests a mechanism of molecular recognition in the expression and/or assembly of the LH1 complex that could be regulated through interactions with reaction center subunits.
History
DepositionOct 23, 2021-
Header (metadata) releaseMay 4, 2022-
Map releaseMay 4, 2022-
UpdateJun 8, 2022-
Current statusJun 8, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32100.png

Downloads & links

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Map

FileDownload / File: emd_32100.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.)
0.81 Å/pix.
x 400 pix.
= 325.6 Å		0.81 Å/pix.
x 400 pix.
= 325.6 Å		0.81 Å/pix.
x 400 pix.
= 325.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.814 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0134
Minimum - Maximum-0.05139761 - 0.10136426
Average (Standard dev.)6.802941e-05 (±0.002903585)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 325.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Photosynthetic LH1-RC complex from the purple phototrophic bacter...

EntireName: Photosynthetic LH1-RC complex from the purple phototrophic bacterium Allochromatium tepidum
Components
  • Complex: Photosynthetic LH1-RC complex from the purple phototrophic bacterium Allochromatium tepidum
    • Protein or peptide: Photosynthetic reaction center cytochrome c subunit
    • Protein or peptide: Photosynthetic reaction center L subunit
    • Protein or peptide: Photosynthetic reaction center M subunit
    • Protein or peptide: Photosynthetic reaction center H subunit
    • Protein or peptide: Light-harvesting protein LH1 alpha2
    • Protein or peptide: Light-harvesting protein LH1 beta1
    • Protein or peptide: Light-harvesting protein LH1 alpha1
    • Protein or peptide: Light-harvesting protein LH1 beta3
    • Protein or peptide: Light-harvesting protein LH1 alpha3
  • Ligand: HEME C
  • Ligand: MAGNESIUM ION
  • Ligand: DIACYL GLYCEROL
  • Ligand: PALMITIC ACID
  • Ligand: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: BACTERIOPHEOPHYTIN A
  • Ligand: Ubiquinone-8
  • Ligand: CARDIOLIPIN
  • Ligand: FE (III) ION
  • Ligand: MENAQUINONE 8
  • Ligand: SPIRILLOXANTHIN
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: CALCIUM ION
  • Ligand: LAURYL DIMETHYLAMINE-N-OXIDE
  • Ligand: water

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Supramolecule #1: Photosynthetic LH1-RC complex from the purple phototrophic bacter...

SupramoleculeName: Photosynthetic LH1-RC complex from the purple phototrophic bacterium Allochromatium tepidum
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Allochromatium tepidum (bacteria)

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Macromolecule #1: Photosynthetic reaction center cytochrome c subunit

MacromoleculeName: Photosynthetic reaction center cytochrome c subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Allochromatium tepidum (bacteria)
Molecular weightTheoretical: 43.659016 KDa
SequenceString: MNLGKQLTLP AVAVVASVVL LGCERPPPEV VQKGYRGVAM EQNYNPRLLE ASLKQNLPVE SLPAAAPGGP KVSDVYQNVQ VLKDLSVAE FTRTMVAVTT WVSPKEGCNY CHVPGNWASD DIYTKVVSRR MFEMVRAANS DWKQHVAVNG TGVTCYTCHR G NPVPKYVW ...String:
MNLGKQLTLP AVAVVASVVL LGCERPPPEV VQKGYRGVAM EQNYNPRLLE ASLKQNLPVE SLPAAAPGGP KVSDVYQNVQ VLKDLSVAE FTRTMVAVTT WVSPKEGCNY CHVPGNWASD DIYTKVVSRR MFEMVRAANS DWKQHVAVNG TGVTCYTCHR G NPVPKYVW VTDPGPNQPS GVKPTGQNYA SSTVAYAALP FDPYTPFLDQ TNEIRVIGQT ALPAGNTTSL KQAEWTYGLM MQ ISDSLGV NCTFCHNSRA FYDWKQSTPQ RTTAWYAIRH VRDINQNYIW PLNDVLPASR KGPYGDPFKV GCMTCHQGAY RPL YGAQMA KDYPALYASA PAEAEVAAPA EAAPVEDVAA APVEEAAPAE AASAEEAPAA EEVAPAPVEE APAAEAAPVE DAAP APQQL

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Macromolecule #2: Photosynthetic reaction center L subunit

MacromoleculeName: Photosynthetic reaction center L subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Allochromatium tepidum (bacteria)
Molecular weightTheoretical: 31.098203 KDa
SequenceString: AMLSFERKYR VRGGTLIGGD LFDFWVGPFY VGFFGVTGFF FALLGVLLIV WGATIGPNAE LQTYNIWQIS IAPPDLSYGL GMAPLTEGG LWQIITICAI GAFVSWALRE VEICRKLGIG FHIPFAFAFA IGAYLVLVVV RPILMGAWGH GFPYGILSHL D WVSNVGYQ ...String:
AMLSFERKYR VRGGTLIGGD LFDFWVGPFY VGFFGVTGFF FALLGVLLIV WGATIGPNAE LQTYNIWQIS IAPPDLSYGL GMAPLTEGG LWQIITICAI GAFVSWALRE VEICRKLGIG FHIPFAFAFA IGAYLVLVVV RPILMGAWGH GFPYGILSHL D WVSNVGYQ FLHFHYNPAH MLAITFFFTN CLALSMHGSL ILSVTNPQKG EEVKTSEHEN TFFRDIVGYS IGALAIHRLG LF LALSAVF WSAVCIVISG PFWTRGWPEW WNWWLELPLW

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Macromolecule #3: Photosynthetic reaction center M subunit

MacromoleculeName: Photosynthetic reaction center M subunit / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Allochromatium tepidum (bacteria)
Molecular weightTheoretical: 36.292117 KDa
SequenceString: PEYQNIFTAV QVRAPAYPGV PLPKGHLPRI GRPIFSYWLG KIGDAQIGPI YLGFTGTLSI IFGFIAIFII GFNMLASVDW NIIQFVKHF FWLGLEPPAP QYGLSIPPLS EGGWWLMAGF FLTMSIILWW VRTYKRAEAL GMSQHLSWAF AAAIFFYLSL G FIRPVMMG ...String:
PEYQNIFTAV QVRAPAYPGV PLPKGHLPRI GRPIFSYWLG KIGDAQIGPI YLGFTGTLSI IFGFIAIFII GFNMLASVDW NIIQFVKHF FWLGLEPPAP QYGLSIPPLS EGGWWLMAGF FLTMSIILWW VRTYKRAEAL GMSQHLSWAF AAAIFFYLSL G FIRPVMMG SWAEAVPFGI FPHLDWTAAF SIRYGNLYYN PFHMLSIAFL YGSALLFAMH GATILAVSRF GGDREIDQIT DR GTAAERA AIFWRWTMGF NASMESIHRW AWWCAVLTVI TAGIGILLTG TVVENWYLWA IKHGVAPAYP EVVTAVDPYA TAT GVTQ

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Macromolecule #4: Photosynthetic reaction center H subunit

MacromoleculeName: Photosynthetic reaction center H subunit / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Allochromatium tepidum (bacteria)
Molecular weightTheoretical: 28.19634 KDa
SequenceString: MSAAITEYMD VAQLTIWAFW FFFAGLIIYL RREDKREGYP LDSDRTERSG GRVKVVGFPD LADPKTFVLP HNAGTVMAPR VEAPTSINA TPVAPFPGAP FEPNGDPMLS GFGPAASPDR AKHCDLTFEG LPKIVPMRVA TDFSIADKDP DPRGMTVVGL D GEVAGTIS ...String:
MSAAITEYMD VAQLTIWAFW FFFAGLIIYL RREDKREGYP LDSDRTERSG GRVKVVGFPD LADPKTFVLP HNAGTVMAPR VEAPTSINA TPVAPFPGAP FEPNGDPMLS GFGPAASPDR AKHCDLTFEG LPKIVPMRVA TDFSIADKDP DPRGMTVVGL D GEVAGTIS DIWVDRSEPQ IRYLEVDVSA TKKKVLLPIG FSRFDKKAGK VKVAAIKAAH FANVPALSKP DQITLYEEDK VC AYYAGGK LYATAERAGP LL

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Macromolecule #5: Light-harvesting protein LH1 alpha2

MacromoleculeName: Light-harvesting protein LH1 alpha2 / type: protein_or_peptide / ID: 5 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Allochromatium tepidum (bacteria)
Molecular weightTheoretical: 5.136131 KDa
SequenceString:
(FME)HKIWQIFDP RRTLVALFGF LFVLGLLIHF ILLSSPAFNW LSGS

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Macromolecule #6: Light-harvesting protein LH1 beta1

MacromoleculeName: Light-harvesting protein LH1 beta1 / type: protein_or_peptide / ID: 6 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Allochromatium tepidum (bacteria)
Molecular weightTheoretical: 5.269103 KDa
SequenceString:
MANSSMTGLT EQEAQEFHGI FVQSMTAFFG IVVIAHILAW LWRPWL

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Macromolecule #7: Light-harvesting protein LH1 alpha1

MacromoleculeName: Light-harvesting protein LH1 alpha1 / type: protein_or_peptide / ID: 7 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Allochromatium tepidum (bacteria)
Molecular weightTheoretical: 7.330739 KDa
SequenceString:
(FME)SPDLWKIWL LIDPRRVLIA VFAFLTILGL AIHMILLSTT EFNWLEDGIP AAKVQQVTPV VPQR

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Macromolecule #8: Light-harvesting protein LH1 beta3

MacromoleculeName: Light-harvesting protein LH1 beta3 / type: protein_or_peptide / ID: 8 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Allochromatium tepidum (bacteria)
Molecular weightTheoretical: 5.504446 KDa
SequenceString:
MADQKSMTGL TEDEAKEFHG IFTQSMTMFF GIVIIAHILA WLWRPWL

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Macromolecule #9: Light-harvesting protein LH1 alpha3

MacromoleculeName: Light-harvesting protein LH1 alpha3 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Allochromatium tepidum (bacteria)
Molecular weightTheoretical: 7.323753 KDa
SequenceString:
MMPQQLYKIW LAFDPRMALI GLGAFLFALA LFIHYMLLSS PGFDWLLGPD HAPVALSAGM SALPAGR

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Macromolecule #10: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 10 / Number of copies: 4 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

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Macromolecule #11: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 11 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #12: DIACYL GLYCEROL

MacromoleculeName: DIACYL GLYCEROL / type: ligand / ID: 12 / Number of copies: 1 / Formula: DGA
Molecular weightTheoretical: 625.018 Da
Chemical component information

ChemComp-DGA:
DIACYL GLYCEROL

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Macromolecule #13: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 13 / Number of copies: 1 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #14: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...

MacromoleculeName: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
type: ligand / ID: 14 / Number of copies: 12 / Formula: PGV
Molecular weightTheoretical: 749.007 Da
Chemical component information

ChemComp-PGV:
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / phospholipid*YM

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Macromolecule #15: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 15 / Number of copies: 36 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

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Macromolecule #16: BACTERIOPHEOPHYTIN A

MacromoleculeName: BACTERIOPHEOPHYTIN A / type: ligand / ID: 16 / Number of copies: 2 / Formula: BPH
Molecular weightTheoretical: 889.215 Da
Chemical component information

ChemComp-BPH:
BACTERIOPHEOPHYTIN A

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Macromolecule #17: Ubiquinone-8

MacromoleculeName: Ubiquinone-8 / type: ligand / ID: 17 / Number of copies: 3 / Formula: UQ8
Molecular weightTheoretical: 727.109 Da
Chemical component information

ChemComp-UQ8:
Ubiquinone-8

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Macromolecule #18: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 18 / Number of copies: 8 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #19: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 19 / Number of copies: 1 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #20: MENAQUINONE 8

MacromoleculeName: MENAQUINONE 8 / type: ligand / ID: 20 / Number of copies: 2 / Formula: MQ8
Molecular weightTheoretical: 717.116 Da
Chemical component information

ChemComp-MQ8:
MENAQUINONE 8

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Macromolecule #21: SPIRILLOXANTHIN

MacromoleculeName: SPIRILLOXANTHIN / type: ligand / ID: 21 / Number of copies: 17 / Formula: CRT
Molecular weightTheoretical: 596.925 Da
Chemical component information

ChemComp-CRT:
SPIRILLOXANTHIN

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Macromolecule #22: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 22 / Number of copies: 18 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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Macromolecule #23: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 23 / Number of copies: 6 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #24: LAURYL DIMETHYLAMINE-N-OXIDE

MacromoleculeName: LAURYL DIMETHYLAMINE-N-OXIDE / type: ligand / ID: 24 / Number of copies: 2 / Formula: LDA
Molecular weightTheoretical: 229.402 Da
Chemical component information

ChemComp-LDA:
LAURYL DIMETHYLAMINE-N-OXIDE / LDAO, detergent*YM

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Macromolecule #25: water

MacromoleculeName: water / type: ligand / ID: 25 / Number of copies: 48 / 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

Concentration3.0 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: LEICA EM GP
DetailsThis sample was monodisperse.

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Average exposure time: 1.5 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: JEOL / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 309706
CTF correctionSoftware - Name: CTFFIND
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 156992
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 4 / Avg.num./class: 158474 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5y5s

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 62 / Target criteria: Correlation coefficient
Output model

PDB-7vrj:
STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF Allochromatium tepidum

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