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- EMDB-39836: Photosynthetic LH1-RC-HiPIP complex from the purple bacterium Hal... -

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Basic information

Entry
Database: EMDB / ID: EMD-39836
TitlePhotosynthetic LH1-RC-HiPIP complex from the purple bacterium Halorhodospira halophila
Map datafull map
Sample
  • Complex: Photosynthetic LH1-RC-HiPIP triple complex from the purple phototrophic bacterium Halorhodospira halophila
    • Complex: LH1-RC-HiPIP complex of Halorhodospira halophila
      • Protein or peptide: x 9 types
  • Ligand: x 15 types
KeywordsLH1-RC / PHOTOSYNTHESIS
Function / homology
Function and homology information


organelle inner membrane / aerobic electron transport chain / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / endomembrane system / 4 iron, 4 sulfur cluster binding / electron transfer activity ...organelle inner membrane / aerobic electron transport chain / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / endomembrane system / 4 iron, 4 sulfur cluster binding / electron transfer activity / iron ion binding / heme binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
High potential iron-sulfur protein / High potential iron-sulphur protein / High potential iron-sulphur protein superfamily / High potential iron-sulfur proteins family profile. / Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit ...High potential iron-sulfur protein / High potential iron-sulphur protein / High potential iron-sulphur protein superfamily / High potential iron-sulfur proteins family profile. / Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / 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, H subunit, N-terminal / PRC-barrel domain / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / Photosynthetic reaction centre, M subunit / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / Multiheme cytochrome superfamily / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Reaction center protein L chain / Reaction center protein M chain / Antenna complex, alpha/beta subunit / Antenna complex, alpha/beta subunit / Photosynthetic reaction center cytochrome c subunit / Antenna complex, alpha/beta subunit / Antenna complex, alpha/beta subunit / High-potential iron-sulfur protein / Photosynthetic reaction centre, H-chain
Similarity search - Component
Biological speciesHalorhodospira halophila (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsTani K / Kanno R / Nagashima KVP / Hiwatashi N / Kawakami M / Nakata K / Nagashima S / Inoue K / Takaichi S / Purba ER ...Tani K / Kanno R / Nagashima KVP / Hiwatashi N / Kawakami M / Nakata K / Nagashima S / Inoue K / Takaichi S / Purba ER / Hall M / Yu L-J / 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: Commun Biol / Year: 2025
Title: A Native LH1-RC-HiPIP Supercomplex from an Extremophilic Phototroph.
Authors: Kazutoshi Tani / Ryo Kanno / Kenji V P Nagashima / Mai Kawakami / Naho Hiwatashi / Kazuna Nakata / Sakiko Nagashima / Kazuhito Inoue / Shinichi Takaichi / Endang R Purba / Malgorzata Hall / ...Authors: Kazutoshi Tani / Ryo Kanno / Kenji V P Nagashima / Mai Kawakami / Naho Hiwatashi / Kazuna Nakata / Sakiko Nagashima / Kazuhito Inoue / Shinichi Takaichi / Endang R Purba / Malgorzata Hall / Long-Jiang Yu / Michael T Madigan / Akira Mizoguchi / Bruno M Humbel / Yukihiro Kimura / Zheng-Yu Wang-Otomo /
Abstract: Halorhodospira (Hlr.) halophila strain BN9622 is an extremely halophilic and alkaliphilic purple phototrophic bacterium and has been widely used as a model for exploring the osmoadaptive and ...Halorhodospira (Hlr.) halophila strain BN9622 is an extremely halophilic and alkaliphilic purple phototrophic bacterium and has been widely used as a model for exploring the osmoadaptive and photosynthetic strategies employed by phototrophic extreme halophiles that enable them to thrive in hypersaline environments. Here we present the cryo-EM structures of (1) a unique native Hlr. halophila triple-complex formed from light-harvesting (LH1), the reaction center (RC), and high-potential iron-sulfur protein (HiPIP) at 2.44 Å resolution, and (2) a HiPIP-free LH1-RC complex at 2.64 Å resolution. Differing from the LH1 in the Hlr. halophila LH1-LH2 co-complex where LH1 encircles LH2, the RC-associated LH1 complex consists of 16 (rather than 18) αβ-subunits circularly surrounding the RC. These distinct forms of LH1 indicate that the number of subunits in a Hlr. halophila LH1 complex is flexible and its size is a function of the photocomplex it encircles. Like LH1 in the LH1-LH2 co-complex, the RC-associated LH1 complex also contained two forms of αβ-polypeptides and both dimeric and monomeric molecules of bacteriochlorophyll a. The majority of the isolated Hlr. halophila LH1-RC complexes contained the electron donor HiPIP bound to the surface of the RC cytochrome subunit near the heme-1 group. The bound HiPIP consisted of an N-terminal functional domain and a long C-terminal extension firmly attached to the cytochrome subunit. Despite overall highly negative surface-charge distributions for both the cytochrome subunit and HiPIP, the interface between the two proteins was relatively uncharged and neutral, forming a pathway for electron tunneling. The structure of the Hlr. halophila LH1-RC-HiPIP complex provides insights into the mechanism of light energy acquisition coupled with a long-distance electron donating process toward the charge separation site in a multi-extremophilic phototroph.
History
DepositionApr 21, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39836.png

Downloads & links

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Map

FileDownload / File: emd_39836.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 400 pix.
= 328. Å		0.82 Å/pix.
x 400 pix.
= 328. Å		0.82 Å/pix.
x 400 pix.
= 328. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.09817035 - 0.21328956
Average (Standard dev.)0.000083308594 (±0.008415245)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 328.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: odd-half map

Fileemd_39836_half_map_1.map
Annotationodd-half map
Projections & Slices
AxesZYX

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Slices (1/2)
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Half map: even-half map

Fileemd_39836_half_map_2.map
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Sample components

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Entire : Photosynthetic LH1-RC-HiPIP triple complex from the purple photot...

EntireName: Photosynthetic LH1-RC-HiPIP triple complex from the purple phototrophic bacterium Halorhodospira halophila
Components
  • Complex: Photosynthetic LH1-RC-HiPIP triple complex from the purple phototrophic bacterium Halorhodospira halophila
    • Complex: LH1-RC-HiPIP complex of Halorhodospira halophila
      • Protein or peptide: Photosynthetic reaction center cytochrome c subunit
      • Protein or peptide: Reaction center protein L chain
      • Protein or peptide: Reaction center protein M chain
      • Protein or peptide: Photosynthetic reaction centre, H-chain
      • Protein or peptide: Antenna complex, alpha/beta subunit
      • Protein or peptide: Antenna complex, alpha/beta subunit
      • Protein or peptide: Antenna complex, alpha/beta subunit
      • Protein or peptide: Antenna complex, alpha/beta subunit
      • Protein or peptide: High-potential iron-sulfur protein
  • Ligand: HEME C
  • Ligand: MAGNESIUM ION
  • Ligand: [(2~{S})-1-dodecanoyloxy-3-oxidanyl-propan-2-yl] pentadecanoate
  • Ligand: PALMITIC ACID
  • Ligand: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: BACTERIOPHEOPHYTIN A
  • Ligand: Ubiquinone-8
  • Ligand: FE (III) ION
  • Ligand: CARDIOLIPIN
  • Ligand: MENAQUINONE 8
  • Ligand: SPIRILLOXANTHIN
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: water

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Supramolecule #1: Photosynthetic LH1-RC-HiPIP triple complex from the purple photot...

SupramoleculeName: Photosynthetic LH1-RC-HiPIP triple complex from the purple phototrophic bacterium Halorhodospira halophila
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Halorhodospira halophila (bacteria) / Strain: BN9622

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Supramolecule #2: LH1-RC-HiPIP complex of Halorhodospira halophila

SupramoleculeName: LH1-RC-HiPIP complex of Halorhodospira halophila / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#5, #7-#8, #6, #9
Source (natural)Organism: Halorhodospira halophila (bacteria) / Strain: BN9622

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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: Halorhodospira halophila (bacteria) / Strain: BN9622
Molecular weightTheoretical: 40.439383 KDa
SequenceString: MSSKMYLNRS LAVGALSAGL AVVVGCERPP VDTEQKGYRG TGMEEVNNPR LRDDDLHLAP EAADPVSAEG PRAGEIYQNV EVLDDLSVA EFTRLMQSMT DWVSPDEGCT YCHDGNDFAS EELYTYQVSR QMIEMNRYVN ANWDSHMDDT GVTCYTCHRG E NLPEESWF ...String:
MSSKMYLNRS LAVGALSAGL AVVVGCERPP VDTEQKGYRG TGMEEVNNPR LRDDDLHLAP EAADPVSAEG PRAGEIYQNV EVLDDLSVA EFTRLMQSMT DWVSPDEGCT YCHDGNDFAS EELYTYQVSR QMIEMNRYVN ANWDSHMDDT GVTCYTCHRG E NLPEESWF AEPTPDVNMA GLGNTMMQNL ASEKTEYTSL PRNAFERYLL GHDDLRVEGD TILPHLDEWD VSLQDTEASY SL MMHMSAA TGSNCTTCHN TGRLGQWDES PEEREISWHG IRMTRDINAN WIEPLEAGQP EVRLGPTGDI AKVQCATCHY GEQ LPLDGA KMVDDYPGLM GEEDADFDFL QFGDLGTDGL RDRNAE

UniProtKB: Photosynthetic reaction center cytochrome c subunit

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Macromolecule #2: Reaction center protein L chain

MacromoleculeName: Reaction center protein L chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Halorhodospira halophila (bacteria) / Strain: BN9622
Molecular weightTheoretical: 30.718809 KDa
SequenceString: MAMLDFEKKY RVRGGTLLGG DLFDFWIGPF YVGIFGVLTA IFAVLGTVLI IYGASQDTFN LWQISIAPPD LSYGLALAPM MEGGLWQII TVCALGAFIT WALRQAEISK KLGMGYHVPV AFAVAILAYA TLVVFRPLLM GAWGHGFPYG ILSHLDWVSN V GYQYLHFH ...String:
MAMLDFEKKY RVRGGTLLGG DLFDFWIGPF YVGIFGVLTA IFAVLGTVLI IYGASQDTFN LWQISIAPPD LSYGLALAPM MEGGLWQII TVCALGAFIT WALRQAEISK KLGMGYHVPV AFAVAILAYA TLVVFRPLLM GAWGHGFPYG ILSHLDWVSN V GYQYLHFH YNPAHMLAVT FFFTTTLALA LHGGLILSVT NPKKGEPVKT AEHENTFFRD VIGYSIGSLG IHRLGLFLAL NA GFWSAVC IIISGPFWTR GWPEWWNWWL NVPIWSWGG

UniProtKB: Reaction center protein L chain

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Macromolecule #3: Reaction center protein M chain

MacromoleculeName: Reaction center protein M chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Halorhodospira halophila (bacteria) / Strain: BN9622
Molecular weightTheoretical: 35.925391 KDa
SequenceString: MAEYQNIFTR VQVRGPTDPG VELPAADWPR TKGATHSWLL GKIGDAQVGP IYLGTTGVMS ILFGIVSIVI IGMNMLASVD WSPLEFIRQ FFWVALEPPP PEYGLSLPPL NDGGWWLIAG FTLTLSVLLW FARTYNRARA LGLGTHVAWA FAAAIFLFLA I GFIWPVLM ...String:
MAEYQNIFTR VQVRGPTDPG VELPAADWPR TKGATHSWLL GKIGDAQVGP IYLGTTGVMS ILFGIVSIVI IGMNMLASVD WSPLEFIRQ FFWVALEPPP PEYGLSLPPL NDGGWWLIAG FTLTLSVLLW FARTYNRARA LGLGTHVAWA FAAAIFLFLA I GFIWPVLM GSWAKSVPFG IFPHLDWTTA FSLRYGNLYY NPFHMLSIVF LFGSALLFAM HGATILAAGR YNAEREIEQI TD RGTAAER SALFWRWTMG FNATMESIHR WGYWFAILCV ITGGIGILLT GTVVENWYLW GVHHGIAPEY PEFFTPAVDP AAG GTE

UniProtKB: Reaction center protein M chain

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Macromolecule #4: Photosynthetic reaction centre, H-chain

MacromoleculeName: Photosynthetic reaction centre, H-chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Halorhodospira halophila (bacteria) / Strain: BN9622
Molecular weightTheoretical: 30.904004 KDa
SequenceString: MEGTGALTDY MNVAQMTLYA FWLFLAGLIV YLRMEDKREG YPLQAEANEN CNRTPEKKLG FPAPPSPKVF KLADGRSIQV PRAEKTDYE LNTQLRAEPT APWDGAPLEP TGNPMVDGLG PAAWAKREDE PEVTHGGKQK ICPLRVATEF EVGMSRDVAR F WPEIDPDP ...String:
MEGTGALTDY MNVAQMTLYA FWLFLAGLIV YLRMEDKREG YPLQAEANEN CNRTPEKKLG FPAPPSPKVF KLADGRSIQV PRAEKTDYE LNTQLRAEPT APWDGAPLEP TGNPMVDGLG PAAWAKREDE PEVTHGGKQK ICPLRVATEF EVGMSRDVAR F WPEIDPDP RGYQVLGCDG KVAGKIVDIW VDRGELRPMY LEMDLSGVGS SGDRVLLPIN FARVGYDSKV RVNAITGQQF TD VPRLREA DRISPQEEDF ITGYFGGGVL YAVPGRTEPF L

UniProtKB: Photosynthetic reaction centre, H-chain

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Macromolecule #5: Antenna complex, alpha/beta subunit

MacromoleculeName: Antenna complex, alpha/beta subunit / type: protein_or_peptide / ID: 5 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Halorhodospira halophila (bacteria) / Strain: BN9622
Molecular weightTheoretical: 7.2755 KDa
SequenceString:
MWRLWKLYDP RRVLIGIFSW LAVLALVIHF ILLSTDRFNW VGGAAVSSVS ESAEEVSALP PRQV

UniProtKB: Antenna complex, alpha/beta subunit

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Macromolecule #6: Antenna complex, alpha/beta subunit

MacromoleculeName: Antenna complex, alpha/beta subunit / type: protein_or_peptide / ID: 6 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Halorhodospira halophila (bacteria) / Strain: BN9622
Molecular weightTheoretical: 8.068154 KDa
SequenceString:
MADNMSLTGL SDEEAKEFHS IFMQSFLIFT AVAVVAHFLA WAWRPWIPGA EGYGSVIEGV HNVTAAVSQI APLAG

UniProtKB: Antenna complex, alpha/beta subunit

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Macromolecule #7: Antenna complex, alpha/beta subunit

MacromoleculeName: Antenna complex, alpha/beta subunit / type: protein_or_peptide / ID: 7 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Halorhodospira halophila (bacteria) / Strain: BN9622
Molecular weightTheoretical: 7.664882 KDa
SequenceString:
MWRMWKILDY RRTVVLAHVG MAVLALLIHF ILLSTENFNW LQGNPYGDAE SAAEVADAAV MPQQREV

UniProtKB: Antenna complex, alpha/beta subunit

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Macromolecule #8: Antenna complex, alpha/beta subunit

MacromoleculeName: Antenna complex, alpha/beta subunit / type: protein_or_peptide / ID: 8 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Halorhodospira halophila (bacteria) / Strain: BN9622
Molecular weightTheoretical: 7.893913 KDa
SequenceString:
MADEMRNVSD EEAKEFHAMF SQAFTVYIGV AVVAHILAWA WRPWIPGDEG FGAALIEGAN AVTAAVQSIA PIAA

UniProtKB: Antenna complex, alpha/beta subunit

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Macromolecule #9: High-potential iron-sulfur protein

MacromoleculeName: High-potential iron-sulfur protein / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Halorhodospira halophila (bacteria) / Strain: BN9622
Molecular weightTheoretical: 15.763442 KDa
SequenceString:
MSKKPCDRSR RKFLRLGLMS TAAIPAASLF GSKAMADDNN NGNDRTWEII SEDAPEAKGI GYVHNQADAD MDHPRFESHQ FCANCLLYV PHEEDGDHGY CAAFGMDEKR LVNANGWCWA WEDAGDAAEV GPRDVPADQL RRG

UniProtKB: High-potential iron-sulfur protein

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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: [(2~{S})-1-dodecanoyloxy-3-oxidanyl-propan-2-yl] pentadecanoate

MacromoleculeName: [(2~{S})-1-dodecanoyloxy-3-oxidanyl-propan-2-yl] pentadecanoate
type: ligand / ID: 12 / Number of copies: 1 / Formula: LJQ
Molecular weightTheoretical: 498.779 Da

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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: 42 / 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: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 15 / Number of copies: 13 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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Macromolecule #16: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 16 / Number of copies: 45 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

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Macromolecule #17: BACTERIOPHEOPHYTIN A

MacromoleculeName: BACTERIOPHEOPHYTIN A / type: ligand / ID: 17 / Number of copies: 2 / Formula: BPH
Molecular weightTheoretical: 889.215 Da
Chemical component information

ChemComp-BPH:
BACTERIOPHEOPHYTIN A

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Macromolecule #18: Ubiquinone-8

MacromoleculeName: Ubiquinone-8 / type: ligand / ID: 18 / Number of copies: 3 / Formula: UQ8
Molecular weightTheoretical: 727.109 Da
Chemical component information

ChemComp-UQ8:
Ubiquinone-8

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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: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 20 / Number of copies: 9 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #21: MENAQUINONE 8

MacromoleculeName: MENAQUINONE 8 / type: ligand / ID: 21 / Number of copies: 1 / Formula: MQ8
Molecular weightTheoretical: 717.116 Da
Chemical component information

ChemComp-MQ8:
MENAQUINONE 8

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Macromolecule #22: SPIRILLOXANTHIN

MacromoleculeName: SPIRILLOXANTHIN / type: ligand / ID: 22 / Number of copies: 9 / Formula: CRT
Molecular weightTheoretical: 596.925 Da
Chemical component information

ChemComp-CRT:
SPIRILLOXANTHIN

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Macromolecule #23: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 23 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #24: water

MacromoleculeName: water / type: ligand / ID: 24 / Number of copies: 5 / 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

Concentration6.0 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: LEICA EM GP
DetailsThis sample was monodisperse.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / 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 / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.1 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 331335
CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING ONLY
Startup modelType of model: OTHER
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 90126
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

5y5s

source_name: PDB, initial_model_type: experimental model

5d8v

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 20 / Target criteria: Correlation coefficient
Output model

PDB-8z82:
Photosynthetic LH1-RC-HiPIP complex from the purple bacterium Halorhodospira halophila

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