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- EMDB-30314: STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF THIORHODOVIBR... -

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Basic information

Entry
Database: EMDB / ID: EMD-30314
TitleSTRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF THIORHODOVIBRIO STRAIN 970
Map data
Sample
  • Complex: light-harvesting-reaction center complex from the purple phototrophic bacterium Thiorhodovibrio strain 970
    • Protein or peptide: x 10 types
  • Ligand: x 14 types
Function / homology
Function and homology information


: / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / electron transfer activity / membrane => GO:0016020 / iron ion binding ...: / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / electron transfer activity / membrane => GO:0016020 / iron ion binding / heme binding / metal ion binding / plasma membrane
Similarity search - Function
: / Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Light-harvesting protein B beta chain / Antenna complex, alpha/beta subunit / Light-harvesting complex / Antenna complex alpha/beta subunit / Multiheme cytochrome c family profile. / Photosynthetic reaction centre, H subunit ...: / Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Light-harvesting protein B beta chain / Antenna complex, alpha/beta subunit / Light-harvesting complex / Antenna complex alpha/beta subunit / Multiheme cytochrome c family profile. / 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 / Multiheme cytochrome 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
Antenna complex alpha/beta subunit / Alpha subunit 1 of light-harvesting 1 complex / Photosynthetic reaction center L subunit / Reaction center protein M chain / Antenna complex alpha/beta subunit / Alpha subunit 2 of light-harvesting 1 complex / Photosynthetic reaction center, subunit H, bacterial / LHC domain-containing protein / Photosynthetic reaction center cytochrome c subunit / Antenna complex alpha/beta subunit
Similarity search - Component
Biological speciesThiorhodovibrio sp. 970 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsTani K / Kanno R / Makino Y / Hall M / Takenouchi M / Imanishi M / Yu L-J / Overmann J / Madigan MT / Kimura Y ...Tani K / Kanno R / Makino Y / Hall M / Takenouchi M / Imanishi M / Yu L-J / Overmann J / Madigan MT / Kimura Y / Mizoguchi A / Humbel BM / Wang-Otomo Z-Y
Funding support Japan, 6 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP20am0101118 Japan
Japan Society for the Promotion of Science (JSPS)JP16H04174 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101116 Japan
Japan Society for the Promotion of Science (JSPS)20H05086 Japan
Japan Society for the Promotion of Science (JSPS)JP18H05153 Japan
Japan Society for the Promotion of Science (JSPS)20H02856 Japan
CitationJournal: Nat Commun / Year: 2020
Title: Cryo-EM structure of a Ca-bound photosynthetic LH1-RC complex containing multiple αβ-polypeptides.
Authors: Kazutoshi Tani / Ryo Kanno / Yuki Makino / Malgorzata Hall / Mizuki Takenouchi / Michie Imanishi / Long-Jiang Yu / Jörg Overmann / Michael T Madigan / Yukihiro Kimura / Akira Mizoguchi / ...Authors: Kazutoshi Tani / Ryo Kanno / Yuki Makino / Malgorzata Hall / Mizuki Takenouchi / Michie Imanishi / Long-Jiang Yu / Jörg Overmann / Michael T Madigan / Yukihiro Kimura / Akira Mizoguchi / Bruno M Humbel / Zheng-Yu Wang-Otomo /
Abstract: The light-harvesting-reaction center complex (LH1-RC) from the purple phototrophic bacterium Thiorhodovibrio strain 970 exhibits an LH1 absorption maximum at 960 nm, the most red-shifted absorption ...The light-harvesting-reaction center complex (LH1-RC) from the purple phototrophic bacterium Thiorhodovibrio strain 970 exhibits an LH1 absorption maximum at 960 nm, the most red-shifted absorption for any bacteriochlorophyll (BChl) a-containing species. Here we present a cryo-EM structure of the strain 970 LH1-RC complex at 2.82 Å resolution. The LH1 forms a closed ring structure composed of sixteen pairs of the αβ-polypeptides. Sixteen Ca ions are present in the LH1 C-terminal domain and are coordinated by residues from the αβ-polypeptides that are hydrogen-bonded to BChl a. The Ca-facilitated hydrogen-bonding network forms the structural basis of the unusual LH1 redshift. The structure also revealed the arrangement of multiple forms of α- and β-polypeptides in an individual LH1 ring. Such organization indicates a mechanism of interplay between the expression and assembly of the LH1 complex that is regulated through interactions with the RC subunits inside.
History
DepositionJun 7, 2020-
Header (metadata) releaseOct 7, 2020-
Map releaseOct 7, 2020-
UpdateOct 14, 2020-
Current statusOct 14, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.037
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.037
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7c9r
  • Surface level: 0.037
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30314.png

Downloads & links

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Map

FileDownload / File: emd_30314.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.84 Å
Density
Contour LevelBy AUTHOR: 0.037 / Movie #1: 0.037
Minimum - Maximum-0.15866552 - 0.26283836
Average (Standard dev.)-0.0000493407 (±0.008591025)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.840.840.84
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z336.000336.000336.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ510510510
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.1590.263-0.000

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Supplemental data

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Sample components

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Entire : light-harvesting-reaction center complex from the purple phototro...

EntireName: light-harvesting-reaction center complex from the purple phototrophic bacterium Thiorhodovibrio strain 970
Components
  • Complex: light-harvesting-reaction center complex from the purple phototrophic bacterium Thiorhodovibrio strain 970
    • Protein or peptide: Photosynthetic reaction center cytochrome c subunit
    • Protein or peptide: L subunit of the reaction center
    • Protein or peptide: Reaction center protein M chainPhotosynthetic reaction centre
    • Protein or peptide: Photosynthetic reaction center, subunit H, bacterialPhotosynthetic reaction centre
    • Protein or peptide: Alpha subunit 1 of light-harvesting 1 complex
    • 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: LHC domain-containing protein
    • Protein or peptide: Alpha subunit 2 of light-harvesting 1 complex
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: MAGNESIUM ION
  • Ligand: CALCIUM IONCalcium
  • Ligand: DIACYL GLYCEROLDiglyceride
  • Ligand: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
  • Ligand: BACTERIOCHLOROPHYLL ABacteriochlorophyll
  • Ligand: BACTERIOPHEOPHYTIN A
  • Ligand: Ubiquinone-8Coenzyme Q10
  • Ligand: Octadecane
  • Ligand: FE (III) ION
  • Ligand: MENAQUINONE 8Vitamin K2
  • Ligand: CARDIOLIPIN
  • Ligand: (6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},24~{E},26~{E})-2,31-dimethoxy-2,6,10,14,19,23,27,31-octamethyl-dotriaconta-6,8,10,12,14,16,18,20,22,24,26-undecaene
  • Ligand: DODECYL-BETA-D-MALTOSIDE

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Supramolecule #1: light-harvesting-reaction center complex from the purple phototro...

SupramoleculeName: light-harvesting-reaction center complex from the purple phototrophic bacterium Thiorhodovibrio strain 970
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Thiorhodovibrio sp. 970 (bacteria)
Molecular weightTheoretical: 400 KDa

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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: Thiorhodovibrio sp. 970 (bacteria)
Molecular weightTheoretical: 42.77891 KDa
SequenceString: MKQRNHHALA LLSLGVAAFI TGCDFPPQDV VQTGYRGLGM QQNYNPKLLQ KVIDATQVPD AIPAATPGGA LAKDVYKNVQ VLGDLSVNE FNRTMVALTT WVAPNEGCTY CHEGTNWESD GVYTKIASRR MLEMTRDTNS NWTGHVADTG VTCYTCHRGK P VPEHVWTT ...String:
MKQRNHHALA LLSLGVAAFI TGCDFPPQDV VQTGYRGLGM QQNYNPKLLQ KVIDATQVPD AIPAATPGGA LAKDVYKNVQ VLGDLSVNE FNRTMVALTT WVAPNEGCTY CHEGTNWESD GVYTKIASRR MLEMTRDTNS NWTGHVADTG VTCYTCHRGK P VPEHVWTT DPGPDIPSVF PSNGQNTIGY NVAYTALPFD PFTPFLLGEN EIRVSGNTDL RNTNRKSIKQ AEWTFALMTH FS EALGVNC TYCHNSRAFM DWNQSTPKRV PAWHAIRNVR DINIQYVEPL GEVLPASRKG PLGDPFKVNC LTCHQGAYKP LFG VPMAKD YPALYETAAV EEEAPAEAAP AAEAEAAPAE AVPVAEAPAE AAPVEAAPAA EAEAAPAEAA PAAPPVPADR

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Macromolecule #2: L subunit of the reaction center

MacromoleculeName: L subunit of the reaction center / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thiorhodovibrio sp. 970 (bacteria)
Molecular weightTheoretical: 30.497693 KDa
SequenceString: MALLNFEKKY RVRGGTLVGG DLFDFWVGPF YVGFFGVSAV FFATLGTMLI LFGAAIGPTL NIWQISIAPP DLSVGLGFAP IREGGLWQV ITICAVGAFV SWALRQVEIA RKLGMGLHVP FAFSFAILAY LTLVFFRPVL LGAWGHAFPY GLFSHLDWVS N VGYQTLHF ...String:
MALLNFEKKY RVRGGTLVGG DLFDFWVGPF YVGFFGVSAV FFATLGTMLI LFGAAIGPTL NIWQISIAPP DLSVGLGFAP IREGGLWQV ITICAVGAFV SWALRQVEIA RKLGMGLHVP FAFSFAILAY LTLVFFRPVL LGAWGHAFPY GLFSHLDWVS N VGYQTLHF HYNPAHMLAI SFFFINTLAL AMHGSLILSV VNPQKGEEVK TAEHENTVFR DIVGYSIGAL AIHRLGLFLA IN AAFWSAV CMILTGPFWT RGWPEWWMWW PNLPIW

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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: Thiorhodovibrio sp. 970 (bacteria)
Molecular weightTheoretical: 36.323215 KDa
SequenceString: MPEYQNIFNK VQVREPAYPG VELPKGSLPR VGKPIFSYWL GKIGDAQIGP LYLGGWGIAS LISGFIALEV IGLNMLASVG WDPRLFLKE FFWLGLEPPP PAYGLSIPPL AEGGWWLIAG LFLTMSLLLW WVRVYKRAKD LGMGTHLSWA FAVAILFFLT L GFIRPVLM ...String:
MPEYQNIFNK VQVREPAYPG VELPKGSLPR VGKPIFSYWL GKIGDAQIGP LYLGGWGIAS LISGFIALEV IGLNMLASVG WDPRLFLKE FFWLGLEPPP PAYGLSIPPL AEGGWWLIAG LFLTMSLLLW WVRVYKRAKD LGMGTHLSWA FAVAILFFLT L GFIRPVLM GSWGEAPPFG IFPHLDWTAA ISIRYGNFYY NPFHGLSIAF MYGSAVLFAM HGGTILAVSR YGGDREIDQI TD RGTAAER AMLFWRWCMG FNASMESIHR WAWWFAVFCI INSILGIILT GTVVDNWYLW AVKHGVAPSY PSELTIDNPY LTQ GVAQ

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Macromolecule #4: Photosynthetic reaction center, subunit H, bacterial

MacromoleculeName: Photosynthetic reaction center, subunit H, bacterial / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thiorhodovibrio sp. 970 (bacteria)
Molecular weightTheoretical: 28.694848 KDa
SequenceString: MEFGYITQYF DLAQVTLWAF WLSLLSVIFF NRREDKREGY PQEAVQIFGK TILTEGFPFM PAPKTFKLPH NGGDVVKPGP ERPQYDFKL EQVDRFAGAA YRPVGNPMLA GVGPGAYAVR ANKPDLTNAG DPRIVPMRVA KHFAVVDKDP DPRGMTVIGA D GQVGGKVT ...String:
MEFGYITQYF DLAQVTLWAF WLSLLSVIFF NRREDKREGY PQEAVQIFGK TILTEGFPFM PAPKTFKLPH NGGDVVKPGP ERPQYDFKL EQVDRFAGAA YRPVGNPMLA GVGPGAYAVR ANKPDLTNAG DPRIVPMRVA KHFAVVDKDP DPRGMTVIGA D GQVGGKVT EIWVDRAEPQ VRYLELEAGN KKKVLVPIAL CVIKGQKREV KVRSINGIHF NDVPTLSNYD QITLAEEDKV SA YYGAGTL YATPNRAESV L

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Macromolecule #5: Alpha subunit 1 of light-harvesting 1 complex

MacromoleculeName: Alpha subunit 1 of light-harvesting 1 complex / type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Thiorhodovibrio sp. 970 (bacteria)
Molecular weightTheoretical: 8.39386 KDa
SequenceString:
MNAKSFDGMH KLWMIMNPVS TLWAIFIFQI FLGLLIHMVV LSSDLNWHDD QIPVGYQLQG ETLPVNLEMK AAQ

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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: 3 / Enantiomer: LEVO
Source (natural)Organism: Thiorhodovibrio sp. 970 (bacteria)
Molecular weightTheoretical: 5.319267 KDa
SequenceString:
MAEKPSTGLT ESEAKEFHGL FMASMTLWFG LVVLAHILSW MYRPWL

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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: 13 / Enantiomer: LEVO
Source (natural)Organism: Thiorhodovibrio sp. 970 (bacteria)
Molecular weightTheoretical: 5.305218 KDa
SequenceString:
MAEKSTTGLT EAESKEFHGI FMASMTLWFG LVVLAHILSW LYRPWL

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Thiorhodovibrio sp. 970 (bacteria)
Molecular weightTheoretical: 9.233694 KDa
SequenceString:
MSNDNFTGTY KMWMFIDPRR ALLFIASFQI LLGILIHMIV LGSDLNWHSD GIPKFYFPNA AEASAPIDMS PIPSARNFKF D

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Macromolecule #9: LHC domain-containing protein

MacromoleculeName: LHC domain-containing protein / type: protein_or_peptide / ID: 9 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Thiorhodovibrio sp. 970 (bacteria)
Molecular weightTheoretical: 8.822363 KDa
SequenceString:
MNAKSFDGMH KLWMIMNPVS TLWAIFIFQI FLGLLIHMVV LSSDLNWHDD QIPVGYQLQG ETLPVNLEMK AALKDAQ

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Macromolecule #10: Alpha subunit 2 of light-harvesting 1 complex

MacromoleculeName: Alpha subunit 2 of light-harvesting 1 complex / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thiorhodovibrio sp. 970 (bacteria)
Molecular weightTheoretical: 9.72239 KDa
SequenceString:
MNSDKFAGMY KLWTFIDPRR TLIFIVAFQI MLGILIHMIV LGSDLNWHND GIPRFYSPRP VDVAVGPAGI PLEIPGSPMP QARNYN

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Macromolecule #11: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 11 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE / Heme B

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Macromolecule #12: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 12 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #13: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 13 / Number of copies: 17 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #14: DIACYL GLYCEROL

MacromoleculeName: DIACYL GLYCEROL / type: ligand / ID: 14 / Number of copies: 1 / Formula: DGA
Molecular weightTheoretical: 625.018 Da
Chemical component information

ChemComp-DGA:
DIACYL GLYCEROL / Diglyceride

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Macromolecule #15: (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: 15 / Number of copies: 19 / 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 / Phosphatidylglycerol

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Macromolecule #16: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 16 / Number of copies: 36 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A / Bacteriochlorophyll

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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 / Pheophytin

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Macromolecule #18: Ubiquinone-8

MacromoleculeName: Ubiquinone-8 / type: ligand / ID: 18 / Number of copies: 2 / Formula: UQ8
Molecular weightTheoretical: 727.109 Da
Chemical component information

ChemComp-UQ8:
Ubiquinone-8

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Macromolecule #19: Octadecane

MacromoleculeName: Octadecane / type: ligand / ID: 19 / Number of copies: 2 / Formula: 8K6
Molecular weightTheoretical: 254.494 Da
Chemical component information

ChemComp-8K6:
Octadecane / Octadecane

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Macromolecule #20: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 20 / Number of copies: 1 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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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 / Vitamin K2

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Macromolecule #22: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 22 / Number of copies: 3 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM / Cardiolipin

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Macromolecule #23: (6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},24~...

MacromoleculeName: (6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},24~{E},26~{E})-2,31-dimethoxy-2,6,10,14,19,23,27,31-octamethyl-dotriaconta-6,8,10,12,14,16,18,20,22,24,26-undecaene
type: ligand / ID: 23 / Number of copies: 17 / Formula: H4X
Molecular weightTheoretical: 600.956 Da
Chemical component information

ChemComp-H4X:
(6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},24~{E},26~{E})-2,31-dimethoxy-2,6,10,14,19,23,27,31-octamethyl-dotriaconta-6,8,10,12,14,16,18,20,22,24,26-undecaene

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Macromolecule #24: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 24 / 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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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
GridModel: Quantifoil R2/2 / Material: MOLYBDENUM / Mesh: 200 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K / Instrument: LEICA EM GP
DetailsThis sample was monodisperse.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average exposure time: 30.6 sec. / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 153004
CTF correctionSoftware - Name: CTFFIND
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: EMAN2
Final 3D classificationNumber classes: 4 / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 105234
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5y5s

RefinementSpace: REAL / Protocol: OTHER / Overall B value: 60 / Target criteria: Correlation coefficient
Output model

PDB-7c9r:
STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF THIORHODOVIBRIO STRAIN 970

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Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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