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- EMDB-34307: Structure of the intact photosynthetic light-harvesting antenna-r... -

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Basic information

Entry
Database: EMDB / ID: EMD-34307
TitleStructure of the intact photosynthetic light-harvesting antenna-reaction center complex from a green sulfur bacterium
Map data
Sample
  • Complex: GsbRC-2FMO complex
    • Protein or peptide: x 7 types
  • Ligand: x 10 types
Function / homology
Function and homology information


thylakoid / bacteriochlorophyll binding / iron-sulfur cluster binding / photosynthesis / electron transfer activity / heme binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Proteolipid membrane potential modulator / Proteolipid membrane potential modulator / Photosystem P840 reaction-centre, cytochrome c-551 / Photosystem P840 reaction-centre cytochrome c-551 / Photosystem I P840 reaction centre protein PscD / Photosystem P840 reaction centre protein PscD / Bacteriochlorophyll A protein / Bacteriochlorophyll A superfamily / Bacteriochlorophyll A protein / Photosystem I PsaA/PsaB ...Proteolipid membrane potential modulator / Proteolipid membrane potential modulator / Photosystem P840 reaction-centre, cytochrome c-551 / Photosystem P840 reaction-centre cytochrome c-551 / Photosystem I P840 reaction centre protein PscD / Photosystem P840 reaction centre protein PscD / Bacteriochlorophyll A protein / Bacteriochlorophyll A superfamily / Bacteriochlorophyll A protein / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / 4Fe-4S dicluster domain / Cytochrome c-like domain superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
Cytochrome c / Bacteriochlorophyll a protein / Photosystem P840 reaction center, large subunit / Photosystem P840 reaction center iron-sulfur protein / P840 reaction center 17 kDa protein / Ric1 protein
Similarity search - Component
Biological speciesChlorobaculum tepidum TLS (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsChen JH / Zhang X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J Integr Plant Biol / Year: 2023
Title: Cryo-electron microscopy structure of the intact photosynthetic light-harvesting antenna-reaction center complex from a green sulfur bacterium.
Authors: Jing-Hua Chen / Weiwei Wang / Chen Wang / Tingyun Kuang / Jian-Ren Shen / Xing Zhang /
Abstract: The photosynthetic reaction center complex (RCC) of green sulfur bacteria (GSB) consists of the membrane-imbedded RC core and the peripheric energy transmitting proteins called Fenna-Matthews-Olson ...The photosynthetic reaction center complex (RCC) of green sulfur bacteria (GSB) consists of the membrane-imbedded RC core and the peripheric energy transmitting proteins called Fenna-Matthews-Olson (FMO). Functionally, FMO transfers the absorbed energy from a huge peripheral light-harvesting antenna named chlorosome to the RC core where charge separation occurs. In vivo, one RC was found to bind two FMOs, however, the intact structure of RCC as well as the energy transfer mechanism within RCC remain to be clarified. Here we report a structure of intact RCC which contains a RC core and two FMO trimers from a thermophilic green sulfur bacterium Chlorobaculum tepidum at 2.9 Å resolution by cryo-electron microscopy. The second FMO trimer is attached at the cytoplasmic side asymmetrically relative to the first FMO trimer reported previously. We also observed two new subunits (PscE and PscF) and the N-terminal transmembrane domain of a cytochrome-containing subunit (PscC) in the structure. These two novel subunits possibly function to facilitate the binding of FMOs to RC core and to stabilize the whole complex. A new bacteriochlorophyll (numbered as 816) was identified at the interspace between PscF and PscA-1, causing an asymmetrical energy transfer from the two FMO trimers to RC core. Based on the structure, we propose an energy transfer network within this photosynthetic apparatus.
History
DepositionSep 16, 2022-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateFeb 15, 2023-
Current statusFeb 15, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34307.png

Downloads & links

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Map

FileDownload / File: emd_34307.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.92 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.5571167 - 1.2976869
Average (Standard dev.)-7.271411e-05 (±0.039397474)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 312.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34307_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34307_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : GsbRC-2FMO complex

EntireName: GsbRC-2FMO complex
Components
  • Complex: GsbRC-2FMO complex
    • Protein or peptide: Bacteriochlorophyll a proteinBacteriochlorophyll
    • Protein or peptide: P840 reaction center 17 kDa protein
    • Protein or peptide: Photosystem P840 reaction center iron-sulfur protein
    • Protein or peptide: Photosystem P840 reaction center, large subunit
    • Protein or peptide: unkown protein
    • Protein or peptide: Ric1 protein
    • Protein or peptide: Cytochrome c
  • Ligand: BACTERIOCHLOROPHYLL ABacteriochlorophyll
  • Ligand: CARDIOLIPIN
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: Bacteriochlorophyll A isomer
  • Ligand: Chlorophyll A ester
  • Ligand: [(2R,3S,4S,5R,6R)-6-[(10E,12E,14E)-2,6,10,14,19,23-hexamethyl-25-(2,3,6-trimethylphenyl)pentacosa-6,8,10,12,14,16,18,20,22,24-decaen-2-yl]oxy-3,4,5-tris(oxidanyl)oxan-2-yl]methyl dodecanoate
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: CALCIUM IONCalcium
  • Ligand: 2-[(1E,3E,5E,7E,9E,11E,13E,15E,17E,19E)-3,7,12,16,20,24-hexamethylpentacosa-1,3,5,7,9,11,13,15,17,19,23-undecaenyl]-1,3,4-trimethyl-benzene

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Supramolecule #1: GsbRC-2FMO complex

SupramoleculeName: GsbRC-2FMO complex / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Chlorobaculum tepidum TLS (bacteria)

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Macromolecule #1: Bacteriochlorophyll a protein

MacromoleculeName: Bacteriochlorophyll a protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Chlorobaculum tepidum TLS (bacteria) / Strain: ATCC 49652 / DSM 12025 / NBRC 103806 / TLS
Molecular weightTheoretical: 40.34343 KDa
SequenceString: MALFGSNDVT TAHSDYEIVL EGGSSSWGKV KARAKVNAPP ASPLLPADCD VKLNVKPLDP AKGFVRISAV FESIVDSTKN KLTIEADIA NETKERRISV GEGMVSVGDF SHTFSFEGSV VNLFYYRSDA VRRNVPNPIY MQGRQFHDIL MKVPLDNNDL I DTWEGTVK ...String:
MALFGSNDVT TAHSDYEIVL EGGSSSWGKV KARAKVNAPP ASPLLPADCD VKLNVKPLDP AKGFVRISAV FESIVDSTKN KLTIEADIA NETKERRISV GEGMVSVGDF SHTFSFEGSV VNLFYYRSDA VRRNVPNPIY MQGRQFHDIL MKVPLDNNDL I DTWEGTVK AIGSTGAFND WIRDFWFIGP AFTALNEGGQ RISRIEVNGL NTESGPKGPV GVSRWRFSHG GSGMVDSISR WA ELFPSDK LNRPAQVEAG FRSDSQGIEV KVDGEFPGVS VDAGGGLRRI LNHPLIPLVH HGMVGKFNNF NVDAQLKVVL PKG YKIRYA APQYRSQNLE EYRWSGGAYA RWVEHVCKGG VGQFEILYAQ

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Macromolecule #2: P840 reaction center 17 kDa protein

MacromoleculeName: P840 reaction center 17 kDa protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlorobaculum tepidum TLS (bacteria) / Strain: ATCC 49652 / DSM 12025 / NBRC 103806 / TLS
Molecular weightTheoretical: 16.633195 KDa
SequenceString:
MQPQLSRPQT ASNQVRKAVS GPWSGNAVHK AEKYFITSAK RDRDGKLQIE LVPASGRRKL SPTPEMIRRL IDGEIEIYIL TTQPDIAID MNKEIIDMEN RYVIDFDKRG VKWTMREIPV FYHEGKGLCV ELHNKIYTLD QFFK

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Macromolecule #3: Photosystem P840 reaction center iron-sulfur protein

MacromoleculeName: Photosystem P840 reaction center iron-sulfur protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlorobaculum tepidum TLS (bacteria) / Strain: ATCC 49652 / DSM 12025 / NBRC 103806 / TLS
Molecular weightTheoretical: 23.383096 KDa
SequenceString: MAEPVENKNQ APAPGAKVPP KGAPAAPKAG APAAPKGPVA PKAGAPAAKT GASAAKQAGK PRLASLGVTL GRSGVRQESA LPYVKPKAV PPPKPAAPAA KGAPAPKGAP AAPAAKAAPG APVAKAAPKA KKHYFIIENL CVGCGLCLDK CPPKVNAIGY K FYGDVQEG ...String:
MAEPVENKNQ APAPGAKVPP KGAPAAPKAG APAAPKGPVA PKAGAPAAKT GASAAKQAGK PRLASLGVTL GRSGVRQESA LPYVKPKAV PPPKPAAPAA KGAPAPKGAP AAPAAKAAPG APVAKAAPKA KKHYFIIENL CVGCGLCLDK CPPKVNAIGY K FYGDVQEG GFRCYIDQAA CISCSACFSG DECPSGALIE VLPDGEVLDF SYTPPERLDF DLRFLHRFHR EA

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Macromolecule #4: Photosystem P840 reaction center, large subunit

MacromoleculeName: Photosystem P840 reaction center, large subunit / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlorobaculum tepidum TLS (bacteria)
Molecular weightTheoretical: 81.784641 KDa
SequenceString: MAEQVKPAGV KPKGTVPPPK GNAPAPKANG APGGASVIKE QDAAKMRRFL FQRTETRSTK WYQIFDTEKL DDEQVVGGHL ALLGVLGFI MGIYYISGIQ VFPWGAPGFH DNWFYLTIKP RMVSLGIDTY STKTADLEAA GARLLGWAAF HFLVGSVLIF G GWRHWTHN ...String:
MAEQVKPAGV KPKGTVPPPK GNAPAPKANG APGGASVIKE QDAAKMRRFL FQRTETRSTK WYQIFDTEKL DDEQVVGGHL ALLGVLGFI MGIYYISGIQ VFPWGAPGFH DNWFYLTIKP RMVSLGIDTY STKTADLEAA GARLLGWAAF HFLVGSVLIF G GWRHWTHN LTNPFTGRCG NFRDFRFLGK FGDVVFNGTS AKSYKEALGP HAVYMSLLFL GWGIVMWAIL GFAPIPDFQT IN SETFMSF VFAVIFFALG IYWWNNPPNA AIHLNDDMKA AFSVHLTAIG YINIALGCIA FVAFQQPSFA PYYKELDKLV FYL YGEPFN RVSFNFVEQG GKVISGAKEF ADFPAYAILP KSGEAFGMAR VVTNLIVFNH IICGVLYVFA GVYHGGQYLL KIQL NGMYN QIKSIWITKG RDQEVQVKIL GTVMALCFAT MLSVYAVIVW NTICELNIFG TNITMSFYWL KPLPIFQWMF ADPSI NDWV MAHVITAGSL FSLIALVRIA FFAHTSPLWD DLGLKKNSYS FPCLGPVYGG TCGVSIQDQL WFAMLWGIKG LSAVCW YID GAWIASMMYG VPAADAKAWD SIAHLHHHYT SGIFYYFWTE TVTIFSSSHL STILMIGHLV WFISFAVWFE DRGSRLE GA DIQTRTIRWL GKKFLNRDVN FRFPVLTISD SKLAGTFLYF GGTFMLVFLF LANGFYQTNS PLPPPVSHAA VSGQQMLA Q LVDTLMKMIA

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Macromolecule #5: unkown protein

MacromoleculeName: unkown protein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlorobaculum tepidum TLS (bacteria)
Molecular weightTheoretical: 4.954098 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)

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Macromolecule #6: Ric1 protein

MacromoleculeName: Ric1 protein / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlorobaculum tepidum TLS (bacteria) / Strain: ATCC 49652 / DSM 12025 / NBRC 103806 / TLS
Molecular weightTheoretical: 6.227533 KDa
SequenceString:
MDIRRLILAF ILPPAAVMNK EAGTIMLTGI LTLWGWIPGV VAALIMISKE QSGKTAEA

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Macromolecule #7: Cytochrome c

MacromoleculeName: Cytochrome c / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlorobaculum tepidum TLS (bacteria) / Strain: ATCC 49652 / DSM 12025 / NBRC 103806 / TLS
Molecular weightTheoretical: 22.741779 KDa
SequenceString: MDKNSNGKLI ALAVGGAVLM GALFFSVSFL TGYIPAPNHS AILTPLRSFM GWFLLIFCAS IIIMGLGKMS SAISDKWFLS FPLSIFVIV MVMFLSLRVY WEKGRTTTVD GKYIRTTAEL KEFLNKPAAT SDVPPAPAGF DFDAAKKLVD VRCNKCHTLD S VADLFRTK ...String:
MDKNSNGKLI ALAVGGAVLM GALFFSVSFL TGYIPAPNHS AILTPLRSFM GWFLLIFCAS IIIMGLGKMS SAISDKWFLS FPLSIFVIV MVMFLSLRVY WEKGRTTTVD GKYIRTTAEL KEFLNKPAAT SDVPPAPAGF DFDAAKKLVD VRCNKCHTLD S VADLFRTK YKKTGQVNLI VKRMQGFPGS GISDDDAKTI GIWLHEKF

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Macromolecule #8: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 8 / Number of copies: 73 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A / Bacteriochlorophyll

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Macromolecule #9: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 9 / Number of copies: 4 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM / Cardiolipin

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Macromolecule #10: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 10 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

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Macromolecule #11: Bacteriochlorophyll A isomer

MacromoleculeName: Bacteriochlorophyll A isomer / type: ligand / ID: 11 / Number of copies: 2 / Formula: GS0
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-GS0:
Bacteriochlorophyll A isomer

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Macromolecule #12: Chlorophyll A ester

MacromoleculeName: Chlorophyll A ester / type: ligand / ID: 12 / Number of copies: 4 / Formula: G2O
Molecular weightTheoretical: 891.473 Da
Chemical component information

ChemComp-G2O:
Chlorophyll A ester

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Macromolecule #13: [(2R,3S,4S,5R,6R)-6-[(10E,12E,14E)-2,6,10,14,19,23-hexamethyl-25-...

MacromoleculeName: [(2R,3S,4S,5R,6R)-6-[(10E,12E,14E)-2,6,10,14,19,23-hexamethyl-25-(2,3,6-trimethylphenyl)pentacosa-6,8,10,12,14,16,18,20,22,24-decaen-2-yl]oxy-3,4,5-tris(oxidanyl)oxan-2-yl]methyl dodecanoate
type: ligand / ID: 13 / Number of copies: 4 / Formula: F39
Molecular weightTheoretical: 895.299 Da
Chemical component information

ChemComp-F39:
[(2R,3S,4S,5R,6R)-6-[(10E,12E,14E)-2,6,10,14,19,23-hexamethyl-25-(2,3,6-trimethylphenyl)pentacosa-6,8,10,12,14,16,18,20,22,24-decaen-2-yl]oxy-3,4,5-tris(oxidanyl)oxan-2-yl]methyl dodecanoate

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Macromolecule #14: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 14 / Number of copies: 7 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

ChemComp-LHG:
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / phospholipid*YM / Phosphatidylglycerol

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Macromolecule #15: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 15 / Number of copies: 2 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

ChemComp-LMG:
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

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Macromolecule #16: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 16 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #17: 2-[(1E,3E,5E,7E,9E,11E,13E,15E,17E,19E)-3,7,12,16,20,24-hexamethy...

MacromoleculeName: 2-[(1E,3E,5E,7E,9E,11E,13E,15E,17E,19E)-3,7,12,16,20,24-hexamethylpentacosa-1,3,5,7,9,11,13,15,17,19,23-undecaenyl]-1,3,4-trimethyl-benzene
type: ligand / ID: 17 / Number of copies: 2 / Formula: F26
Molecular weightTheoretical: 532.841 Da
Chemical component information

ChemComp-F26:
2-[(1E,3E,5E,7E,9E,11E,13E,15E,17E,19E)-3,7,12,16,20,24-hexamethylpentacosa-1,3,5,7,9,11,13,15,17,19,23-undecaenyl]-1,3,4-trimethyl-benzene

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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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 152200 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Specialist opticsSpherical aberration corrector: 2.7mm / Chromatic aberration corrector: 2.7mm / Energy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 80.0 K / Max: 90.0 K
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 2297 / Average exposure time: 8.0 sec. / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1961370
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6m32

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.0)
Final 3D classificationNumber classes: 4 / Avg.num./class: 106600 / Software - Name: cryoSPARC (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.0)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.0) / Number images used: 227038

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