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- EMDB-24023: Reconstruction of the Legionella pneumophila Dot/Icm T4SS 3DVA Map 3 -

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Basic information

Entry
Database: EMDB / ID: EMD-24023
TitleReconstruction of the Legionella pneumophila Dot/Icm T4SS 3DVA Map 3
Map dataReconstruction of the Legionella pneumophila Dot/Icm T4SS 3DVA Map 3
Sample
  • Complex: Legionella pneumophila Dot/Icm T4SS 3DVA Map 3
    • Protein or peptide: x 11 types
KeywordsDot/Icm / Secretion / T4SS / TRANSLOCASE
Function / homology
Function and homology information


: / : / Putative auto-transporter adhesin, head GIN domain / Putative auto-transporter adhesin, head GIN domain / Putative type IV secretory system protein / Type IV secretory system, conjugal DNA-protein transfer / DotD protein / DotD superfamily / DotD protein / Putative outer membrane core complex of type IVb secretion ...: / : / Putative auto-transporter adhesin, head GIN domain / Putative auto-transporter adhesin, head GIN domain / Putative type IV secretory system protein / Type IV secretory system, conjugal DNA-protein transfer / DotD protein / DotD superfamily / DotD protein / Putative outer membrane core complex of type IVb secretion / Putative outer membrane core complex of type IVb secretion / Pentapeptide repeats (9 copies) / Pentapeptide repeat / Type IV secretion system, VirB10/TrbI / Bacterial conjugation TrbI-like protein / Type IV secretion system, VirB10 / TraB / TrbI / : / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Putative auto-transporter adhesin head GIN domain-containing protein / Neurogenic locus notch / Type IV secretion protein IcmK / DotD / DotC / Inner membrane lipoprotein YiaD / IcmE protein / DotF / Outer membrane protein, OmpA family protein
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsSheedlo MJ / Durie CL
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01AI118932 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)F32 AI150027-01 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)2T32DK007673 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD020011 United States
CitationJournal: Elife / Year: 2021
Title: Cryo-EM reveals new species-specific proteins and symmetry elements in the Dot/Icm T4SS.
Authors: Michael J Sheedlo / Clarissa L Durie / Jeong Min Chung / Louise Chang / Jacquelyn Roberts / Michele Swanson / Dana Borden Lacy / Melanie D Ohi /
Abstract: is an opportunistic pathogen that causes the potentially fatal pneumonia known as Legionnaires' disease. The pathology associated with infection depends on bacterial delivery of effector proteins ... is an opportunistic pathogen that causes the potentially fatal pneumonia known as Legionnaires' disease. The pathology associated with infection depends on bacterial delivery of effector proteins into the host via the membrane spanning Dot/Icm type IV secretion system (T4SS). We have determined sub-3.0 Å resolution maps of the Dot/Icm T4SS core complex by single particle cryo-EM. The high-resolution structural analysis has allowed us to identify proteins encoded outside the Dot/Icm genetic locus that contribute to the core T4SS structure. We can also now define two distinct areas of symmetry mismatch, one that connects the C18 periplasmic ring (PR) and the C13 outer membrane cap (OMC) and one that connects the C13 OMC with a 16-fold symmetric dome. Unexpectedly, the connection between the PR and OMC is DotH, with five copies sandwiched between the OMC and PR to accommodate the symmetry mismatch. Finally, we observe multiple conformations in the reconstructions that indicate flexibility within the structure.
History
DepositionMay 14, 2021-
Header (metadata) releaseOct 6, 2021-
Map releaseOct 6, 2021-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.25
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 2.25
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7muv
  • Surface level: 2.25
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7muv
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24023.png

Downloads & links

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Map

FileDownload / File: emd_24023.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the Legionella pneumophila Dot/Icm T4SS 3DVA Map 3
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.24 Å/pix.
x 250 pix.
= 561. Å		2.24 Å/pix.
x 250 pix.
= 561. Å		2.24 Å/pix.
x 250 pix.
= 561. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.244 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.25 / Movie #1: 2.25
Minimum - Maximum-3.6210568 - 9.229272999999999
Average (Standard dev.)0.09089534 (±0.54645485)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 561.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.2442.2442.244
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z561.000561.000561.000
α/β/γ90.00090.00090.000
start NX/NY/NZ484647
NX/NY/NZ97101117
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean-3.6219.2290.091

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Supplemental data

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Sample components

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Entire : Legionella pneumophila Dot/Icm T4SS 3DVA Map 3

EntireName: Legionella pneumophila Dot/Icm T4SS 3DVA Map 3
Components
  • Complex: Legionella pneumophila Dot/Icm T4SS 3DVA Map 3
    • Protein or peptide: IcmE protein
    • Protein or peptide: Type IV secretion protein IcmK
    • Protein or peptide: Inner membrane lipoprotein YiaD
    • Protein or peptide: Outer membrane protein, OmpA family protein
    • Protein or peptide: Neurogenic locus notch
    • Protein or peptide: Unknown protein fragment
    • Protein or peptide: Unknown protein fragment
    • Protein or peptide: DotD
    • Protein or peptide: DotF
    • Protein or peptide: DotC
    • Protein or peptide: DUF2807 domain-containing protein

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Supramolecule #1: Legionella pneumophila Dot/Icm T4SS 3DVA Map 3

SupramoleculeName: Legionella pneumophila Dot/Icm T4SS 3DVA Map 3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Legionella pneumophila (bacteria)

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Macromolecule #1: IcmE protein

MacromoleculeName: IcmE protein / type: protein_or_peptide / ID: 1 / Number of copies: 34 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 107.911891 KDa
SequenceString: MASKKENLKS LFSNTRTRVI IIFTAALLII AVVIGFFKIR GATTGSIAAA EVSTVPGGIQ SIPGVLDPTA QYAKLQEEQN ITQAQVAEK TGGSAIPTII RTQALGEGVG VIGSQSGVGF AALAQEELGG PQRSLWIQEL QDGSCSKSVI TKVVNQGAQL T DLKAACSC ...String:
MASKKENLKS LFSNTRTRVI IIFTAALLII AVVIGFFKIR GATTGSIAAA EVSTVPGGIQ SIPGVLDPTA QYAKLQEEQN ITQAQVAEK TGGSAIPTII RTQALGEGVG VIGSQSGVGF AALAQEELGG PQRSLWIQEL QDGSCSKSVI TKVVNQGAQL T DLKAACSC VQLKDSGYGL QELEQVCECK ELKSAGYNAR QLKEAGYSAG RLRNCGFDAC ELRNAGFTAQ EMKDGGFSDG EL KGAGFSD AEIAKASGLP DGITADDVRK AGCGAAALAK LRQAGVSASA IRKISGCTAE QLKAAGYTAK ELKDAGFSAA DLR RAGFSA AELKDAGFTA RDLLNAGFTP ADLAKAGFSD AQIKAAQAEL PPGITPQDVK NAGCDVEALK KEREAGVSAA LIRQ YAGCS AQALKAAGFT DADLANAGFT PAQISAATPL SDAEIKAAGC DPDKLKKLFS AGVSAKRIKE LNGCSAEALK AAGYD AQSL LAAGFTPQEL LAAGFTPKQL EDAGLNPVSI IADGRVADCS VESLKKARAA GVSALTIKQT LGCSAAALKA AGYTAK ELK DAGFTAAELK AAGFSAKELK DAGFTAKELR DAGFSAQELK DVGFSAKDLK DAGFSAAELK AAGFTAAQLK AAGFSAK DL KDAGFSAAEL KAAGFSAKEL KDAGFSASDL KNAGFSAKEL KDAGFSASDL KSAGFSASEL KNAGYSADEL KKAGYTSA E LRNAGFSPQE SAVAGLQGPD LQQLDSSITG IPSIPGATPR PTTSDAASSA EQLQAILQKQ NEQLAEQKYQ QEIQQRTSD MLTAATQLVQ DWKQVETQVY TEGTEETKTS GGESAVPGTG TGTGSNNQPV DQGAVSAQNQ AIIKTGDIMF AVLDTSVNSD EPGPILATI VTGKLKGSKL IGSFNLPSNA DKMVITFNTM SIPGAEKTIS ISAYAIDPNT ARTALASRTN HHYLMRYGSL F ASSFLQGF GNAFQSANTT ITIGGTGGGN NITVANGVGR STLENAVIGL ATVGKAWSQQ AQQLFNTPTT VEVYSGTGLG IL FTQDVTT I

UniProtKB: IcmE protein

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Macromolecule #2: Type IV secretion protein IcmK

MacromoleculeName: Type IV secretion protein IcmK / type: protein_or_peptide / ID: 2 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 38.958926 KDa
SequenceString: MMKKYDQLCK YCLVIGLTFS MSCSIYAADQ SDDAQQALQQ LRMLQQKLSQ NPSPDAQSGA GDGGDNAASD STQQPNQSGQ ANAPAANQT ATAGGDGQII SQDDAEVIDK KAFKDMTRNL YPLNPEQVVK LKQIYETSEY AKAATPGTPP KPTATSQFVN L SPGSTPPV ...String:
MMKKYDQLCK YCLVIGLTFS MSCSIYAADQ SDDAQQALQQ LRMLQQKLSQ NPSPDAQSGA GDGGDNAASD STQQPNQSGQ ANAPAANQT ATAGGDGQII SQDDAEVIDK KAFKDMTRNL YPLNPEQVVK LKQIYETSEY AKAATPGTPP KPTATSQFVN L SPGSTPPV IRLSQGFVSS LVFLDSTGAP WPIAAYDLGD PSSFNIQWDK TSNTLMIQAT KLYNYGNLAV RLRGLNTPVM LT LIPGQKA VDYRVDLRVQ GYGPNAKSMP TEEGIPPSAN DLLLHVLEGV PPPGSRRLVV SGGDARAWLS NEKMYVRTNL TIL SPGWLA SMTSADGTHA YEMQKSPVLL VSWHGKVMQL KVEGL

UniProtKB: Type IV secretion protein IcmK

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Macromolecule #3: Inner membrane lipoprotein YiaD

MacromoleculeName: Inner membrane lipoprotein YiaD / type: protein_or_peptide / ID: 3 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 21.096492 KDa
SequenceString:
MRSLRTNYIY VLFKTTGLLF LLLLSACNRS GYIPENEVPK LPCRVDGACD ATIIKMMTDL NKKGIKVASV GQNYLISIPA SALFADQSP RLNWASYSLL NEIAAFLKQF RKIAITVTSY SSKYVSVKRE RALTLARSRV VSEYLWSQGV DSRIIFTQGL G SDKPITSY TLGGDRSPNA RVEITFRRAV A

UniProtKB: Inner membrane lipoprotein YiaD

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Macromolecule #4: Outer membrane protein, OmpA family protein

MacromoleculeName: Outer membrane protein, OmpA family protein / type: protein_or_peptide / ID: 4 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 27.582047 KDa
SequenceString: MRNLMRCLIM IKSLIKGVDM SRKLAKTRIL GYGLMICFLA GCFHPPYNNF QPDRRAVKRV GVDTGIGAVA GAIASGTASG TLIGAAAGG TVGLVASIYR DSKRKIIRDL QKQDIQYVEY GDTRTLIIPT DKYFMFSSPR LNEICYPGLN NVIRLLNFYP Q STIYVAGF ...String:
MRNLMRCLIM IKSLIKGVDM SRKLAKTRIL GYGLMICFLA GCFHPPYNNF QPDRRAVKRV GVDTGIGAVA GAIASGTASG TLIGAAAGG TVGLVASIYR DSKRKIIRDL QKQDIQYVEY GDTRTLIIPT DKYFMFSSPR LNEICYPGLN NVIRLLNFYP Q STIYVAGF TDNVGSRSHK RKLSQAQAET MMTFLWANGI AAKRLKAEGY GDKNAISDNA IIHGSAQNRR IEIQWFTSPA QP PQPQMAY VK

UniProtKB: Outer membrane protein, OmpA family protein

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Macromolecule #5: Neurogenic locus notch

MacromoleculeName: Neurogenic locus notch / type: protein_or_peptide / ID: 5 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 13.598854 KDa
SequenceString:
MLFLKIKTNQ RTTMNILKPK AFLLASVFVL SISPAFAADG CCSKMGGINY CDSSAGRLVC NNGFYSTCYC TRHAVMDLQF LMGCCLWHG GVYPQLNSSG LVVCNDGYVS EECSLQKPVE QISVY

UniProtKB: Neurogenic locus notch

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Macromolecule #6: Unknown protein fragment

MacromoleculeName: Unknown protein fragment / type: protein_or_peptide / ID: 6 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 783.958 Da
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #7: Unknown protein fragment

MacromoleculeName: Unknown protein fragment / type: protein_or_peptide / ID: 7 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 4.103049 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)

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Macromolecule #8: DotD

MacromoleculeName: DotD / type: protein_or_peptide / ID: 8 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 17.860678 KDa
SequenceString:
MNNNKIVIMF IFSALLAGCA GTMKFKKPPI NNPSDDATIK LAEAAVSVSD SMLEMAKVEK VITPPSKDNT LTIPNAYNLQ ARASVDWSG PIEELTARIA KAAHFRFRVL GKSPSVPVLI SISTKDESLA EILRDIDYQA GKKASIHVYP NSQVVELRYA K IYS

UniProtKB: DotD

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Macromolecule #9: DotF

MacromoleculeName: DotF / type: protein_or_peptide / ID: 9 / Number of copies: 31 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 29.729969 KDa
SequenceString: MMAEHDQNND EYKFAELDSY DMDQAGESDL DSEASYQSGK EGLTKKKDIK RNALIAIGAV VFIMVMYKII GWMFFSDKSS QVTSKPAIP PVTQVATPQP VQTIPTTTPI QQVQPTTIIE DDPDLKKKVS AIEMTQQSLR SEVNALSEQI NAVNNNIKNL N AQIVNLNQ ...String:
MMAEHDQNND EYKFAELDSY DMDQAGESDL DSEASYQSGK EGLTKKKDIK RNALIAIGAV VFIMVMYKII GWMFFSDKSS QVTSKPAIP PVTQVATPQP VQTIPTTTPI QQVQPTTIIE DDPDLKKKVS AIEMTQQSLR SEVNALSEQI NAVNNNIKNL N AQIVNLNQ IIGNMSNQIA RQSEVINVLM ARTTPKKVVK VSRPIVQARI IYYIQAVIPG RAWLIGSNGS TLTVREGSKI PG YGMVKLI DSLQGRILTS SGQVIKFSQE DS

UniProtKB: DotF

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Macromolecule #10: DotC

MacromoleculeName: DotC / type: protein_or_peptide / ID: 10 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 34.162441 KDa
SequenceString: MRKFILSLSI LLSALLVACS SRNHYGDTGS LAGLQAMADS KYTRAQKKQK MGKIREMALK ETALSVGAQA GLAWRAKIID EQLNKQARN LDAIYDFNSL VLEHNILPPV LLEGRNTLNL ADAQSIRISD RTYKVAKQAH FITTPPTWRQ YLWMDYVKPE A PNVTLLPK ...String:
MRKFILSLSI LLSALLVACS SRNHYGDTGS LAGLQAMADS KYTRAQKKQK MGKIREMALK ETALSVGAQA GLAWRAKIID EQLNKQARN LDAIYDFNSL VLEHNILPPV LLEGRNTLNL ADAQSIRISD RTYKVAKQAH FITTPPTWRQ YLWMDYVKPE A PNVTLLPK TKAEKEIWCI YTERGWKNGI DQANTILEEN IARIKEDFGG MILYRKLLAM NMVSPPYVSH TDLGVTGDGS EI HIDDRVL RITALPELNV NSAEWRAAVA KDENALERFK NMEKLANQAK IVITNKSWQP IIAPVS

UniProtKB: DotC

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Macromolecule #11: DUF2807 domain-containing protein

MacromoleculeName: DUF2807 domain-containing protein / type: protein_or_peptide / ID: 11 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 36.095367 KDa
SequenceString: MLKRCYLLIL LMFVLASCAH HKPQTPPAEV KKQGTSSTRQ FRQVSSFNQI VVQGRLNVNL HTGYNKPEVM LRGDPRDLVQ VRTIVKQNT LYVSLGQGYP DYGAVTVDIK TKFLNRFRYE GAGVVTGNNL RTSYLDLYLA NEGTTRLAGN IGLQKLEAVG N GVTQINGV ...String:
MLKRCYLLIL LMFVLASCAH HKPQTPPAEV KKQGTSSTRQ FRQVSSFNQI VVQGRLNVNL HTGYNKPEVM LRGDPRDLVQ VRTIVKQNT LYVSLGQGYP DYGAVTVDIK TKFLNRFRYE GAGVVTGNNL RTSYLDLYLA NEGTTRLAGN IGLQKLEAVG N GVTQINGV SSRNLQIVLK GDPKVLISGF VNLRQLDMYG KGTLSLYWIK SDTLTIRAKK AAKIQLAGIV NRLDVELWDF AQ FKGKYLR AQRSFVKTHD KSVAEISAVN HQSSLATDAS DIYYYNLSKT RADFMAFNGS VLDMREWGQS DLKDFDRYNK QFP

UniProtKB: Putative auto-transporter adhesin head GIN domain-containing protein

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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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 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

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 64698
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-7muv:
Reconstruction of the Legionella pneumophila Dot/Icm T4SS 3DVA Map 3

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