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- EMDB-22081: Cryo-EM Structure of the Helicobacter pylori OMC -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-22081
TitleCryo-EM Structure of the Helicobacter pylori OMC
Map dataHelicobacter pylori OMC
Sample
  • Complex: Helicobacter pylori Cag T4SS OMC
    • Protein or peptide: Type IV secretion system apparatus protein Cag3
    • Protein or peptide: Type IV secretion system apparatus protein CagM
    • Protein or peptide: Type IV secretion system apparatus protein CagT
    • Protein or peptide: Unknown protein fragment
    • Protein or peptide: Type IV secretion system apparatus protein CagX
    • Protein or peptide: Cag pathogenicity island protein (Cag7)
KeywordsHelicobacter / T4SS / Secretion / Cag / PROTEIN TRANSPORT
Function / homology
Function and homology information


Cag pathogenicity island protein Cag12 / Cag pathogenicity island protein Cag12 / CagY type 1 repeat / CagY type 1 repeat / DC-EC / DC-EC Repeat / Type IV secretion system CagX conjugation protein / Conjugal transfer, TrbG/VirB9/CagX / VirB9/CagX/TrbG, C-terminal / VirB9/CagX/TrbG, C-terminal domain superfamily ...Cag pathogenicity island protein Cag12 / Cag pathogenicity island protein Cag12 / CagY type 1 repeat / CagY type 1 repeat / DC-EC / DC-EC Repeat / Type IV secretion system CagX conjugation protein / Conjugal transfer, TrbG/VirB9/CagX / VirB9/CagX/TrbG, C-terminal / VirB9/CagX/TrbG, C-terminal domain superfamily / Conjugal transfer protein / Type IV secretion system, VirB10/TrbI / Bacterial conjugation TrbI-like protein / Type IV secretion system, VirB10 / TraB / TrbI / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Type IV secretion system apparatus protein Cag3 / Sodium:calcium antiporter / Type IV secretion system apparatus protein CagX / Cag pathogenicity island protein (Cag7) / Cag pathogenicity island protein
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsSheedlo MJ / Chung JM
Funding support United States, 7 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI118932 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA116087 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI039657 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)2T32DK007673 United States
National Institutes of Health/Office of the DirectorS10OD020011 United States
Other government1I01BX004447 United States
CitationJournal: Elife / Year: 2020
Title: Cryo-EM reveals species-specific components within the Cag type IV secretion system core complex.
Authors: Michael J Sheedlo / Jeong Min Chung / Neha Sawhney / Clarissa L Durie / Timothy L Cover / Melanie D Ohi / D Borden Lacy /
Abstract: The pathogenesis of -associated gastric cancer is dependent on delivery of CagA into host cells through a type IV secretion system (T4SS). The Cag T4SS includes a large membrane-spanning core ...The pathogenesis of -associated gastric cancer is dependent on delivery of CagA into host cells through a type IV secretion system (T4SS). The Cag T4SS includes a large membrane-spanning core complex containing five proteins, organized into an outer membrane cap (OMC), a periplasmic ring (PR) and a stalk. Here, we report cryo-EM reconstructions of a core complex lacking Cag3 and an improved map of the wild-type complex. We define the structures of two unique species-specific components (Cag3 and CagM) and show that Cag3 is structurally similar to CagT. Unexpectedly, components of the OMC are organized in a 1:1:2:2:5 molar ratio (CagY:CagX:CagT:CagM:Cag3). CagX and CagY are components of both the OMC and the PR and bridge the symmetry mismatch between these regions. These results reveal that assembly of the T4SS core complex is dependent on incorporation of interwoven species-specific components.
History
DepositionMay 29, 2020-
Header (metadata) releaseOct 7, 2020-
Map releaseOct 7, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6x6s
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6x6s
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22081.png

Downloads & links

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Map

FileDownload / File: emd_22081.map.gz / Format: CCP4 / Size: 506 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHelicobacter pylori OMC
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.64 Å/pix.
x 510 pix.
= 836.4 Å		1.64 Å/pix.
x 510 pix.
= 836.4 Å		1.64 Å/pix.
x 510 pix.
= 836.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.64 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.056124672 - 0.13887374
Average (Standard dev.)0.00016198565 (±0.0035887666)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions510510510
Spacing510510510
CellA=B=C: 836.39996 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.641.641.64
M x/y/z510510510
origin x/y/z0.0000.0000.000
length x/y/z836.400836.400836.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ510510510
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS510510510
D min/max/mean-0.0560.1390.000

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Supplemental data

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Sample components

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Entire : Helicobacter pylori Cag T4SS OMC

EntireName: Helicobacter pylori Cag T4SS OMC
Components
  • Complex: Helicobacter pylori Cag T4SS OMC
    • Protein or peptide: Type IV secretion system apparatus protein Cag3
    • Protein or peptide: Type IV secretion system apparatus protein CagM
    • Protein or peptide: Type IV secretion system apparatus protein CagT
    • Protein or peptide: Unknown protein fragment
    • Protein or peptide: Type IV secretion system apparatus protein CagX
    • Protein or peptide: Cag pathogenicity island protein (Cag7)

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Supramolecule #1: Helicobacter pylori Cag T4SS OMC

SupramoleculeName: Helicobacter pylori Cag T4SS OMC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Helicobacter pylori (bacteria)

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Macromolecule #1: Type IV secretion system apparatus protein Cag3

MacromoleculeName: Type IV secretion system apparatus protein Cag3 / type: protein_or_peptide / ID: 1 / Number of copies: 70 / Enantiomer: LEVO
Source (natural)Organism: Helicobacter pylori (bacteria)
Molecular weightTheoretical: 55.105828 KDa
SequenceString: MFRKLATAVS LIGLLTSNTL YAKEISEADK VIKATKETKE TKKEAKRLKK EAKQRQQIPD HKKPQYVSVD DTKTQALFDI YDTLNVNDK SFGDWFGNSA LKDKTYLYAM DLLDYNNYLS IENPIIKTRA MGTYADLIII TGSLEQVNGY YNILKALNKR N AKFVLKIN ...String:
MFRKLATAVS LIGLLTSNTL YAKEISEADK VIKATKETKE TKKEAKRLKK EAKQRQQIPD HKKPQYVSVD DTKTQALFDI YDTLNVNDK SFGDWFGNSA LKDKTYLYAM DLLDYNNYLS IENPIIKTRA MGTYADLIII TGSLEQVNGY YNILKALNKR N AKFVLKIN ENMPYAQATF LRVPKRSDPN AHTLDKGASI DENKLFEQQK KMYFNYANDV ICRPDDEVCS PLRDEMVAMP TS DSVTQKP NIIAPYSLYR LKETNNANEA QPSPYATATA PENSKEKLIE ELIANSQLVA NEEEREKKLL AEKEKQEAEL AKY KLKDLE NQKKLKALEA ELKKKNAKKP RVVEVPVSPQ TSNSDETMRV VKEKENYNGL LVDKETTIKR SYEGTLISEN SYSK KTPLN PNDLRSLEEE IKSYYIKSNG LCYTNGINLY VKIKNDPYKE GMLCGYESVQ NLLSPLKDKL KYDKQKLQKA LLKDS K

UniProtKB: Type IV secretion system apparatus protein Cag3

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Macromolecule #2: Type IV secretion system apparatus protein CagM

MacromoleculeName: Type IV secretion system apparatus protein CagM / type: protein_or_peptide / ID: 2 / Number of copies: 28 / Enantiomer: LEVO
Source (natural)Organism: Helicobacter pylori (bacteria)
Molecular weightTheoretical: 43.830027 KDa
SequenceString: MLAKIVFSSL VAFGVLSANV EQFGSFFNEI KKEQEEVAAK EDALKARKKL LNNTHDFLED LIFRKQKIKE LMDHRAKVLS DLENKYKKE KEALEKETRG KILTAKSKAY GDLEQALKDN PLYRKLLPNP YAYVLNQETF TKEDRERLSY YYPQVKTSSI F KKTTATTK ...String:
MLAKIVFSSL VAFGVLSANV EQFGSFFNEI KKEQEEVAAK EDALKARKKL LNNTHDFLED LIFRKQKIKE LMDHRAKVLS DLENKYKKE KEALEKETRG KILTAKSKAY GDLEQALKDN PLYRKLLPNP YAYVLNQETF TKEDRERLSY YYPQVKTSSI F KKTTATTK DKAQALLQMG VFSLDEEQNK KASRLALSYK QAIEEYSNNV SNLLSRKELD NIDYYLQLER NKFDSKAKDI AQ KATNTLI FNSERLAFSM AIDKINEKYL RGYEAFSNLL KNVKDDVELN TLTKNFTNQK LSFAQKQKLC LLVLDSFNFD TQS KKSILK KTNEYNIFVD SDPMMSDKTT MQKEHYKIFN FFKTVVSAYR NNVAKNNPFE

UniProtKB: Sodium:calcium antiporter

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Macromolecule #3: Type IV secretion system apparatus protein CagT

MacromoleculeName: Type IV secretion system apparatus protein CagT / type: protein_or_peptide / ID: 3 / Number of copies: 28 / Enantiomer: LEVO
Source (natural)Organism: Helicobacter pylori (bacteria)
Molecular weightTheoretical: 32.418971 KDa
SequenceString: MKLRASVLIG ATILCLILSA CSNYAKKVVK QKNHVYTPVY NELIEKYSEI PLNDKLKDTP FMVQVKLPNY KDYLLDNKQV VLTFKLVHH SKKITLIGDA NKILQYKNYF QANGARSDID FYLQPTLNQK GVVMIASNYN DNPNSKEKPQ TFDVLQGSQP M LGANTKNL ...String:
MKLRASVLIG ATILCLILSA CSNYAKKVVK QKNHVYTPVY NELIEKYSEI PLNDKLKDTP FMVQVKLPNY KDYLLDNKQV VLTFKLVHH SKKITLIGDA NKILQYKNYF QANGARSDID FYLQPTLNQK GVVMIASNYN DNPNSKEKPQ TFDVLQGSQP M LGANTKNL HGYDVSGANN KQVINEVARE KAQLEKINQY YKTLLQDKEQ EYTTRKNNQR EILETLSNRA GYQMRQNVIS SE IFKNGNL NMQAKEEEVR EKLQEERENE YLRNQIRSLL SGK

UniProtKB: Cag pathogenicity island protein

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Macromolecule #4: Unknown protein fragment

MacromoleculeName: Unknown protein fragment / type: protein_or_peptide / ID: 4 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Helicobacter pylori (bacteria)
Molecular weightTheoretical: 13.634798 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)(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)(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 #5: Type IV secretion system apparatus protein CagX

MacromoleculeName: Type IV secretion system apparatus protein CagX / type: protein_or_peptide / ID: 5 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Helicobacter pylori (bacteria)
Molecular weightTheoretical: 60.72048 KDa
SequenceString: MGQAFFKKIV GCFCLGYLFL SSAIEAAALD IKNFNRGRVK VVNKKIAYLG DEKPITIWTS LDNVTVIQLE KDETISYITT GFNKGWSIV PNSNHIFIQP KSVKSNLMFE KEAVNFALMT RDYQEFLKTK KLIVDAPDPK ELEEQKKALE KEKEAKEQAQ K AQKDKREK ...String:
MGQAFFKKIV GCFCLGYLFL SSAIEAAALD IKNFNRGRVK VVNKKIAYLG DEKPITIWTS LDNVTVIQLE KDETISYITT GFNKGWSIV PNSNHIFIQP KSVKSNLMFE KEAVNFALMT RDYQEFLKTK KLIVDAPDPK ELEEQKKALE KEKEAKEQAQ K AQKDKREK RKEERAKNRA NLENLTNAMS NPQNLSNNKN LSEFIKQQRE NELDQMERLE DMQEQAQANA LKQIEELNKK QA EETIKQR AKDKINIKTD KPQKSPEDNS IELSPSDSAW RTNLVVRTNK ALYQFILRIA QKDNFASAYL TVKLEYPQRH EVS SVIEEE LKKREEAKRQ KELIKQENLN TTAYINRVMM ASNEQIINKE KIREEKQKII LDQAKALETQ YVHNALKRNP VPRN YNYYQ APEKRSKHIM PSEIFDDGTF TYFGFKNITL QPAIFVVQPD GKLSMTDAAI DPNMTNSGLR WYRVNEIAEK FKLIK DKAL VTVINKGYGK NPLTKNYNIK NYGELERVIK KLPLVRDK

UniProtKB: Type IV secretion system apparatus protein CagX

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Macromolecule #6: Cag pathogenicity island protein (Cag7)

MacromoleculeName: Cag pathogenicity island protein (Cag7) / type: protein_or_peptide / ID: 6 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Helicobacter pylori (bacteria)
Molecular weightTheoretical: 219.748641 KDa
SequenceString: MNEENDKLET SKKAQQDSPQ DLSNEEATEA NHFENLLKES KESSDHHLDN PTETQTHFDG DKSEETQTQM DSEGNETSES SNGSLADKL FKKARKLVDN KKPFTQQKNL DEETQELNEE DDQENNEYQE ETQTDLIDDE TSKKTQQHSP QDLSNEEATE A NHFENLLK ...String:
MNEENDKLET SKKAQQDSPQ DLSNEEATEA NHFENLLKES KESSDHHLDN PTETQTHFDG DKSEETQTQM DSEGNETSES SNGSLADKL FKKARKLVDN KKPFTQQKNL DEETQELNEE DDQENNEYQE ETQTDLIDDE TSKKTQQHSP QDLSNEEATE A NHFENLLK ESKESSDHHL DNPTETQTNF DGDKSEETQT QMDSEGNETS ESSNGSLADK LFKKARKLVD NKKPFTQQKN LD EETQELN EEDDQENNEY QEETQTDLID DETSKKTQQH SPQDLSNEEA TEANHFENLL KESKESSDHH LDNPTETQTN FDG DKSEEI TDDSNDQEII KGSKKKYIIG GIVVAVLIVI ILFSRSIFHY FMPLEDKSSR FSKDRNLYVN DEIQIRQEYN RLLK ERNEK GNMIDKNLFF NDDPNRTLYN YLNIAEIEDK NPLRAFYECI SNGGNYEECL KLIKDKKLQD QMKKTLEAYN DCIKN AKTE EERIKCLDLI KDENLKKSLL NQQKVQVALD CLKNAKTDEE RNECLKLIND PEIREKFRKE LELQKELQEY KDCIKN AKT EAEKNKCLKG LSKEAIERLK QQALDCLKNA KTDEERNECL KNIPQDLQKE LLADMSVKAY KDCVSKARNE KEKQECE KL LTPEARKKLE QQVLDCLKNA KTDEERKKCL KDLPKDLQSD ILAKESLKAY KDCVSQAKTE AEKKECEKLL TPEAKKLL E EEAKESVKAY LDCVSQAKTE AEKKECEKLL TPEAKKKLEE AKKSVKAYLD CVSRARNEKE KKECEKLLTP EAKKLLEQQ ALDCLKNAKT DKERKKCLKD LPKDLQKKVL AKESVKAYLD CVSQAKTEAE KKECEKLLTP EARKLLEEAK KSVKAYLDCV SQAKTEAEK KECEKLLTPE ARKLLEE(UNK)AK ESVKAYLDCV SQAKNEAEKK ECEKLLTLES KKKLEEAKKS VKAYLDC VS QAKTEAEKKE CEKLLTPEAK KLLEQQALDC LKNAKTEADK KRCVKDLPKD LQKKVLAKES LKAYKDCVSK ARNEKEKK E CEKLLTPEAK KLLEEAKKSV KAYLDCVSQA KTEAEKKECE KLLTPEARKL LEEAKESVKA YKDCVSKARN EKEKKECEK LLTPEAKKLL EQQVLDCLKN AKTEADKKRC VKDLPKDLQK KVLAKESVKA YLDCVSRARN EKEKKECEKL LTPEAKKLLE EAKESLKAY KDCLSQARNE EERRACEKLL TPEARKLLEQ EVKKSIKAYL DCVSRARNEK EKKECEKLLT PEARKFLAKQ V LNCLEKAG NEEERKACLK NLPKDLQENI LAKESLKAYK DCLSQARNEE ERRACEKLLT PEARKLLEQE VKKSVKAYLD CV SRARNEK EKKECEKLLT PEARKFLAKE LQQKDKAIKD CLKNADPNDR AAIMKCLDGL SDEEKLKYLQ EAREKAVADC LAM AKTDEE KRKCQNLYSD LIQEIQNKRT QNKQNQLSKT ERLHQASECL DNLDDPTDQE AIEQCLEGLS DSERALILGI KRQA DEVDL IYSDLRNRKT FDNMAAKGYP LLPMDFKNGG DIATINATNV DADKIASDNP IYASIEPDIA KQYETEKTIK DKNLE AKLA KALGGNKKDD DKEKSKKSTA EAKAENNKID KDVAETAKNI SEIALKNKKE KSGEFVDENG NPIDDKKKAE KQDETS PVK QAFIGKSDPT FVLAQYTPIE ITLTSKVDAT LTGIVSGVVA KDVWNMNGTM ILLDKGTKVY GNYQSVKGGT PIMTRLM IV FTKAITPDGV IIPLANAQAA GMLGEAGVDG YVNNHFMKRI GFAVIASVVN SFLQTAPIIA LDKLIGLGKG RSERTPEF N YALGQAINGS MQSSAQMSNQ ILGQLMNIPP SFYKNEGDSI KILTMDDIDF SGVYDVKITN KSVVDEIIKQ STKTLSREH EEITTSPKGG N

UniProtKB: Cag pathogenicity island protein (Cag7)

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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: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Average electron dose: 59.2 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #1 - Average electron dose: 59.0 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

Image recording ID1
Startup modelType of model: EMDB MAP
Final reconstructionApplied symmetry - Point group: C14 (14 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 47440
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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