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- EMDB-79055: LPT translocon complex from Bacteroides thetaiotaomicron - focus ... -

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Basic information

Entry
Database: EMDB / ID: EMD-79055
TitleLPT translocon complex from Bacteroides thetaiotaomicron - focus volume, membrane and extracellular region
Map datarefinement volume
Sample
  • Complex: LPT translocon complex
    • Protein or peptide: x 11 types
KeywordsLPS transport SLP transport outer membrane protein complex / MEMBRANE PROTEIN
Biological speciesBacteroides thetaiotaomicron (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsLea SM / Berks BC
Funding support United States, European Union, 3 items
OrganizationGrant numberCountry
Other private United States
European Research Council (ERC)101201241European Union
European Research Council (ERC)833713European Union
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionSep 13, 2026-
Header (metadata) releaseOct 21, 2026-
Map releaseOct 21, 2026-
UpdateOct 21, 2026-
Current statusOct 21, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_79055.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationrefinement volume
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 380 pix.
= 499.7 Å
1.32 Å/pix.
x 380 pix.
= 499.7 Å
1.32 Å/pix.
x 380 pix.
= 499.7 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.315 Å
Density
Contour LevelBy AUTHOR: 0.295
Minimum - Maximum-0.74536544 - 1.7073375
Average (Standard dev.)0.00043593897 (±0.029642224)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 499.7 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_79055_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: deepEMhanced volume

Fileemd_79055_additional_1.map
AnnotationdeepEMhanced volume
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: half map B

Fileemd_79055_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: half map A

Fileemd_79055_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : LPT translocon complex

EntireName: LPT translocon complex
Components
  • Complex: LPT translocon complex
    • Protein or peptide: LptA
    • Protein or peptide: LptE
    • Protein or peptide: LptQ
    • Protein or peptide: LptT
    • Protein or peptide: LptV
    • Protein or peptide: LptD
    • Protein or peptide: LptN
    • Protein or peptide: LptP
    • Protein or peptide: LptR
    • Protein or peptide: LptR
    • Protein or peptide: LptU

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Supramolecule #1: LPT translocon complex

SupramoleculeName: LPT translocon complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacteroides thetaiotaomicron (bacteria)

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Macromolecule #1: LptA

MacromoleculeName: LptA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron (bacteria)
Molecular weightTheoretical: 45.297156 KDa
SequenceString: MLKQNKKDKQ QDGHRWLLIG FLCLFAVCLV AQVKPTGQTK KAETPAAKTP NGTKQTDKDI KKEPENKKTK VYLLHANQGQ ADKLARPDVQ VLIGNVKLRH DSMYMFCDSA LIYEKTNSVE AFSNVRMEQG DTLFIYGDYL YYDGMTQIAQ IRENVKMINR NTTLLTDSLN ...String:
MLKQNKKDKQ QDGHRWLLIG FLCLFAVCLV AQVKPTGQTK KAETPAAKTP NGTKQTDKDI KKEPENKKTK VYLLHANQGQ ADKLARPDVQ VLIGNVKLRH DSMYMFCDSA LIYEKTNSVE AFSNVRMEQG DTLFIYGDYL YYDGMTQIAQ IRENVKMINR NTTLLTDSLN YDRLYDLGYY FEGGTLMDEE NVLTSDWGEY SPATKQSVFN HDVKLVNPKF VLTSDTLKYN TFSKIATILG PSNIVSDNNH IYSERGFYNT LSEQAELLDR SILTNEGKKL IGDSLFYDRK VGYGEAFDNI RMTDTINKNM LTGDYCFYNE LADSAFATKR AVAIDYSQGD SLFMHGDTLQ LISYNLNTDS VFRLMKAYHK VRMYRTDVQG VCDSLVYNSK DSCLTMYTDP ILWNEGQQLL GEEIKIYMND STINWAHIIN QALTVEMKDS VHYNQVSGKE MKAYFENGDM RHIEVIGNVM TAFYPEEKDS TMTGFNNMEG SVLHLYMKEK KMEKGMFVGK SNGTLYPMDQ IPPDKLRLST FAWFDYVRPL NKEDIFNWRG KKEGETLKPT TDRKPKTDKR SLINMK

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Macromolecule #2: LptE

MacromoleculeName: LptE / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron (bacteria)
Molecular weightTheoretical: 16.416078 KDa
SequenceString:
MNWIKKIARP LILIVLPAVI IACSVSYKFN GSSINYDKVK TISIADFPIK SEYVYAPLAT KFNEDLKDIF IRQTRLQLLK PNQNADLQID GEITGYNQYN QAVSADGYSS ETKLTITVNV RFVNNTNHAE DFEQQFSAFR TYDSSQLLTA VQDGLIAEMS KEITDQIFNA TVANW

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Macromolecule #3: LptQ

MacromoleculeName: LptQ / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron (bacteria)
Molecular weightTheoretical: 23.029232 KDa
SequenceString: VLLLFCIGIP TIAQQQRPTP VQKRDQKKKE AVVDTIPFYN GTYVGVDIYG IGSKMLGGDF MSSEVSIGVN LKNKFIPTIE FGMGGTDTWN ETGIHYKSKT APFFRIGVDY NTMAKKKEKN SYLYVGLRYA FSSFKYDVST LPVDDPIWGG SIGNPSLEDD YWGGSVPFSH ...String:
VLLLFCIGIP TIAQQQRPTP VQKRDQKKKE AVVDTIPFYN GTYVGVDIYG IGSKMLGGDF MSSEVSIGVN LKNKFIPTIE FGMGGTDTWN ETGIHYKSKT APFFRIGVDY NTMAKKKEKN SYLYVGLRYA FSSFKYDVST LPVDDPIWGG SIGNPSLEDD YWGGSVPFSH LGMKGSMQWF ELVVGVKVRI YKNFNMGWSV RMKYKTNAST NEYANPWYVP GYGKFKSNNM GITYSLIYKL PL

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Macromolecule #4: LptT

MacromoleculeName: LptT / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron (bacteria)
Molecular weightTheoretical: 16.168415 KDa
SequenceString: MTRKSKKYQL PIITLLLCFL QVAGIDVYAQ EPVTPVQKDS IIQSREAPKA RARRHRDPAQ VMDSLKKDSI KILHPERLQA TDSLSAVKIQ IADSLDAANK KELKKIEQPA PIVVKTDTVP PVQDLNKKLF IPNPTKATWL AVVFPGGGQI YNRKYWKLPI IYGGFAGCAY ...String:
MTRKSKKYQL PIITLLLCFL QVAGIDVYAQ EPVTPVQKDS IIQSREAPKA RARRHRDPAQ VMDSLKKDSI KILHPERLQA TDSLSAVKIQ IADSLDAANK KELKKIEQPA PIVVKTDTVP PVQDLNKKLF IPNPTKATWL AVVFPGGGQI YNRKYWKLPI IYGGFAGCAY ALSWNGKMYK DYSQAYLDIM DSNPNTKSYE DLLPPNAQYN EEQLKNTLKR RKDSFRRFRD LSIFAFIGVY LISIIDAYVD AELSNFDISP DLSMKLEPTV IDNNSQFRSN SYKNKSVGLQ CVLRF

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Macromolecule #5: LptV

MacromoleculeName: LptV / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron (bacteria)
Molecular weightTheoretical: 23.92599 KDa
SequenceString: MTKIKSLLIA ASLMMGLALP ATAQIGEPRQ NFSVGFNGGV NLNSASFTPK IKQNSLMGIT GGLTARYISE KYFAMICGAQ VELNISQRGW DELFEVPGEN GEPVEDPTRK YTRKMTYLDI PFLAHLAFGN EKGLQFFINA GPQIGLLIGE SESMENIDMN ALTDTQKAVY ...String:
MTKIKSLLIA ASLMMGLALP ATAQIGEPRQ NFSVGFNGGV NLNSASFTPK IKQNSLMGIT GGLTARYISE KYFAMICGAQ VELNISQRGW DELFEVPGEN GEPVEDPTRK YTRKMTYLDI PFLAHLAFGN EKGLQFFINA GPQIGLLIGE SESMENIDMN ALTDTQKAVY GDKIQNKFDY GIAGGGGIEF RTKKAGSFLL EGRYYFALSD FYSTTKKDYF SRAAHGTITV KLTYLFDLKK

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Macromolecule #6: LptD

MacromoleculeName: LptD / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron (bacteria)
Molecular weightTheoretical: 89.284461 KDa
SequenceString: MAPLRAKIII SFILLIVLLM LPDEATSQRR RRGMIASNTA QTDSLNRKDS LGADTVVVRV DSVWSHPQFE KGGGSGGGSG GSAWSHPQFE KVDSVAPTKK QPFVAPVIYE SNDSTTFTLG GAATLYGSGK VNYQNIELAA EVISMNLDSS TVHAYGIKDT TGTIKGKPVF ...String:
MAPLRAKIII SFILLIVLLM LPDEATSQRR RRGMIASNTA QTDSLNRKDS LGADTVVVRV DSVWSHPQFE KGGGSGGGSG GSAWSHPQFE KVDSVAPTKK QPFVAPVIYE SNDSTTFTLG GAATLYGSGK VNYQNIELAA EVISMNLDSS TVHAYGIKDT TGTIKGKPVF KEGETAYDTE TISYNFKSKK AGITDIITQQ GEGYVTGSRA KKGANDEIFM EHGRYTTCDH HDHPHFYMQL TRAKVRPKKN VVTGPAYLVV EDVPLPLAVP FFFFPFSSSY SSGFIMPTYM DDSSRGFGLA EGGYYFAMSD IMDLKLTGDI FTKGSWRLSG LTNYNKRYKY SGTLQADYQV TKTGDKGMPD YTVAKDFKVV WNHRQDAKAS PNSTFSASVN FSTSSYERSN INNLYNSQLL TQNTKTSSIS YSRSFPDIGL TLSGTTNIAQ TMRDSSIAVT LPDLNITLSR LFPFKRKKAA GAERWYEKIS VSYTGRLTNS IRTKDDRLFK TGISGWENAM NHNIPVSATF TLFKYLQVNP SVNYTERWYT RKINQTYNEE TGRLEQNLND TINGFYRVSN YSASLSLSTK LYGMYKPLFM KKKEIQIRHV VTPQVGISGA PAFSKYWEEY TDNNGNTQYY SPYTGQPFGV PSREGSGTVS FSIANNLEMK YYDAKKDTLK KVSLIDDLSV NMSYNMAAKE KPWSPLSMNL RLKLTKNYTF NMNASFATYA YTFDKSGNVV EGNRTEWSYG RFGRFQGYGS SFNYTFNNDT WKKWFGPKED EKDKDKKESE DGDGEDSEGT EDGTTTKKVE KAQADPDGYQ VFKMPWSLSF SYSFNIREDR TKPINRYSMR YPFTYTHNIN MNGNVKISNN WSLSFNSGYD FQAKEITQTS CTISRDLHCF NLSASLSPFG RWKYYNVTIR ANASILQDLK YEQRSQTQSN IQWY

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Macromolecule #7: LptN

MacromoleculeName: LptN / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron (bacteria)
Molecular weightTheoretical: 72.931789 KDa
SequenceString: MRRILLLYIL FSVVGLSAIH AQLNPARQQI DENGRDQYGN QVDPAMIPDK LDSANVEVQG LPPTLYMWRI KNQLGDRTMI PADTTYHHFQ NTNLTEGITG HYNYLANLGS PRLSRIFFER RYPEPTIFME SFSSFFIRPT EFNFTNSNVP YTNLTYHKAG NKQNGEERFK ...String:
MRRILLLYIL FSVVGLSAIH AQLNPARQQI DENGRDQYGN QVDPAMIPDK LDSANVEVQG LPPTLYMWRI KNQLGDRTMI PADTTYHHFQ NTNLTEGITG HYNYLANLGS PRLSRIFFER RYPEPTIFME SFSSFFIRPT EFNFTNSNVP YTNLTYHKAG NKQNGEERFK SYFSVNVNKK LAFGFNIDYL YGRGYYNNQN TSYFNAALFG SYIGDRYQVQ GIYSNNYLKT NENGGITDDR YITAPEEMAE GRKEYESVNI PTVLNASANR NHDFYVFLTQ RYNLGFHRDI PQAENDTMPA KQEFVPVTSF IHTIQVERSR HNFRSDDNVE NYYKQTLLDK ENTFVRDSTV YIGVKNTIGI ALLEGFNKYA KAGLTAFASH KLSKYSLMSL DPLKQDKYNE TEIYIGGELT KKQGNFLHYH AIGEVGMAGK AIGQFDVKGD IDLNIPLWKD TVSVIARGEI SNKLAPFYMR HYHSKHFWWD DDMDKEFRTR IEGELSIANW GTRLRAGVEN IKNYTYFNQQ ALPEQKGGSL QVVSACFNQD FKVGIFHLDN EVIWQKSSDQ AVLPLPELSL YHNFYMQFKL AKKVLSVQLG ADVRYFTKYD APAYMPATQQ FYLQPEEGKV EIGGYPIVNV YANLHLKRTR FYVMMYHVNQ GMSKPNYFLA PHYPINPRVL KFGLSWNFYD

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Macromolecule #8: LptP

MacromoleculeName: LptP / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron (bacteria)
Molecular weightTheoretical: 61.967645 KDa
SequenceString: MLQFENQKIK HIVRKALPVI ALVAILYSCA SIGRPEGGPK DYDPPRFVGS TPAAGAINNK RTKVSLQFDE FIKLEKATEK VVVSPPQIQQ PEIKASGKKI QVNLLDSLKP NTTYTIDFSD AIVDNNEGNP LGNFAFTFST GAQIDTMEVS GTVLDASNLE PIKGILVGLH ...String:
MLQFENQKIK HIVRKALPVI ALVAILYSCA SIGRPEGGPK DYDPPRFVGS TPAAGAINNK RTKVSLQFDE FIKLEKATEK VVVSPPQIQQ PEIKASGKKI QVNLLDSLKP NTTYTIDFSD AIVDNNEGNP LGNFAFTFST GAQIDTMEVS GTVLDASNLE PIKGILVGLH ANLNDSAFTK LPFDRVARTD SRGRFSIRGV APGKYRIFGL MDSDQNFAFT QKSEVIAFND SLIIPRMEER LRMDTAWVDS LTYDTIVEKK YMHYLPDDVI LRAFKELNYS QYLIKSERLV PQKFTFYFAG KADTLPVLKG LNFDEKEAFV IEKNQRNDTI HYWVKDSLLY KQDTLALSLT YLYTDTLNQL IPRTDTLKLV SKQKTLTKEE PEKKKKKKKK EGEEDEPIPT KFLPVNVNAP SSMDVYGYVS LNFEEPIASF DTAAIHLRQK VDTIWKDIPF EFEQDSLNLR RFNLYPENDW EPTMEYEFSV DSTAFHGIYG LFTDKIKQSF KVRSEDEYFT LHFIVTGADP QAFVELLDTQ DKVVRRRLVE DGRADFYYLN PGKYAARLIN DRNGNGEWDT GDYAKGIQPE EVYYFPKVVE YKALWDVDQN WDIHATPVDK QKLDELKKQK PDEDKKKKER ERDRNNQNRN RR

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Macromolecule #9: LptR

MacromoleculeName: LptR / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron (bacteria)
Molecular weightTheoretical: 15.897076 KDa
SequenceString:
MKNLIRIFLI VVIVGAGISI GSSCSDENDC SLAGRPMMYC TLYTIDEITD LRVNDTLDSL TITALGTDSI ILNNQKKVHT LMLPLRYTSD TTVFILWYNP NSPTNKKDVD TLYIIQKNTP YFQSMECGYM MKQNILSTKF GNTKNSSERI DSLHIQNKEA NTNEIENLQI FYRYRDRTPP TIE

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Macromolecule #10: LptR

MacromoleculeName: LptR / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron (bacteria)
Molecular weightTheoretical: 16.839123 KDa
SequenceString:
MKNLIRIFLI VVIVGAGISI GSSCSDENDC SLAGRPMMYC TLYTIDEITD LRVNDTLDSL TITALGTDSI ILNNQKKVHT LMLPLRYTSD TTVFILWYNP NSPTNKKDVD TLYIIQKNTP YFQSMECGYM MKQNILSTKF GNTKNSSERI DSLHIQNKEA NTNEIENLQI FYRYRDRTPP TIE

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Macromolecule #11: LptU

MacromoleculeName: LptU / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron (bacteria)
Molecular weightTheoretical: 39.418219 KDa
SequenceString: MTNLRKILLI PALIVVSVSS FFSCGVDRWP EYAHLTELDT WMYDIMQQNY LWYQYMPGYD EVNLFQDPAT FLSKAKWDKD SYSFVDSVLE APLPTYGFDY SLVKSQDNDT AYNALITYVI PESPAEKAGL QRGDWIMKVD TSYISKKYET QLLQGTIARE LSMGVWKEVE ...String:
MTNLRKILLI PALIVVSVSS FFSCGVDRWP EYAHLTELDT WMYDIMQQNY LWYQYMPGYD EVNLFQDPAT FLSKAKWDKD SYSFVDSVLE APLPTYGFDY SLVKSQDNDT AYNALITYVI PESPAEKAGL QRGDWIMKVD TSYISKKYET QLLQGTIARE LSMGVWKEVE EEPEEGEEVP EEPVMVYKVV PNGVTLDLGA AQSIEDQPVH KYKILTLDNG AKVGYLMYNS FTAGTNNDPE KYNNELRKVS TIFQEANVQA TILDLRYNEG GSLDCVQLLA TILVPNARMG TPMAYLEYND KNLDKDATIN FDQEVLKTGV NLNQNTLVAI TSGTTAGAAE MLLTSLYKEE QAPNIIVMGS ASKGQTVATE QFINETYRWS VNPVVCTVYN SDHDAGEDAF VLVPSDKFKI SETSINGTTD YSQFLPFGNP KERMLSIAIQ TLEGTYPPKD EDKEEETRST KSIKIEKSVS SPASRRFAGG LRIK

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
DetailsData were collected at both 200kV and 300kV on two different Titan Krios and an Arctica
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Details: Data were collected on three microscopes Titan Krios / Gatan K3 BioQuantum Titan Krios / Falcon 4i Arctica / Gatan K3 BioQuantum
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsData were combined from two different Gatan K3 Bioquantum detectors and a Falcon 4i
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 130464
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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