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- EMDB-43118: The secreted adhesin EtpA of Enterotoxigenic Escherichia coli in ... -

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Basic information

Entry
Database: EMDB / ID: EMD-43118
TitleThe secreted adhesin EtpA of Enterotoxigenic Escherichia coli in complex with the mouse mAb 1C08
Map data
Sample
  • Complex: EtpA in complex with the mAb 1C08 Fab
    • Protein or peptide: EtpA
    • Protein or peptide: mAb 1C08 Heavy Chain
    • Protein or peptide: mAb 1C08 Light Chain
  • Ligand: beta-D-glucopyranose
KeywordsAdhesin / glycoprotein / lectin / antibody-antigen complex / CELL ADHESION
Function / homology
Function and homology information


periplasmic space / cell surface
Similarity search - Function
: / Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain / haemagglutination activity domain / ESPR domain / Extended Signal Peptide of Type V secretion system / Parallel beta-helix repeat / Parallel beta-helix repeats / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
Biological speciesEscherichia coli ETEC H10407 (bacteria) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsBerndsen ZT / Ward AB
Funding support United States, 7 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI126887 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI089894 United States
Department of Veterans Affairs (VA, United States)5I01BX001469-05). United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32AI007172 United States
Consortia for HIV/AIDS Vaccine DevelopmentUM1 AI144462 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI100663 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI113867 United States
CitationJournal: To Be Published
Title: Structure and Antigenicity of the Secreted Glycoprotein Adhesin EtpA of Enterotoxigenic Escherichia coli
Authors: Berndsen ZT / Akhtar M / Thapa M / Vickers T / Schmitz A / Torres JL / Baboo S / Kumar P / Khatoom N / Sheikh A / Hamrick M / Diedrich JK / Bartolome SM / Garrett PT / Yates III JR / Turner ...Authors: Berndsen ZT / Akhtar M / Thapa M / Vickers T / Schmitz A / Torres JL / Baboo S / Kumar P / Khatoom N / Sheikh A / Hamrick M / Diedrich JK / Bartolome SM / Garrett PT / Yates III JR / Turner JS / Dell A / Haslam S / Paulson JC / Ellebedy AH / Fleckenstein JM / Ward AB
History
DepositionDec 12, 2023-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43118.png

Downloads & links

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Map

FileDownload / File: emd_43118.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 400 pix.
= 290. Å		0.73 Å/pix.
x 400 pix.
= 290. Å		0.73 Å/pix.
x 400 pix.
= 290. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.725 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0688
Minimum - Maximum-0.61490315 - 0.84248
Average (Standard dev.)0.00003713283 (±0.014598826)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 290.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_43118_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_43118_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_43118_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : EtpA in complex with the mAb 1C08 Fab

EntireName: EtpA in complex with the mAb 1C08 Fab
Components
  • Complex: EtpA in complex with the mAb 1C08 Fab
    • Protein or peptide: EtpA
    • Protein or peptide: mAb 1C08 Heavy Chain
    • Protein or peptide: mAb 1C08 Light Chain
  • Ligand: beta-D-glucopyranose

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Supramolecule #1: EtpA in complex with the mAb 1C08 Fab

SupramoleculeName: EtpA in complex with the mAb 1C08 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Escherichia coli ETEC H10407 (bacteria)
Molecular weightTheoretical: 220 KDa

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Macromolecule #1: EtpA

MacromoleculeName: EtpA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli ETEC H10407 (bacteria)
Molecular weightTheoretical: 157.456922 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MNRIYKLKFD KRRNELVVVS EITTGVGNAK ATGSVEGEKS PRRGVRAMAL SLLSGMMIMA HPAMSANLPT GGQIVAGSGS IQTPSGNQM NIHQNSQNMV ANWNSFDIGK GNTVQFDQPS SSAVALNRVV GGGESQIMGN LKANGQVFLV NPNGVLFGEG A SVSTSGFV ...String:
MNRIYKLKFD KRRNELVVVS EITTGVGNAK ATGSVEGEKS PRRGVRAMAL SLLSGMMIMA HPAMSANLPT GGQIVAGSGS IQTPSGNQM NIHQNSQNMV ANWNSFDIGK GNTVQFDQPS SSAVALNRVV GGGESQIMGN LKANGQVFLV NPNGVLFGEG A SVSTSGFV ASTRDIKNDD FMNRRYTFSG GQKAGAAIVN QGELTTNAGG YIVLAADRVS NSGTIRTPGG KTVLAASERI TL QLDNGGL MSVQVTGDVV NALVENRGLV SARDGQVYLT ALGRGMLMNT VLNVSGVVEA SGMHRQDGNI VLDGGDSGVV HLS GTLQAD NASGQGGKVV VQGKNILLDK GSNITATGGQ GGGEVYVGGG WQGKDSNIRN ADKVVMQGGA RIDVSATQQG NGGT AVLWS DSYTNFHGQI GAKGGETGGN GGRVETSSHG NLQAFGTVSA SAKKGKAGNW LLDSADITIV NGSNVSKTET TQSPP HTQF APTAAGSAVS NTSINNRLNN GTSVTILTHR TRTGTAQGGN ITVNAAINKG NGSDVNLTLQ AGGNITVNNS ITSTEG KLN VNLSGARTSN GSITISNNAN ITTNGGDITV GTTNTSNRVN ISINNTTLNA SNGNIQLTGT GTDSGILFAG NNRLTAS NI ALTGNSTSGN AINLTGTATL NATNNITLTG SSTSGNAINL KGNNTLTASN ITLTGESTSG NAINHTDTTG TTTLNATN N ITMQGTRVQI KHSNITAGNF ALNATVAGSE ISNTTLTATN NINLAAKTNS ASSGVYLKDA RITSTNGSIT ANGTATANG KATHLDGNVT LNASNGRIKL TGNGHGSASG ILFAGNNRLT ASNIALTGNS TSGNAINLTG TATLNATNDI TLTGSSTSGN AINLTGTAT LNATNNITLT GSSTSGNAIN LKGNNTLTAS NITLTGESTS GNAINLTDTT GTTTLNATNN ITMQGTRVQI K HSNITAGN FALNATVAGS EISNTTLTAT NNINLAAKTN SASSGVYLKD ARITSTNGSI TANGTATANG KATHLDGNVT LN ASNGRIK LTGNGHGSAS GILFAGNNRL TASNIALTGN STSGNAINLT GTATLNATND ITLTGSNTSG NAINLTGTAT LNA TNNITL TGSSTSGNAI NLKGNNTLTA SNITLTGEST SGNAINLTDT TGTTTLNATN NITMQGTRVQ IKHSNITAGN FALN ATVAG SEISNTTLTA TNNINLAAKT NSASSGVYLK DARITSTNGS ITANGTATAN GKATHLDGNV TLNASNGRIK LTGNG HGSA SGILFAGNNR LTASNIALTG NSTSGNAINL TGTATLNATN DITLTGSSTS GNAINLTGTA TLNATNNITL TGSSTS GNA INLKGNNTLT ASNITLTGES TSGNAINLTD TTGTTTLNAT NNITMQGTRV QIKHSNITAG NFALNATVAG SEISNTT LT ATNNINLAAK TNSASSGVYL KDARITSTNG SITANGTAPA NDNATYLDGN VTLNASNGSI KLTGNGNGST SGILFAGN N TLTASNITLT GNSEVYWQKL GPEQKLISEE DLNSAVDHHH HHH

UniProtKB: EtpA

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Macromolecule #2: mAb 1C08 Heavy Chain

MacromoleculeName: mAb 1C08 Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 50.965383 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHSE VQLQQSGGEL MKPGASVKLS CKATGYTFTG YWIEWVEQRP GHGLEWIGEI LPGSGSTDYN EKFKGKATC SADTSSNTAY MKLSSLTTED SAIYYCARKS PYAMEYWGQG TSVTVSSAST KGPSVFPLAP SSKSTSGGTA A LGCLVKDY ...String:
MGWSCIILFL VATATGVHSE VQLQQSGGEL MKPGASVKLS CKATGYTFTG YWIEWVEQRP GHGLEWIGEI LPGSGSTDYN EKFKGKATC SADTSSNTAY MKLSSLTTED SAIYYCARKS PYAMEYWGQG TSVTVSSAST KGPSVFPLAP SSKSTSGGTA A LGCLVKDY FPEPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKRVEPKS CD KTHTCPP CPAPELLGGP SVFLFPPKPK DTLMISRTPE VTCVVVDVSH EDPEVKFNWY VDGVEVHNAK TKPREEQYNS TYR VVSVLT VLHQDWLNGK EYKCKVSNKA LPAPIEKTIS KAKGQPREPQ VYTLPPSREE MTKNQVSLTC LVKGFYPSDI AVEW ESNGQ PENNYKTTPP VLDSDGSFFL YSKLTVDKSR WQQGNVFSCS VMHEALHNHY TQKSLSLSPG K

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Macromolecule #3: mAb 1C08 Light Chain

MacromoleculeName: mAb 1C08 Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 25.339232 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHSD IQMTQSPASL SVSVGETVTI TCRASENIYS NLAWLHQKQG KSPQLLVYGA TNLADGVPSR FSGSGSGTQ YSLKINSLQS EDFGTYYCQQ FWGSPYTFGG GTKLEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY P REAKVQWK ...String:
MGWSCIILFL VATATGVHSD IQMTQSPASL SVSVGETVTI TCRASENIYS NLAWLHQKQG KSPQLLVYGA TNLADGVPSR FSGSGSGTQ YSLKINSLQS EDFGTYYCQQ FWGSPYTFGG GTKLEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY P REAKVQWK VDNALQSGNS QESVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC

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Macromolecule #4: beta-D-glucopyranose

MacromoleculeName: beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 39 / Formula: BGC
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-BGC:
beta-D-glucopyranose

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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

Concentration1 mg/mL
BufferpH: 6
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 47.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 215360
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8vba:
The secreted adhesin EtpA of Enterotoxigenic Escherichia coli in complex with the mouse mAb 1C08

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