[English] 日本語
Yorodumi
- EMDB-21429: Density-fitted Model Structure of Antibody Variable Domains of Ty... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-21429
TitleDensity-fitted Model Structure of Antibody Variable Domains of TyTx11 in Complex with Typhoid Toxin
Map dataFull map
Sample
  • Complex: Complex of TyTx11 Fab with Typhoid toxin
    • Complex: Typhoid toxin
      • Protein or peptide: Pertussis like toxin subunit B
      • Protein or peptide: Pertussis toxin-like subunit ArtA
      • Protein or peptide: Cytolethal distending toxin subunit B
    • Complex: TyTx11 Fab
      • Protein or peptide: Variable Domain of Kappa Chain of TyTx11 Antibody
      • Protein or peptide: Variable Domain of Heavy Chain of Antibody TyTx11
Function / homology
Function and homology information


Transferases; Glycosyltransferases; Pentosyltransferases / : / NAD+ ADP-ribosyltransferase activity / toxin activity / endonuclease activity / Hydrolases; Acting on ester bonds / hydrolase activity / extracellular region
Similarity search - Function
Cytolethal distending toxin B / Bordetella pertussis toxin A / Pertussis toxin, subunit 1 / Bordetella pertussis toxin B, subunit 2/3, C-terminal / Pertussis toxin, subunit 2 and 3, C-terminal domain / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Enterotoxin / Endonuclease/exonuclease/phosphatase superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Pertussis like toxin subunit B / Pertussis-like toxin subunit ArtA / Cytolethal distending toxin S-CDT / Pertussis-like toxin subunit / Pertussis toxin-like subunit ArtA / Cytolethal distending toxin subunit B homolog
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhi str. CT18 (bacteria) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsNguyen T / Song J
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R03 AI135767 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM098621 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM116942 United States
CitationJournal: iScience / Year: 2021
Title: Mechanisms of typhoid toxin neutralization by antibodies targeting glycan receptor binding and nuclease subunits.
Authors: Changhwan Ahn / Yi-An Yang / Durga P Neupane / Tri Nguyen / Angelene F Richards / Ji Hyun Sim / Nicholas J Mantis / Jeongmin Song /
Abstract: Nearly all clinical isolates of Typhi, the cause of typhoid fever, are antibiotic resistant. All Typhi isolates secrete an AB exotoxin called typhoid toxin to benefit the pathogen during infection. ...Nearly all clinical isolates of Typhi, the cause of typhoid fever, are antibiotic resistant. All Typhi isolates secrete an AB exotoxin called typhoid toxin to benefit the pathogen during infection. Here, we demonstrate that antibiotic-resistant Typhi secretes typhoid toxin continuously during infection regardless of antibiotic treatment. We characterize typhoid toxin antibodies targeting glycan-receptor-binding PltB or nuclease CdtB, which neutralize typhoid toxin and , as demonstrated by using typhoid toxin secreted by antibiotic-resistant Typhi during human cell infection and lethal dose typhoid toxin challenge to mice. TyTx11 generated in this study neutralizes typhoid toxin effectively, comparable to TyTx4 that binds to all PltB subunits available per holotoxin. Cryoelectron microscopy explains that the binding of TyTx11 to CdtB makes this subunit inactive through CdtB catalytic-site conformational change. The identified toxin-neutralizing epitopes are conserved across all Typhi clinical isolates, offering critical insights into typhoid toxin-neutralizing strategies.
History
DepositionFeb 21, 2020-
Header (metadata) releaseFeb 24, 2021-
Map releaseFeb 24, 2021-
UpdateJul 14, 2021-
Current statusJul 14, 2021Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6vx4
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21429.png

Downloads & links

-
Map

FileDownload / File: emd_21429.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map
Voxel sizeX=Y=Z: 1.23 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.047669347 - 0.12601173
Average (Standard dev.)1.5912465e-06 (±0.0033823168)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions208208208
Spacing208208208
CellA=B=C: 255.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.231.231.23
M x/y/z208208208
origin x/y/z0.0000.0000.000
length x/y/z255.840255.840255.840
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ410410410
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS208208208
D min/max/mean-0.0480.1260.000

-
Supplemental data

-
Mask #1

Fileemd_21429_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: RELION 3 Postprocess Map

Fileemd_21429_additional_1.map
AnnotationRELION 3 Postprocess Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: RELION 3 Postprocess Map - Masked

Fileemd_21429_additional_2.map
AnnotationRELION 3 Postprocess Map - Masked
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 1

Fileemd_21429_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 2

Fileemd_21429_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex of TyTx11 Fab with Typhoid toxin

EntireName: Complex of TyTx11 Fab with Typhoid toxin
Components
  • Complex: Complex of TyTx11 Fab with Typhoid toxin
    • Complex: Typhoid toxin
      • Protein or peptide: Pertussis like toxin subunit B
      • Protein or peptide: Pertussis toxin-like subunit ArtA
      • Protein or peptide: Cytolethal distending toxin subunit B
    • Complex: TyTx11 Fab
      • Protein or peptide: Variable Domain of Kappa Chain of TyTx11 Antibody
      • Protein or peptide: Variable Domain of Heavy Chain of Antibody TyTx11

-
Supramolecule #1: Complex of TyTx11 Fab with Typhoid toxin

SupramoleculeName: Complex of TyTx11 Fab with Typhoid toxin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Map of Fab segment of IgG antibody TyTx11 in complex with purified Typhoid toxin

-
Supramolecule #2: Typhoid toxin

SupramoleculeName: Typhoid toxin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2, #4-#5 / Details: S. Typhi A2B5 toxin wild type
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhi str. CT18 (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

-
Supramolecule #3: TyTx11 Fab

SupramoleculeName: TyTx11 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1, #3 / Details: Fab segment of IgG antibody TyTx11
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Mus musculus (house mouse) / Recombinant cell: Hybridoma

-
Macromolecule #1: Variable Domain of Kappa Chain of TyTx11 Antibody

MacromoleculeName: Variable Domain of Kappa Chain of TyTx11 Antibody / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse) / Cell: Hybridoma
Molecular weightTheoretical: 11.689935 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString:
DIQMTQSSSY LSVSQGDRVT ITCKASDHID NWLAWYQQKP GNAPRLLISG ATSLKTGLPS RFSGSGSGKD FSLSITNLQT EDVASYYCQ QYWRTPYTFG GGTKLEI

-
Macromolecule #2: Pertussis like toxin subunit B

MacromoleculeName: Pertussis like toxin subunit B / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhi str. CT18 (bacteria)
Molecular weightTheoretical: 12.563042 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
EWTGDNTNAY YSDEVISELH VGQIDTSPYF CIKTVKANGS GTPVVACAVS KQSIWAPSFK ELLDQARYFY STGQSVRIHV QKNIWTYPL FVNTFSANAL VGLSSCSATQ CFGPK

-
Macromolecule #3: Variable Domain of Heavy Chain of Antibody TyTx11

MacromoleculeName: Variable Domain of Heavy Chain of Antibody TyTx11 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 20.049723 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString:
EVQLQQSGPV LVKPGPSVKI SCKASGYSFI DYFMNWVMQS HGKSLEWIGR IDPYSGDTFY NQKFKGKATL TVDKSSTTAH MELRSLASE DSAVYYCARE VLNYYAMDYW GQGTSVTVSS AKTTPPSVYP LAPGSAAQTN SMVTLGCLVK GYFPEPVTVT W NSGSPWYI SFLKLNKIF(UNK) RE(UNK)

-
Macromolecule #4: Pertussis toxin-like subunit ArtA

MacromoleculeName: Pertussis toxin-like subunit ArtA / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhi str. CT18 (bacteria)
Molecular weightTheoretical: 25.117145 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: VDFVYRVDST PPDVIFRDGF SLLGYNRNFQ QFISGRSCSG GSSDSRYIAT TSSVNQTYAI ARAYYSRSTF KGNLYRYQIR ADNNFYSLL PSITYLETQG GHFNAYEKTM MRLQREYVST LSILPENIQK AVALVYDSAT GLVKDGVSTM NASYLGLSTT S NPGVIPFL ...String:
VDFVYRVDST PPDVIFRDGF SLLGYNRNFQ QFISGRSCSG GSSDSRYIAT TSSVNQTYAI ARAYYSRSTF KGNLYRYQIR ADNNFYSLL PSITYLETQG GHFNAYEKTM MRLQREYVST LSILPENIQK AVALVYDSAT GLVKDGVSTM NASYLGLSTT S NPGVIPFL PEPQTYTQQR IDAFGPLISS CFSIGSVCHS HRGQRADVYN MSFYDARPVI ELILSK

-
Macromolecule #5: Cytolethal distending toxin subunit B

MacromoleculeName: Cytolethal distending toxin subunit B / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhi str. CT18 (bacteria)
Molecular weightTheoretical: 28.149777 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: NISDYKVMTW NLQGSSASTE SKWNVNVRQL LSGTAGVDIL MVQEAGAVPT SAVPTGRHIQ PFGVGIPIDE YTWNLGTTSR QDIRYIYHS AIDVGARRVN LAIVSRQRAD NVYVLRPTTV ASRPVIGIGL GNDVFLTAHA LASGGPDAAA IVRVTINFFR Q PQMRHLSW ...String:
NISDYKVMTW NLQGSSASTE SKWNVNVRQL LSGTAGVDIL MVQEAGAVPT SAVPTGRHIQ PFGVGIPIDE YTWNLGTTSR QDIRYIYHS AIDVGARRVN LAIVSRQRAD NVYVLRPTTV ASRPVIGIGL GNDVFLTAHA LASGGPDAAA IVRVTINFFR Q PQMRHLSW FLAGDFNRSP DRLENDLMTE HLERVVAVLA PTEPTQIGGG ILDYGVIVDR APYSQRVEAL RNPQLASDHY PV AFLARSC LEHHHHHH

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
15.0 mMTristris(hydroxymethyl)aminomethane
150.0 mMNaClsodium chloride
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 2.0 second before plunging.
DetailsFreshly prepared size-exclusion-chromatography purified complex of TyTx11 IgG and Typhoid toxin wild-type

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.7 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 63000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: Gctf
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4k6l

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 61478
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

4k6l


6gff

chain_id: K

1f11

chain_id: B
DetailsInitial local fitting was done using Chimera and then Coot was used for rebuilding Fab variable domains into correct sequences. Refinement was performed using Real Space Refine in PHENIX and was iterated with manual building in Coot.
Output model

PDB-6vx4:
Density-fitted Model Structure of Antibody Variable Domains of TyTx11 in Complex with Typhoid Toxin

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more