[English] 日本語
Yorodumi
- EMDB-74629: Shigella flexneri type III secretion system (T3SS) protein IpaD b... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-74629
TitleShigella flexneri type III secretion system (T3SS) protein IpaD bound to hemolysis blocking Fab D02-F2 and hemolysis enhancing Fab D02-E4
Map data
Sample
  • Complex: Shigella flexneri type III secretion system (T3SS) protein IpaD bound to hemolysis blocking Fab D02-F2 and hemolysis enhancing Fab D02-E4, both stablized by an anti-Fab nanobody.
    • Complex: Shigella flexneri type III secretion system (T3SS) protein IpaD
      • Protein or peptide: Invasin IpaD
    • Complex: Hemolysis blocking antibody fragment D02-F2
      • Protein or peptide: D02-F2 antibody fragment heavy chain
      • Protein or peptide: D02-F2 antibody fragment light chain
    • Complex: Hemolysis enhancing antibody fragment D02-E4
      • Protein or peptide: D02-E4 antibody fragment heavy chain
      • Protein or peptide: D02-E4 antibody fragment light chain
KeywordsT3SS / epitope / vaccine antigen / SipD homolog / PROTEIN TRANSPORT
Function / homologyeffector-mediated activation of host programmed cell death by symbiont / Type III secretion systems tip complex components / BipD-like superfamily / Type III secretion systems tip complex components / extracellular region / Invasin IpaD
Function and homology information
Biological speciesShigella flexneri (bacteria) / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsGilman MSA / Kruse AC / Schmidt HR
Funding support United States, United Kingdom, 5 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)Hanna H. Gray Fellows Program United States
Wellcome TrustWellcome Trust RESISTANT grant United Kingdom
National Institutes of Health/Office of the DirectorP51OD011106 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)RR15459-01 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)RR020141-01 United States
CitationJournal: Sci Transl Med / Year: 2026
Title: Multifunctional antibody responses from a primate outbreak inform vaccine design.
Authors: Robert M Gallant / Paul Savarino / Sophia Pulido / Morgan S A Gilman / Ti Lu / Jennifer Hayes / Nicholas L Xerri / Torrey Williams / Mark A Ochoa / Zackary Dietz / Eric Peterson / Timothy ...Authors: Robert M Gallant / Paul Savarino / Sophia Pulido / Morgan S A Gilman / Ti Lu / Jennifer Hayes / Nicholas L Xerri / Torrey Williams / Mark A Ochoa / Zackary Dietz / Eric Peterson / Timothy Scott / Faye Hartmann / Stephen G Baker / Robert W Kaminski / Devin Sok / Andrew C Kruse / Wendy Picking / Saverio V Capuano / Hayden R Schmidt /
Abstract: There is currently no approved vaccine for spp., a leading cause of diarrhea with increasing rates of antimicrobial resistance. vaccine development is complicated in part by an incomplete ...There is currently no approved vaccine for spp., a leading cause of diarrhea with increasing rates of antimicrobial resistance. vaccine development is complicated in part by an incomplete understanding of the structural and molecular determinants of immunity. To address this, we isolated monoclonal antibodies against candidate vaccine antigens using samples from a outbreak in a nonhuman primate (NHP) research facility. We found that antibodies targeting the O-antigen can undergo substantial affinity maturation (>10%) to acquire broad cross-reactivity across serotypes. We also found that the virulence-associated type III secretion system (T3SS) proteins IpaD and IpaB elicit moderate T cell and robust antibody responses. T3SS antibodies could either inhibit or enhance bacterial virulence in vitro and differed in vivo depending on their epitope specificity. Collectively, these findings provide insights into protective and deleterious immune responses against that directly inform vaccine immunogen design.
History
DepositionDec 20, 2025-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_74629.png

Downloads & links

-
Map

FileDownload / File: emd_74629.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.48918566 - 0.77686393
Average (Standard dev.)0.00020307236 (±0.008361891)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_74629_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_74629_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Shigella flexneri type III secretion system (T3SS) protein IpaD b...

EntireName: Shigella flexneri type III secretion system (T3SS) protein IpaD bound to hemolysis blocking Fab D02-F2 and hemolysis enhancing Fab D02-E4, both stablized by an anti-Fab nanobody.
Components
  • Complex: Shigella flexneri type III secretion system (T3SS) protein IpaD bound to hemolysis blocking Fab D02-F2 and hemolysis enhancing Fab D02-E4, both stablized by an anti-Fab nanobody.
    • Complex: Shigella flexneri type III secretion system (T3SS) protein IpaD
      • Protein or peptide: Invasin IpaD
    • Complex: Hemolysis blocking antibody fragment D02-F2
      • Protein or peptide: D02-F2 antibody fragment heavy chain
      • Protein or peptide: D02-F2 antibody fragment light chain
    • Complex: Hemolysis enhancing antibody fragment D02-E4
      • Protein or peptide: D02-E4 antibody fragment heavy chain
      • Protein or peptide: D02-E4 antibody fragment light chain

-
Supramolecule #1: Shigella flexneri type III secretion system (T3SS) protein IpaD b...

SupramoleculeName: Shigella flexneri type III secretion system (T3SS) protein IpaD bound to hemolysis blocking Fab D02-F2 and hemolysis enhancing Fab D02-E4, both stablized by an anti-Fab nanobody.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Antibody fragments were prepared by papain digest. Only the variable domains were modeled. Although two copies of an anti-Fab single-domain antibody were present in the sample, these were not modeled.

-
Supramolecule #2: Shigella flexneri type III secretion system (T3SS) protein IpaD

SupramoleculeName: Shigella flexneri type III secretion system (T3SS) protein IpaD
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Shigella flexneri (bacteria)

-
Supramolecule #3: Hemolysis blocking antibody fragment D02-F2

SupramoleculeName: Hemolysis blocking antibody fragment D02-F2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

-
Supramolecule #4: Hemolysis enhancing antibody fragment D02-E4

SupramoleculeName: Hemolysis enhancing antibody fragment D02-E4 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4-#5
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

-
Macromolecule #1: Invasin IpaD

MacromoleculeName: Invasin IpaD / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Shigella flexneri (bacteria)
Molecular weightTheoretical: 39.605887 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHGLN DIFEAQKIEW HEGSGSNITT LTNSISTSSF SPNNTNGSST ETVNSDIKTT TSSHPVSSLT MLNDTLHNIR TTNQALKKE LSQKTLTKTS LEEIALHSSQ ISMDVNKSAQ LLDILSRNEY PINKDARELL HSAPKEAELD GDQMISHREL W AKIANSIN ...String:
MHHHHHHGLN DIFEAQKIEW HEGSGSNITT LTNSISTSSF SPNNTNGSST ETVNSDIKTT TSSHPVSSLT MLNDTLHNIR TTNQALKKE LSQKTLTKTS LEEIALHSSQ ISMDVNKSAQ LLDILSRNEY PINKDARELL HSAPKEAELD GDQMISHREL W AKIANSIN DINEQYLKVY EHAVSSYTQM YQDFSAVLSS LAGWISPGGN DGNSVKLQVN SLKKALEELK EKYKDKPLYP AN NTVSQEQ ANKWLTELGG TIGKVSQKNG GYVVSINMTP IDNMLKSLDN LGGNGEVVLD NAKYQAWNAG FSAEDETMKN NLQ TLVQKY SNANSIFDNL VKVLSSTISS CTDTDKLFLH F

UniProtKB: Invasin IpaD

-
Macromolecule #2: D02-F2 antibody fragment heavy chain

MacromoleculeName: D02-F2 antibody fragment heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 23.364023 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQESGPG LVKPSETLSL TCAVSDGSVS SSYWTWIRQP PGKGLEWIGF IYGGNGNTGY NPSLKSRVTI STDMSKNQFS LNLDSVTAA DTAVYHCVRG HSSLDRWGQG VLVTVSSAST KGPSVFPLAP SSRSTSESTA ALGCLVKDYF PEPVTVSWNS G SLTSGVHT ...String:
QVQLQESGPG LVKPSETLSL TCAVSDGSVS SSYWTWIRQP PGKGLEWIGF IYGGNGNTGY NPSLKSRVTI STDMSKNQFS LNLDSVTAA DTAVYHCVRG HSSLDRWGQG VLVTVSSAST KGPSVFPLAP SSRSTSESTA ALGCLVKDYF PEPVTVSWNS G SLTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYV CNVNHKPSNT KVDKRVEIKT CGGG

-
Macromolecule #3: D02-F2 antibody fragment light chain

MacromoleculeName: D02-F2 antibody fragment light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 23.820412 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVMTQSPLS LSVTPGQPAS ISCVSSQSLV HSNGNTYLAW YHQRPGQPPR RLIYEVSDRD SGAPDRFRGS GAGTDFTLKI SRVEAEDVG VYYCGQGTHL PFTFGPGTKV DIKRTVAAPS VFIFPPSEDQ VKSGTVSVVC LLNNFYPREA SVKWKVDGAL K TGNSQESV ...String:
DIVMTQSPLS LSVTPGQPAS ISCVSSQSLV HSNGNTYLAW YHQRPGQPPR RLIYEVSDRD SGAPDRFRGS GAGTDFTLKI SRVEAEDVG VYYCGQGTHL PFTFGPGTKV DIKRTVAAPS VFIFPPSEDQ VKSGTVSVVC LLNNFYPREA SVKWKVDGAL K TGNSQESV TEQDSKDNTY SLSSTLTLSS TEYQSHKVYA CEVTHQGLSS PVTKSFNRGE C

-
Macromolecule #4: D02-E4 antibody fragment heavy chain

MacromoleculeName: D02-E4 antibody fragment heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 23.783611 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQESGPG LVKPSETLSL TCAVSGGSIS SNYWWIWIRQ PPGRGLEWIG NIGGSIDTTY YNPSLKSRVT ISKDMSKNQF SLKLNSVTT ADTAIYYCAR HSRAAAGDSW GQGVVVTVSS ASTKGPSVFP LAPSSRSTSE STAALGCLVK DYFPEPVTVS W NSGSLTSG ...String:
QVQLQESGPG LVKPSETLSL TCAVSGGSIS SNYWWIWIRQ PPGRGLEWIG NIGGSIDTTY YNPSLKSRVT ISKDMSKNQF SLKLNSVTT ADTAIYYCAR HSRAAAGDSW GQGVVVTVSS ASTKGPSVFP LAPSSRSTSE STAALGCLVK DYFPEPVTVS W NSGSLTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYVCNVNHKP SNTKVDKRVE IKTCGGG

-
Macromolecule #5: D02-E4 antibody fragment light chain

MacromoleculeName: D02-E4 antibody fragment light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 23.318811 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LFASVGDRVT ITCQASQPIS DWLAWYQQKP GKAPKRLIYA ASSLESGVPS RFSGSGSGTE FTLTISSLQP EDFATYYCQ QHDSYPLTFG GGTKVEIKRT VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGALKTGNS Q ESVTEQDS ...String:
DIQMTQSPSS LFASVGDRVT ITCQASQPIS DWLAWYQQKP GKAPKRLIYA ASSLESGVPS RFSGSGSGTE FTLTISSLQP EDFATYYCQ QHDSYPLTFG GGTKVEIKRT VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGALKTGNS Q ESVTEQDS KDNTYSLSST LTLSSTEYQS HKVYACEVTH QGLSSPVTKS FNRGEC

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.3 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio model generated using cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 1/2 BIT CUT-OFF / Software - Name: cryoSPARC / Number images used: 73375
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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://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