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- EMDB-74630: Shigella flexneri type III secretion system (T3SS) protein IpaD b... -

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Basic information

Entry
Database: EMDB / ID: EMD-74630
TitleShigella flexneri type III secretion system (T3SS) protein IpaD bound to hemolysis blocking antibody fragment D13r-34
Map dataIpaD with D13r-34 Fab and anti-Fab Nb
Sample
  • Complex: Shigella flexneri type III secretion system (T3SS) protein IpaD bound to hemolysis blocking antibody fragment D13r-34 stablized by anti-Fab nanobody
    • Complex: Shigella flexneri type III secretion system (T3SS) protein IpaD
      • Protein or peptide: Invasin IpaD
    • Complex: Hemolysis blocking antibody fragment D13r-34
      • Protein or peptide: D13r-34 antibody fragment heavy chain
      • Protein or peptide: D13r-34 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: 3.3 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

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Structure visualization

Supplemental images

emd_74630.png

Downloads & links

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Map

FileDownload / File: emd_74630.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIpaD with D13r-34 Fab and anti-Fab Nb
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 420 pix.
= 309.54 Å		0.74 Å/pix.
x 420 pix.
= 309.54 Å		0.74 Å/pix.
x 420 pix.
= 309.54 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.737 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.33
Minimum - Maximum-1.2747631 - 2.0085385
Average (Standard dev.)-0.000028831215 (±0.035092074)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 309.54 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map B

Fileemd_74630_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_74630_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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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 antibody fragment D13r-34 stablized by anti-Fab nanobody
Components
  • Complex: Shigella flexneri type III secretion system (T3SS) protein IpaD bound to hemolysis blocking antibody fragment D13r-34 stablized by anti-Fab nanobody
    • Complex: Shigella flexneri type III secretion system (T3SS) protein IpaD
      • Protein or peptide: Invasin IpaD
    • Complex: Hemolysis blocking antibody fragment D13r-34
      • Protein or peptide: D13r-34 antibody fragment heavy chain
      • Protein or peptide: D13r-34 antibody fragment light chain

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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 antibody fragment D13r-34 stablized by 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 an anti-Fab single-domain antibody was present in the sample, this was not modeled.

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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)

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Supramolecule #3: Hemolysis blocking antibody fragment D13r-34

SupramoleculeName: Hemolysis blocking antibody fragment D13r-34 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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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

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Macromolecule #2: D13r-34 antibody fragment heavy chain

MacromoleculeName: D13r-34 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: 24.644561 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLAESGPG LVKPLETLSL TCAVSGDYIR NAHYWSWIRQ VPGKGPEWMG GIDGRSSSTD YNPSLESRVT VSTDTSNNQL SLKLTSVTA ADTAVYYCAR DARTGVIFMP TNWFELWGLG VLVTVSSAST KGPSVFPLAP SSRSTSESTA ALGCLVKDYF P EPVTVSWN ...String:
EVQLAESGPG LVKPLETLSL TCAVSGDYIR NAHYWSWIRQ VPGKGPEWMG GIDGRSSSTD YNPSLESRVT VSTDTSNNQL SLKLTSVTA ADTAVYYCAR DARTGVIFMP TNWFELWGLG VLVTVSSAST KGPSVFPLAP SSRSTSESTA ALGCLVKDYF P EPVTVSWN SGSLTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYV CNVNHKPSNT KVDKRVEIKT CGGG

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Macromolecule #3: D13r-34 antibody fragment light chain

MacromoleculeName: D13r-34 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: 23.44515 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVMTQSPSS LSACVGDRVT ITCRASQDIG AFLNWYQQKP GKAPKFLVLD RNRLEGGVPS RFSGSGSGTE FTLTISSLQP EDFATYYCQ QHKNFPFTFG PGTKVEIKRT VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGALKTGNS Q ESVTEQDS ...String:
DIVMTQSPSS LSACVGDRVT ITCRASQDIG AFLNWYQQKP GKAPKFLVLD RNRLEGGVPS RFSGSGSGTE FTLTISSLQP EDFATYYCQ QHKNFPFTFG PGTKVEIKRT VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGALKTGNS Q ESVTEQDS KDNTYSLSST LTLSSTEYQS HKVYACEVTH QGLSSPVTKS FNRGEC

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 51.6 e/Å2
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: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 26038
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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