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- PDB-9zrt: Shigella flexneri type III secretion system (T3SS) protein IpaD b... -

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Basic information

Entry
Database: PDB / ID: 9zrt
TitleShigella flexneri type III secretion system (T3SS) protein IpaD bound to hemolysis blocking antibody fragment D13r-34
Components
  • D13r-34 antibody fragment heavy chain
  • D13r-34 antibody fragment light chain
  • Invasin IpaD
KeywordsPROTEIN TRANSPORT / T3SS / epitope / vaccine antigen / SipD homolog
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsGilman, M.S.A. / Kruse, A.C. / Schmidt, H.R.
Funding support United States, United Kingdom, 5items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 16, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Invasin IpaD
H: D13r-34 antibody fragment heavy chain
L: D13r-34 antibody fragment light chain


Theoretical massNumber of molelcules
Total (without water)87,6963
Polymers87,6963
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Invasin IpaD / 36 kDa membrane antigen


Mass: 39605.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ipaD, CP0126 / Production host: Escherichia coli (E. coli) / References: UniProt: P18013
#2: Antibody D13r-34 antibody fragment heavy chain


Mass: 24644.561 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#3: Antibody D13r-34 antibody fragment light chain


Mass: 23445.150 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeDetails (eV)Entity IDParent-IDSource
1Shigella flexneri type III secretion system (T3SS) protein IpaD bound to hemolysis blocking antibody fragment D13r-34 stablized by anti-Fab nanobodyCOMPLEXAntibody 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.all0MULTIPLE SOURCES
2Shigella flexneri type III secretion system (T3SS) protein IpaDCOMPLEX#11RECOMBINANT
3Hemolysis blocking antibody fragment D13r-34COMPLEX#2-#31RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
42Shigella flexneri (bacteria)623
53Macaca mulatta (Rhesus monkey)9544
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
42Escherichia coli (E. coli)562
53Homo sapiens (human)9606
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 51.6 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26038 / Symmetry type: POINT

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