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- PDB-9p1v: Structure of MAb PhtD3 in complex with PhtD -

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Basic information

Entry
Database: PDB / ID: 9p1v
TitleStructure of MAb PhtD3 in complex with PhtD
Components
  • Histidine triad protein D
  • MAb PhtD3 antibody heavy chain
  • MAb PhtD3 antibody light chain
KeywordsANTIMICROBIAL PROTEIN / A complex of an antibody / PhtD3 / with Pneumococcal histidine triad protein D / PhtD.
Function / homologyStreptococcal histidine triad repeat / Histidine triad protein / PhtA domain superfamily / Streptococcal histidine triad protein / Histidine triad protein D
Function and homology information
Biological speciesStreptococcus pneumoniae (bacteria)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsDu, J. / Cui, J. / Lin, Z. / Eisenhauer, J. / Weiner, D.B. / Pallesen, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI141236 United States
CitationJournal: To Be Published
Title: Fc-engineering and structural characterization of a broadly reactive monoclonal antibody targeting the pneumococcal histidine triad protein D (PhtD) on the surface of Streptococcus pneumoniae
Authors: Eisenhauer, J. / Gingerich, A.D. / Du, J. / Parzych, E.M. / Li, Y. / McCormick, A.L. / Lin, Z.J. / Cui, J. / Cassel, J. / Bhardwaj, B. / Chu, J.D. / Smith, T. / Patel, A. / Mousa, J.J. / ...Authors: Eisenhauer, J. / Gingerich, A.D. / Du, J. / Parzych, E.M. / Li, Y. / McCormick, A.L. / Lin, Z.J. / Cui, J. / Cassel, J. / Bhardwaj, B. / Chu, J.D. / Smith, T. / Patel, A. / Mousa, J.J. / Pallesen, J. / Weiner, D.B.
History
DepositionJun 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histidine triad protein D
L: MAb PhtD3 antibody light chain
H: MAb PhtD3 antibody heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,5064
Polymers171,4413
Non-polymers651
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 Histidine triad protein D


Mass: 93795.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: phtD / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E3JFL0
#2: Antibody MAb PhtD3 antibody light chain


Mass: 25767.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody MAb PhtD3 antibody heavy chain


Mass: 51877.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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
IDNameTypeEntity IDParent-IDSourceDetails (eV)
1MAb PhtD3 fab complex with Pneumococcal histidine triad protein D.COMPLEX#1-#30MULTIPLE SOURCES
2MAb PhtD3 fab light chain.COMPLEX#21RECOMBINANTFab fragment generated by proteolytic cleavage of mAb PhtD3 antibody.
3MAb PhtD3 fab heavy chain.COMPLEX#31RECOMBINANTFab fragment generated by proteolytic cleavage of mAb PhtD3 antibody.
4Pneumococcal histidine triad protein D.COMPLEX#11RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Streptococcus pneumoniae (bacteria)1313
32Homo sapiens (human)9606
43Homo sapiens (human)9606
54Streptococcus pneumoniae (bacteria)1313
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli (E. coli)562
32Homo sapiens (human)9606
43Homo sapiens (human)9606
54Escherichia coli (E. coli)562
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1058309 / Symmetry type: POINT

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