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- PDB-9pms: Epitope editing of CD90 protects hematopoietic stem cells from im... -

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Basic information

Entry
Database: PDB / ID: 9pms
TitleEpitope editing of CD90 protects hematopoietic stem cells from immunotherapy and enables targeted enrichment for gene therapy
Components
  • (Antibody heavy ...) x 2
  • (Antibody light ...) x 2
  • Thy-1 membrane glycoprotein
KeywordsANTITUMOR PROTEIN / Antibody / Antigen / Complex
Function / homology
Function and homology information


negative regulation of neuron projection regeneration / positive regulation of cellular extravasation / GPI anchor binding / regulation of cell-matrix adhesion / retinal cone cell development / Post-translational modification: synthesis of GPI-anchored proteins / negative regulation of axonogenesis / focal adhesion assembly / heterotypic cell-cell adhesion / neuronal cell body membrane ...negative regulation of neuron projection regeneration / positive regulation of cellular extravasation / GPI anchor binding / regulation of cell-matrix adhesion / retinal cone cell development / Post-translational modification: synthesis of GPI-anchored proteins / negative regulation of axonogenesis / focal adhesion assembly / heterotypic cell-cell adhesion / neuronal cell body membrane / receptor clustering / positive regulation of GTPase activity / positive regulation of focal adhesion assembly / negative regulation of T cell receptor signaling pathway / axolemma / negative regulation of protein kinase activity / cytoskeleton organization / negative regulation of cell migration / dendrite membrane / integrin-mediated signaling pathway / positive regulation of release of sequestered calcium ion into cytosol / GTPase activator activity / cell-cell adhesion / integrin binding / positive regulation of T cell activation / T cell receptor signaling pathway / cell-cell signaling / presynapse / growth cone / angiogenesis / postsynapse / apical plasma membrane / membrane raft / external side of plasma membrane / focal adhesion / dendrite / glutamatergic synapse / cell surface / endoplasmic reticulum / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Thy-1 membrane glycoprotein / Immunoglobulin / Immunoglobulin domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Thy-1 membrane glycoprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.56 Å
AuthorsChoo, S. / Radtke, S. / Rupert, P.B. / Tong, A.H. / Swing, K. / Repele, A. / Starrs, M. / Humphreys, T. / Darari, A. / Strong, R.K. / Keim, H.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P30 CA015704-40 United States
CitationJournal: To Be Published
Title: Epitope editing of CD90 protects hematopoietic stem cells from immunotherapy and enables targeted enrichment for gene therapy
Authors: Choo, S. / Radtke, S. / Rupert, P.B. / Tong, A.H. / Swing, K. / Repele, A. / Starrs, M. / Humphreys, T. / Darari, A. / Strong, R.K. / Keim, H.P.
History
DepositionJul 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 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

Downloads & links

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Assembly

Deposited unit
A: Antibody heavy chain
B: Antibody light chain
C: Thy-1 membrane glycoprotein
H: Antibody heavy chain
L: Antibody light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,3138
Polymers105,6505
Non-polymers6643
Water00
1


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

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Components

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Antibody , 4 types, 4 molecules ABHL

#1: Antibody Antibody heavy chain


Mass: 23984.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Antibody light chain


Mass: 23724.041 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#4: Antibody Antibody heavy chain


Mass: 22645.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#5: Antibody Antibody light chain


Mass: 22535.779 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)

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Protein / Sugars , 2 types, 4 molecules C

#3: Protein Thy-1 membrane glycoprotein / CDw90 / Thy-1 antigen


Mass: 12759.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THY1 / Production host: Homo sapiens (human) / References: UniProt: P04216
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

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

ComponentName: Ternary complex of CD90 with antibody 5E10 and MAB20671
Type: COMPLEX / Details: 5E10 Fab fragment generated by Papain digest / Entity ID: #1-#5 / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7
Buffer component
IDConc.NameFormulaBuffer-ID
1139 mMolsodium chlorideNaCl1
22.7 mMolpotassium chlorideKCl1
310 mMolphosphatePhosphate1
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
12cryoSPARC3D reconstruction
13PHENIX1.21.1_5286model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 231849 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
RefinementHighest resolution: 3.56 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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