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- EMDB-71742: Epitope editing of CD90 protects hematopoietic stem cells from im... -

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Basic information

Entry
Database: EMDB / ID: EMD-71742
TitleEpitope editing of CD90 protects hematopoietic stem cells from immunotherapy and enables targeted enrichment for gene therapy
Map data
Sample
  • Complex: Ternary complex of CD90 with antibody 5E10 and MAB20671
    • Protein or peptide: Antibody heavy chain
    • Protein or peptide: Antibody light chain
    • Protein or peptide: Thy-1 membrane glycoprotein
    • Protein or peptide: Antibody heavy chain
    • Protein or peptide: Antibody light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsAntibody / Antigen / Complex / ANTITUMOR PROTEIN
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 speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.56 Å
AuthorsChoo S / Radtke S / Rupert PB / Tong AH / Swing K / Repele A / Starrs M / Humphreys T / Darari A / Strong RK / Keim HP
Funding support United States, 1 items
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 PB / Tong AH / Swing K / Repele A / Starrs M / Humphreys T / Darari A / Strong RK / Keim HP
History
DepositionJul 18, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71742.png

Downloads & links

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Map

FileReleased
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 400 pix.
= 448.8 Å		1.12 Å/pix.
x 400 pix.
= 448.8 Å		1.12 Å/pix.
x 400 pix.
= 448.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.122 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.744525 - 2.575234
Average (Standard dev.)0.00017053878 (±0.024286311)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 448.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_71742_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_71742_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of CD90 with antibody 5E10 and MAB20671

EntireName: Ternary complex of CD90 with antibody 5E10 and MAB20671
Components
  • Complex: Ternary complex of CD90 with antibody 5E10 and MAB20671
    • Protein or peptide: Antibody heavy chain
    • Protein or peptide: Antibody light chain
    • Protein or peptide: Thy-1 membrane glycoprotein
    • Protein or peptide: Antibody heavy chain
    • Protein or peptide: Antibody light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Ternary complex of CD90 with antibody 5E10 and MAB20671

SupramoleculeName: Ternary complex of CD90 with antibody 5E10 and MAB20671
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 / Details: 5E10 Fab fragment generated by Papain digest
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Antibody heavy chain

MacromoleculeName: Antibody heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.984859 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QVQLLQPGAE LVRPGASVRL SCKTSGYTFT SYWINWVKQR PGQGLEWIGK IFPSDSHTNY NQKFKDKATL TVDKSSSTAY MQLISPTSE DSAVYYCTRD FDTQFYAMEY WGQGTSVTVS SAKTTPPSVY PLAPGSAAQT NSMVTLGCLV KGYFPEPVTV T WNSGSLSS ...String:
QVQLLQPGAE LVRPGASVRL SCKTSGYTFT SYWINWVKQR PGQGLEWIGK IFPSDSHTNY NQKFKDKATL TVDKSSSTAY MQLISPTSE DSAVYYCTRD FDTQFYAMEY WGQGTSVTVS SAKTTPPSVY PLAPGSAAQT NSMVTLGCLV KGYFPEPVTV T WNSGSLSS GVHTFPAVLQ SDLYTLSSSV TVPSSTWPSE TVTCNVAHPA SSTKVDKKIV PR

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Macromolecule #2: Antibody light chain

MacromoleculeName: Antibody light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.724041 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: DIQMTQTTSS LSASLGDRVT ISCRASQDIS NYLNWYQQKP DGTFKLLIYY TSRLHSGVPS RFSGGGSGTD YSLTISNLEK EDIATYFCQ QGNTLPRTFG GGTRLEVKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS ...String:
DIQMTQTTSS LSASLGDRVT ISCRASQDIS NYLNWYQQKP DGTFKLLIYY TSRLHSGVPS RFSGGGSGTD YSLTISNLEK EDIATYFCQ QGNTLPRTFG GGTRLEVKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS KDSTYSMSST LTLTKDEYER HNSYTCEATH KTSTSPIVKS FNRNES

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Macromolecule #3: Thy-1 membrane glycoprotein

MacromoleculeName: Thy-1 membrane glycoprotein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.75941 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QKVTSLTACL VDQSLRLDCR HENTSSSPIQ YEFSLTRETK KHVLFGTVGV PEHTYRSRTN FTSKYNMKVL YLSAFTSKDE GTYTCALHH SGHSPPISSQ NVTVLRDKLV KCEG

UniProtKB: Thy-1 membrane glycoprotein

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Macromolecule #4: Antibody heavy chain

MacromoleculeName: Antibody heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 22.645531 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QVQLLQPGAE LVRPGASVRL SCKTSAAAAA AAWINWVKQR PGQGLEWIGK IAAAAAATNY NQKFKDKATL TVDKSSSTAY MQLISPTSE DSAVYYCTRA AAAAAAAAWG QGTSVTVSSA KTTPPSVYPL APGSAAQTNS MVTLGCLVKG YFPEPVTVTW N SGSLSSGV ...String:
QVQLLQPGAE LVRPGASVRL SCKTSAAAAA AAWINWVKQR PGQGLEWIGK IAAAAAATNY NQKFKDKATL TVDKSSSTAY MQLISPTSE DSAVYYCTRA AAAAAAAAWG QGTSVTVSSA KTTPPSVYPL APGSAAQTNS MVTLGCLVKG YFPEPVTVTW N SGSLSSGV HTFPAVLQSD LYTLSSSVTV PSSTWPSETV TCNVAHPASS TKVDKKIVPR

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Macromolecule #5: Antibody light chain

MacromoleculeName: Antibody light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 22.535779 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: DIQMTQTTSS LSASLGDRVT ISCAAAAAAA AAAAWYQQKP DGTFKLLIYA AAAAAAGVPS RFSGGGSGTD YSLTISNLEK EDIATYFCA AAAAAAAAFG GGTRLEVKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS ...String:
DIQMTQTTSS LSASLGDRVT ISCAAAAAAA AAAAWYQQKP DGTFKLLIYA AAAAAAGVPS RFSGGGSGTD YSLTISNLEK EDIATYFCA AAAAAAAAFG GGTRLEVKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS KDSTYSMSST LTLTKDEYER HNSYTCEATH KTSTSPIVKS FNRNES

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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
Component:
ConcentrationFormulaName
139.0 mMolNaClsodium chloride
2.7 mMolKClpotassium chloride
10.0 mMolPhosphatephosphate
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 231849
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9pms:
Epitope editing of CD90 protects hematopoietic stem cells from immunotherapy and enables targeted enrichment for gene therapy

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