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- EMDB-45577: Cryo-EM Structural Analysis of Human Integrin Heterodimer bound t... -

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Basic information

Entry
Database: EMDB / ID: EMD-45577
TitleCryo-EM Structural Analysis of Human Integrin Heterodimer bound to DNA Aptamer
Map data
Sample
  • Complex: human integrin alpha4 beta1 heterodimer in complex with DNA aptamer
    • DNA: DNA aptamer
    • Protein or peptide: human integrin alpha 4
    • Protein or peptide: human integrin beta 1
KeywordsDNA aptamer / Human integrin / Cryo-EM / CELL ADHESION
Function / homologyIsoform 1 of Integrin beta-1 / Isoform 1 of Integrin alpha-4
Function and homology information
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsWang T
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: ACS Appl Mater Interfaces / Year: 2025
Title: DNA Aptamer-Polymer Conjugates for Selective Targeting of Integrin α4β1 T-Lineage Cancers.
Authors: Ian I Cardle / Jai Raman / Dinh Chuong Nguyen / Tong Wang / Abe Y Wu / Drew L Sellers / Trey J Pichon / Emmeline L Cheng / Nataly Kacherovsky / Stephen J Salipante / Michael C Jensen / Suzie H Pun /
Abstract: Selective therapeutic targeting of T-cell malignancies is difficult due to the shared lineage between healthy and malignant T cells. Current front-line chemotherapy for these cancers is largely ...Selective therapeutic targeting of T-cell malignancies is difficult due to the shared lineage between healthy and malignant T cells. Current front-line chemotherapy for these cancers is largely nonspecific, resulting in frequent cases of relapsed/refractory disease. The development of targeting approaches for effectively treating T-cell leukemia and lymphoma thus remains a critical goal for the oncology field. Here, we report the discovery of a DNA aptamer, named HR7A1, that displays low nanomolar affinity for the integrin α4β1 (VLA-4), a marker associated with chemoresistance and relapse in leukemia patients. After truncation of HR7A1 to a minimal binding motif, we demonstrate elevated binding of the aptamer to T-lineage cancer cells over healthy immune cells. Using cryo-EM and competition studies, we find that HR7A1 shares an overlapping binding site on α4β1 with fibronectin and VCAM-1, which has implications for sensitizing blood cancers to chemotherapy. We last characterize barriers to aptamer translation, including serum stability, temperature-sensitive binding, and short circulation half-life, and synthesize an aptamer-polymer conjugate that addresses these challenges. Future work will seek to validate targeting of α4β1 tumors with the conjugate, establishing an aptamer-based biomaterial that can be readily adapted for targeted treatment of T-cell malignancies.
History
DepositionJun 28, 2024-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45577.png

Downloads & links

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Map

FileDownload / File: emd_45577.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 256 pix.
= 216.704 Å		0.85 Å/pix.
x 256 pix.
= 216.704 Å		0.85 Å/pix.
x 256 pix.
= 216.704 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8465 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.0006134698 - 0.22423492
Average (Standard dev.)0.00030551633 (±0.0044311094)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 216.704 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_45577_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_45577_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : human integrin alpha4 beta1 heterodimer in complex with DNA aptamer

EntireName: human integrin alpha4 beta1 heterodimer in complex with DNA aptamer
Components
  • Complex: human integrin alpha4 beta1 heterodimer in complex with DNA aptamer
    • DNA: DNA aptamer
    • Protein or peptide: human integrin alpha 4
    • Protein or peptide: human integrin beta 1

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Supramolecule #1: human integrin alpha4 beta1 heterodimer in complex with DNA aptamer

SupramoleculeName: human integrin alpha4 beta1 heterodimer in complex with DNA aptamer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 320 KDa

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Macromolecule #1: DNA aptamer

MacromoleculeName: DNA aptamer / type: dna / ID: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString:
CTCCTTACTA GATGCAACCC GACTACTAAC GTCGTAAGAG AG

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Macromolecule #2: human integrin alpha 4

MacromoleculeName: human integrin alpha 4 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: YNVDTESALL YQGPHNTLFG YSVVLHS HG ANRWLLVGAP TANWLANASV INPGAIYRCR IGKNPGQTCE QLQLGSPNGE PCGKTCLE E RDNQWLGVTL SRQPGENGSI VTCGHRWKNI FYIKNENKLP TGGCYGVPPD LRTELSKRI APCYQDYVKK FGENFASCQA ...String:
YNVDTESALL YQGPHNTLFG YSVVLHS HG ANRWLLVGAP TANWLANASV INPGAIYRCR IGKNPGQTCE QLQLGSPNGE PCGKTCLE E RDNQWLGVTL SRQPGENGSI VTCGHRWKNI FYIKNENKLP TGGCYGVPPD LRTELSKRI APCYQDYVKK FGENFASCQA GISSFYTKDL IVMGAPGSSY WTGSLFVYNI TTNKYKAFLD KQNQVKFGS YLGYSVGAGH FRSQHTTEVV GGAPQHEQIG KAYIFSIDEK ELNILHEMKG K KLGSYFGA SVCAVDLNAD GFSDLLVGAP MQSTIREEGR VFVYINSGSG AVMNAMETNL VG SDKYAAR FGESIVNLGD IDNDGFEDVA IGAPQEDDLQ GAIYIYNGRA DGISSTFSQR IEG LQISKS LSMFGQSISG QIDADNNGYV DVAVGAFRSD SAVLLRTRPV VIVDASLSHP ESVN RTKFD CVENGWPSVC IDLTLCFSYK GKEVPGYIVL FYNMSLDVNR KAESPPRFYF SSNGT SDVI TGSIQVSSRE ANCRTHQAFM RKDVRDILTP IQIEAAYHLG PHVISKRSTE EFPPLQ PIL QQKKEKDIMK KTINFARFCA HENCSADLQV SAKIGFLKPH ENKTYLAVGS MKTLMLN VS LFNAGDDAYE TTLHVKLPVG LYFIKILELE EKQINCEVTD NSGVVQLDCS IGYIYVDH L SRIDISFLLD VSSLSRAEED LSITVHATCE NEEEMDNLKH SRVTVAIPLK YEVKLTVHG FVNPTSFVYG SNDENEPETC MVEKMNLTFH VINTGNSMAP NVSVEIMVPN SFSPQTDKLF NILDVQTTT GECHFENYQR VCALEQQKSA MQTLKGIVRF LSKTDKRLLY CIKADPHCLN F LCNFGKME SGKEASVHIQ LEGRPSILEM DETSALKFEI RATGFPEPNP RVIELNKDEN VA HVLLEGL HHQRPKRYFT

UniProtKB: Isoform 1 of Integrin alpha-4

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Macromolecule #3: human integrin beta 1

MacromoleculeName: human integrin beta 1 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QTDENRCLKA NAKSCGECIQ AGPNCGWCTN STFLQEGMPT SARCDDLEA LKKKGCPPDD IENPRGSKDI KKNKNVTNRS KGTAEKLKPE DITQIQPQQL V LRLRSGEP QTFTLKFKRA EDYPIDLYYL MDLSYSMKDD LENVKSLGTD LMNEMRRITS DF RIGFGSF ...String:
QTDENRCLKA NAKSCGECIQ AGPNCGWCTN STFLQEGMPT SARCDDLEA LKKKGCPPDD IENPRGSKDI KKNKNVTNRS KGTAEKLKPE DITQIQPQQL V LRLRSGEP QTFTLKFKRA EDYPIDLYYL MDLSYSMKDD LENVKSLGTD LMNEMRRITS DF RIGFGSF VEKTVMPYIS TTPAKLRNPC TSEQNCTSPF SYKNVLSLTN KGEVFNELVG KQR ISGNLD SPEGGFDAIM QVAVCGSLIG WRNVTRLLVF STDAGFHFAG DGKLGGIVLP NDGQ CHLEN NMYTMSHYYD YPSIAHLVQK LSENNIQTIF AVTEEFQPVY KELKNLIPKS AVGTL SANS SNVIQLIIDA YNSLSSEVIL ENGKLSEGVT ISYKSYCKNG VNGTGENGRK CSNISI GDE VQFEISITSN KCPKKDSDSF KIRPLGFTEE VEVILQYICE CECQSEGIPE SPKCHEG NG TFECGACRCN EGRVGRHCEC STDEVNSEDM DAYCRKENSS EICSNNGECV CGQCVCRK R DNTNEIYSGK FCECDNFNCD RSNGLICGGN GVCKCRVCEC NPNYTGSACD CSLDTSTCE ASNGQICNGR GICECGVCKC TDPKFQGQTC EMCQTCLGVC AEHKECVQCR AFNKGEKKDT CTQECSYFN ITKVESRDKL PQPVQPDPVS HCKEKDVDDC WFYFTYSVNG NNEVMVHVVE N PECPTGPD

UniProtKB: Isoform 1 of Integrin beta-1

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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
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 76.56 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 37000
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN

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Image processing

Startup modelType of model: OTHER / Details: Ab-initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Details: the resolution is calculated with unmasked FSC. / Number images used: 155996
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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