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- EMDB-44387: Integrin alpha-5 beta-1 in complex with MINT1526A Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-44387
TitleIntegrin alpha-5 beta-1 in complex with MINT1526A Fab
Map dataprimary EM map
Sample
  • Complex: Protein complex of integrin alpha-5 beta-1 with MINT1526A Fab
    • Protein or peptide: Integrin alpha-5 light chain
    • Protein or peptide: Integrin beta-1
    • Protein or peptide: MINT1526A Fab Heavy Chain
    • Protein or peptide: MINT1526A Fab Light Chain
  • Ligand: CALCIUM ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsIntegrin / Antibody Fab / Inhibitory / SIGNALING PROTEIN
Function / homology
Function and homology information


integrin alpha8-beta1 complex / : / integrin alpha3-beta1 complex / integrin alpha5-beta1 complex / integrin alpha6-beta1 complex / integrin alpha7-beta1 complex / integrin alpha10-beta1 complex / integrin alpha11-beta1 complex / positive regulation of glutamate uptake involved in transmission of nerve impulse / myoblast fate specification ...integrin alpha8-beta1 complex / : / integrin alpha3-beta1 complex / integrin alpha5-beta1 complex / integrin alpha6-beta1 complex / integrin alpha7-beta1 complex / integrin alpha10-beta1 complex / integrin alpha11-beta1 complex / positive regulation of glutamate uptake involved in transmission of nerve impulse / myoblast fate specification / integrin alpha9-beta1 complex / regulation of collagen catabolic process / cardiac cell fate specification / integrin binding involved in cell-matrix adhesion / integrin alpha4-beta1 complex / cell-cell adhesion mediated by integrin / integrin alpha1-beta1 complex / collagen binding involved in cell-matrix adhesion / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / integrin alpha2-beta1 complex / reactive gliosis / formation of radial glial scaffolds / Other semaphorin interactions / cerebellar climbing fiber to Purkinje cell synapse / Formation of the ureteric bud / positive regulation of fibroblast growth factor receptor signaling pathway / CD40 signaling pathway / Fibronectin matrix formation / calcium-independent cell-matrix adhesion / basement membrane organization / regulation of synapse pruning / integrin alphav-beta1 complex / myelin sheath abaxonal region / CHL1 interactions / RUNX2 regulates genes involved in cell migration / cardiac muscle cell myoblast differentiation / alphav-beta3 integrin-vitronectin complex / MET interacts with TNS proteins / Laminin interactions / leukocyte tethering or rolling / cardiac muscle cell differentiation / germ cell migration / cell projection organization / Platelet Adhesion to exposed collagen / vascular endothelial growth factor receptor 2 binding / myoblast fusion / positive regulation of vascular endothelial growth factor signaling pathway / Elastic fibre formation / mesodermal cell differentiation / cell-substrate junction assembly / platelet-derived growth factor receptor binding / axon extension / myoblast differentiation / cell migration involved in sprouting angiogenesis / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / positive regulation of fibroblast migration / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of cell-substrate adhesion / wound healing, spreading of epidermal cells / integrin complex / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / heterotypic cell-cell adhesion / regulation of spontaneous synaptic transmission / epidermal growth factor receptor binding / lamellipodium assembly / dendrite morphogenesis / sarcomere organization / Molecules associated with elastic fibres / MET activates PTK2 signaling / Basigin interactions / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / negative regulation of vasoconstriction / leukocyte cell-cell adhesion / cell adhesion mediated by integrin / positive regulation of wound healing / muscle organ development / Syndecan interactions / response to muscle activity / positive regulation of neuroblast proliferation / maintenance of blood-brain barrier / negative regulation of Rho protein signal transduction / positive regulation of sprouting angiogenesis / cell-substrate adhesion / endodermal cell differentiation / homophilic cell adhesion via plasma membrane adhesion molecules / TGF-beta receptor signaling activates SMADs / establishment of mitotic spindle orientation / cleavage furrow / fibronectin binding / negative regulation of anoikis / cellular response to low-density lipoprotein particle stimulus / RHOG GTPase cycle / glial cell projection / intercalated disc / neuroblast proliferation / negative regulation of neuron differentiation / RAC2 GTPase cycle / ECM proteoglycans / RAC3 GTPase cycle / Integrin cell surface interactions
Similarity search - Function
Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / : / Integrin alpha Ig-like domain 3 / Integrin EGF domain / Integrin beta subunit, tail ...Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / : / Integrin alpha Ig-like domain 3 / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / EGF-like domain, extracellular / EGF-like domain / Integrins beta chain EGF (I-EGF) domain profile. / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1.
Similarity search - Domain/homology
Integrin beta-1 / Integrin alpha-5
Similarity search - Component
Biological speciesHomo sapiens (human) / unidentified (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsNguyen A / Azumaya CM / Campbell MG
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM147414-01 United States
The Pew Charitable Trusts United States
Other privateP30 CA015704-40
CitationJournal: bioRxiv / Year: 2025
Title: Structural and functional characterization of integrin α5-targeting antibodies for anti-angiogenic therapy.
Authors: Adam Nguyen / Joel B Heim / Gabriele Cordara / Matthew C Chan / Hedda Johannesen / Cristine Charlesworth / Ming Li / Caleigh M Azumaya / Benjamin Madden / Ute Krengel / Alexander Meves / Melody G Campbell /
Abstract: Integrins are a large family of heterodimeric receptors important for cell adhesion and signaling. Integrin α5β1, also known as the fibronectin receptor, is a key mediator of angiogenesis and its ...Integrins are a large family of heterodimeric receptors important for cell adhesion and signaling. Integrin α5β1, also known as the fibronectin receptor, is a key mediator of angiogenesis and its dysregulation is associated with tumor proliferation, progression, and metastasis. Despite numerous efforts, α5β1-targeting therapeutics have been unsuccessful in large part due to efficacy and off-target effects. To mediate activation and signaling, integrins undergo drastic conformational changes. However, how therapeutics influence or are affected by integrin conformation remains incompletely characterized. Using cell biology, biophysics, and electron microscopy, we shed light on these relationships by characterizing two potentially therapeutic anti-α5β1 antibodies, BIIG2 and MINT1526A. We show that both antibodies bind α5β1 with nanomolar affinity and reduce angiogenesis . We demonstrate BIIG2 reduces tumor growth in two human xenograft mouse models and exhibits a strong specificity for connective tissue-resident fibroblasts and melanoma cells. Using electron microscopy, we map out the molecular interfaces mediating the integrin-antibody interactions and reveal that although both antibodies have overlapping epitopes and block fibronectin binding via steric hindrance, the effect on the conformational equilibrium is drastically different. While MINT1526A constricts α5β1's range of flexibility, BIIG2 binds without restricting the available conformational states. These mechanistic insights, coupled with the functional analysis, guide which aspects should be prioritized to avoid off-target effects or partial agonism in the design of future integrin-targeted therapeutics.
History
DepositionApr 2, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44387.png

Downloads & links

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Map

FileDownload / File: emd_44387.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprimary EM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 352 pix.
= 394.944 Å		1.12 Å/pix.
x 352 pix.
= 394.944 Å		1.12 Å/pix.
x 352 pix.
= 394.944 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: 0.3
Minimum - Maximum-0.7104602 - 1.6691222
Average (Standard dev.)-0.00002537017 (±0.026204854)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 394.944 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Additional EM map

Fileemd_44387_additional_1.map
AnnotationAdditional EM map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: primary EM map half B

Fileemd_44387_half_map_1.map
Annotationprimary EM map half B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: primary EM map half A

Fileemd_44387_half_map_2.map
Annotationprimary EM map half A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Protein complex of integrin alpha-5 beta-1 with MINT1526A Fab

EntireName: Protein complex of integrin alpha-5 beta-1 with MINT1526A Fab
Components
  • Complex: Protein complex of integrin alpha-5 beta-1 with MINT1526A Fab
    • Protein or peptide: Integrin alpha-5 light chain
    • Protein or peptide: Integrin beta-1
    • Protein or peptide: MINT1526A Fab Heavy Chain
    • Protein or peptide: MINT1526A Fab Light Chain
  • Ligand: CALCIUM ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Protein complex of integrin alpha-5 beta-1 with MINT1526A Fab

SupramoleculeName: Protein complex of integrin alpha-5 beta-1 with MINT1526A Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Integrin alpha-5 light chain

MacromoleculeName: Integrin alpha-5 light chain / type: protein_or_peptide / ID: 1
Details: Integrin alpha-5 ectodomain with cleaved linker, HRV 3C cute site, acid coil and Strep-Tag II.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 108.693734 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MGSRTPESPL HAVQLRWGPR RRPPLLPLLL LLLPPPPRVG GFNLDAEAPA VLSGPPGSFF GFSVEFYRPG TDGVSVLVGA PKANTSQPG VLQGGAVYLC PWGASPTQCT PIEFDSKGSR LLESSLSSSE GEEPVEYKSL QWFGATVRAH GSSILACAPL Y SWRTEKEP ...String:
MGSRTPESPL HAVQLRWGPR RRPPLLPLLL LLLPPPPRVG GFNLDAEAPA VLSGPPGSFF GFSVEFYRPG TDGVSVLVGA PKANTSQPG VLQGGAVYLC PWGASPTQCT PIEFDSKGSR LLESSLSSSE GEEPVEYKSL QWFGATVRAH GSSILACAPL Y SWRTEKEP LSDPVGTCYL STDNFTRILE YAPCRSDFSW AAGQGYCQGG FSAEFTKTGR VVLGGPGSYF WQGQILSATQ EQ IAESYYP EYLINLVQGQ LQTRQASSIY DDSYLGYSVA VGEFSGDDTE DFVAGVPKGN LTYGYVTILN GSDIRSLYNF SGE QMASYF GYAVAATDVN GDGLDDLLVG APLLMDRTPD GRPQEVGRVY VYLQHPAGIE PTPTLTLTGH DEFGRFGSSL TPLG DLDQD GYNDVAIGAP FGGETQQGVV FVFPGGPGGL GSKPSQVLQP LWAASHTPDF FGSALRGGRD LDGNGYPDLI VGSFG VDKA VVYRGRPIVS ASASLTIFPA MFNPEERSCS LEGNPVACIN LSFCLNASGK HVADSIGFTV ELQLDWQKQK GGVRRA LFL ASRQATLTQT LLIQNGARED CREMKIYLRN ESEFRDKLSP IHIALNFSLD PQAPVDSHGL RPALHYQSKS RIEDKAQ IL LDCGEDNICV PDLQLEVFGE QNHVYLGDKN ALNLTFHAQN VGEGGAYEAE LRVTAPPEAE YSGLVRHPGN FSSLSCDY F AVNQSRLLVC DLGNPMKAGA SLWGGLRFTV PHLRDTKKTI QFDFQILSKN LNNSQSDVVS FRLSVEAQAQ VTLNGVSKP EAVLFPVSDW HPRDQPQKEE DLGPAVHHVY ELINQGPSSI SQGVLELSCP QALEGQQLLY VTRVTGLNCT TNHPINPKGL ELDPEGSLH HQQKREAPSR SSASSGPQIL KCPEAECFRL RCELGPLHQQ ESQSLQLHFR VWAKTFLQRE HQPFSLQCEA V YKALKMPY RILPRQLPQK ERQVATAVQW TKAEGSY

UniProtKB: Integrin alpha-5

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Macromolecule #2: Integrin beta-1

MacromoleculeName: Integrin beta-1 / type: protein_or_peptide / ID: 2
Details: Integrin beta-1 ectodomain with cleaved linker, HRV 3C cut site, base coil, and 6x His-tag.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 80.653781 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MNLQPIFWIG LISSVCCVFA QTDENRCLKA NAKSCGECIQ AGPNCGWCTN STFLQEGMPT SARCDDLEAL KKKGCPPDDI ENPRGSKDI KKNKNVTNRS KGTAEKLKPE DITQIQPQQL VLRLRSGEPQ TFTLKFKRAE DYPIDLYYLM DLSYSMKDDL E NVKSLGTD ...String:
MNLQPIFWIG LISSVCCVFA QTDENRCLKA NAKSCGECIQ AGPNCGWCTN STFLQEGMPT SARCDDLEAL KKKGCPPDDI ENPRGSKDI KKNKNVTNRS KGTAEKLKPE DITQIQPQQL VLRLRSGEPQ TFTLKFKRAE DYPIDLYYLM DLSYSMKDDL E NVKSLGTD LMNEMRRITS DFRIGFGSFV EKTVMPYIST TPAKLRNPCT SEQNCTSPFS YKNVLSLTNK GEVFNELVGK QR ISGNLDS PEGGFDAIMQ VAVCGSLIGW RNVTRLLVFS TDAGFHFAGD GKLGGIVLPN DGQCHLENNM YTMSHYYDYP SIA HLVQKL SENNIQTIFA VTEEFQPVYK ELKNLIPKSA VGTLSANSSN VIQLIIDAYN SLSSEVILEN GKLSEGVTIS YKSY CKNGV NGTGENGRKC SNISIGDEVQ FEISITSNKC PKKDSDSFKI RPLGFTEEVE VILQYICECE CQSEGIPESP KCHEG NGTF ECGACRCNEG RVGRHCECST DEVNSEDMDA YCRKENSSEI CSNNGECVCG QCVCRKRDNT NEIYSGKFCE CDNFNC DRS NGLICGGNGV CKCRVCECNP NYTGSACDCS LDTSTCEASN GQICNGRGIC ECGVCKCTDP KFQGQTCEMC QTCLGVC AE HKECVQCRAF NKGEKKDTCT QECSYFNITK VESRDKLPQP VQPDPVSHCK EKDVDDCWFY FTYSVNGNNE VMVHVVEN P ECPTGPD

UniProtKB: Integrin beta-1

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Macromolecule #3: MINT1526A Fab Heavy Chain

MacromoleculeName: MINT1526A Fab Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 13.398053 KDa
SequenceString:
EVHLVESGGD LVQPGSSLKL SCAASGFTFS NRWLYWVKQA PGKGLEWVGG LKTKPNLYAT EYADSVKGRF TISRDDSKNS LYLQMNTLR VDDTALYYCT SLTGMRYFDY WGQGTMVTVS S

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Macromolecule #4: MINT1526A Fab Light Chain

MacromoleculeName: MINT1526A Fab Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 11.978021 KDa
SequenceString:
LDVLTQSPSA SASLGNSVKL TCTLSSQHST YTIGWYQAGH PDKAPKYVMY LNSDGSHNKG DGLPDRFSGS SSGAHRYLSI SNIQPEDEA DYFCGSSYSS GYVFGSGTKV ELK

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Macromolecule #9: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 9 / Number of copies: 7 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #10: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 10 / Number of copies: 1 / 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

Concentration0.10 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMTris-HClTris hydrochloride
150.0 mMNaClsodium chloride
5.0 mMCaCl2calcium chloride
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 3079 / 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 / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 36000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 1339328
Startup modelType of model: INSILICO MODEL
In silico model: Ab initio model from selected particles within the dataset
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 342608
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

7nxd

chain_id: A, source_name: PDB, initial_model_type: experimental model

7nxd

chain_id: B, source_name: PDB, initial_model_type: experimental model
DetailsInitial local fitting was done using ChimeraX and then Phenix, ISOLDE and COOT for flexible fitting and modeling.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 106.4 / Target criteria: Cross-correlation coefficient
Output model

PDB-9b9k:
Integrin alpha-5 beta-1 in complex with MINT1526A Fab

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