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- EMDB-45655: Cryo-EM structure of alpha5beta1 integrin in complex with NeoNectin -

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Basic information

Entry
Database: EMDB / ID: EMD-45655
TitleCryo-EM structure of alpha5beta1 integrin in complex with NeoNectin
Map dataSharpened map 3.19Angstrom
Sample
  • Complex: Protein complex of wild type integrin alpha-5 beta-1 with computationally designed protein NeoNectin
    • Protein or peptide: Integrin alpha-5
    • Protein or peptide: Integrin beta-1
    • Protein or peptide: NeoNectin
  • Ligand: CALCIUM ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: MANGANESE (II) ION
Keywordsa5B1 / de novo / tissue regeneration / extracellular matrix protein / 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) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsWerther R / Nguyen A / Estrada Alamo KA / Wang X / Campbell MG
Funding support United States, 4 items
OrganizationGrant numberCountry
The Pew Charitable Trusts United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM147414-01 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30 CA015704-40; RRID:SCR_022611 United States
Other privateSeattle Cancer Consortium Safeway Inc Pilot Grant
CitationJournal: bioRxiv / Year: 2024
Title: De Novo Design of Integrin α5β1 Modulating Proteins for Regenerative Medicine.
Authors: Xinru Wang / Jordi Guillem-Marti / Saurav Kumar / David S Lee / Daniel Cabrerizo-Aguado / Rachel Werther / Kevin Alexander Estrada Alamo / Yan Ting Zhao / Adam Nguyen / Irina Kopyeva / Buwei ...Authors: Xinru Wang / Jordi Guillem-Marti / Saurav Kumar / David S Lee / Daniel Cabrerizo-Aguado / Rachel Werther / Kevin Alexander Estrada Alamo / Yan Ting Zhao / Adam Nguyen / Irina Kopyeva / Buwei Huang / Jing Li / Yuxin Hao / Xinting Li / Aritza Brizuela-Velasco / Analisa Murray / Stacey Gerben / Anindya Roy / Cole A DeForest / Timothy Springer / Hannele Ruohola-Baker / Jonathan A Cooper / Melody G Campbell / Jose Maria Manero / Maria-Pau Ginebra / David Baker /
Abstract: Integrin α5β1 is crucial for cell attachment and migration in development and tissue regeneration, and α5β1 binding proteins could have considerable utility in regenerative medicine and next- ...Integrin α5β1 is crucial for cell attachment and migration in development and tissue regeneration, and α5β1 binding proteins could have considerable utility in regenerative medicine and next-generation therapeutics. We use computational protein design to create de novo α5β1-specific modulating miniprotein binders, called NeoNectins, that bind to and stabilize the open state of α5β1. When immobilized onto titanium surfaces and throughout 3D hydrogels, the NeoNectins outperform native fibronectin and RGD peptide in enhancing cell attachment and spreading, and NeoNectin-grafted titanium implants outperformed fibronectin and RGD-grafted implants in animal models in promoting tissue integration and bone growth. NeoNectins should be broadly applicable for tissue engineering and biomedicine.
History
DepositionJul 9, 2024-
Header (metadata) releaseJul 17, 2024-
Map releaseJul 17, 2024-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45655.png

Downloads & links

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Map

FileDownload / File: emd_45655.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map 3.19Angstrom
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)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.122 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.24
Minimum - Maximum-1.0254947 - 2.0571992
Average (Standard dev.)0.000040452403 (±0.033777367)
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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Mask #1

Fileemd_45655_msk_1.map
Projections & Slices
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Additional map: Additional unsharpened map 3.19Angstrom

Fileemd_45655_additional_1.map
AnnotationAdditional unsharpened map 3.19Angstrom
Projections & Slices
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Additional map: Additional sharpened map 3.28Angstrom

Fileemd_45655_additional_2.map
AnnotationAdditional sharpened map 3.28Angstrom
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Additional map: Additional unsharpened map 3.28Angstrom

Fileemd_45655_additional_3.map
AnnotationAdditional unsharpened map 3.28Angstrom
Projections & Slices
AxesZYX

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Half map: Half Map B from 3.19Angstrom map

Fileemd_45655_half_map_1.map
AnnotationHalf Map B from 3.19Angstrom map
Projections & Slices
AxesZYX

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Half map: Half Map A from 3.19Angstrom map

Fileemd_45655_half_map_2.map
AnnotationHalf Map A from 3.19Angstrom map
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Sample components

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Entire : Protein complex of wild type integrin alpha-5 beta-1 with computa...

EntireName: Protein complex of wild type integrin alpha-5 beta-1 with computationally designed protein NeoNectin
Components
  • Complex: Protein complex of wild type integrin alpha-5 beta-1 with computationally designed protein NeoNectin
    • Protein or peptide: Integrin alpha-5
    • Protein or peptide: Integrin beta-1
    • Protein or peptide: NeoNectin
  • Ligand: CALCIUM ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: MANGANESE (II) ION

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Supramolecule #1: Protein complex of wild type integrin alpha-5 beta-1 with computa...

SupramoleculeName: Protein complex of wild type integrin alpha-5 beta-1 with computationally designed protein NeoNectin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Integrin alpha-5

MacromoleculeName: Integrin alpha-5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 109.695867 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 TKAEGSYGTG GLEVLFQ

UniProtKB: Integrin alpha-5

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Macromolecule #2: Integrin beta-1

MacromoleculeName: Integrin beta-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 81.743961 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 ECPTGPDDTS GLEVLFQ

UniProtKB: Integrin beta-1

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Macromolecule #3: NeoNectin

MacromoleculeName: NeoNectin / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 11.270766 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGLNDIFEAQ KIEWHEGGSG GSELIIHGRG DFPSSELERL RERFERLGIK VRVDHKVLTL IGISEEEAER LARELRKRGI WVEIRKGGS LEHHHHHH

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Macromolecule #7: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 7 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #9: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 9 / Number of copies: 3 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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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

Concentration0.1 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMTrisTris
150.0 mMNaClsodium chloride
1.0 mMMnCl2manganese chloride
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
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: 3 / Average electron dose: 50.0 e/Å2 / Details: Collection at 30 degrees tilt
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: 2.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 36000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 72604
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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