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Yorodumi- EMDB-45655: Cryo-EM structure of alpha5beta1 integrin in complex with NeoNectin -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-45655 | |||||||||||||||
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Title | Cryo-EM structure of alpha5beta1 integrin in complex with NeoNectin | |||||||||||||||
Map data | Sharpened map 3.19Angstrom | |||||||||||||||
Sample |
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Keywords | a5B1 / de novo / tissue regeneration / extracellular matrix protein / SIGNALING PROTEIN | |||||||||||||||
Function / homology | Function and homology information integrin alpha6-beta1 complex / integrin alpha8-beta1 complex / integrin alpha3-beta1 complex / integrin alpha5-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 / regulation of inward rectifier potassium channel activity ...integrin alpha6-beta1 complex / integrin alpha8-beta1 complex / integrin alpha3-beta1 complex / integrin alpha5-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 / regulation of inward rectifier potassium channel activity / regulation of collagen catabolic process / integrin alpha9-beta1 complex / integrin alpha4-beta1 complex / cardiac cell fate specification / integrin binding involved in cell-matrix adhesion / cell-cell adhesion mediated by integrin / integrin alpha1-beta1 complex / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / regulation of synapse pruning / reactive gliosis / formation of radial glial scaffolds / cerebellar climbing fiber to Purkinje cell synapse / Other semaphorin interactions / Formation of the ureteric bud / CD40 signaling pathway / positive regulation of vascular endothelial growth factor signaling pathway / calcium-independent cell-matrix adhesion / integrin alphav-beta1 complex / positive regulation of fibroblast growth factor receptor signaling pathway / Fibronectin matrix formation / basement membrane organization / myelin sheath abaxonal region / alphav-beta3 integrin-vitronectin complex / CHL1 interactions / cardiac muscle cell myoblast differentiation / Laminin interactions / RUNX2 regulates genes involved in cell migration / MET interacts with TNS proteins / germ cell migration / leukocyte tethering or rolling / cardiac muscle cell differentiation / vascular endothelial growth factor receptor 2 binding / cell projection organization / Platelet Adhesion to exposed collagen / myoblast fusion / Elastic fibre formation / mesodermal cell differentiation / cell-substrate junction assembly / platelet-derived growth factor receptor binding / axon extension / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / positive regulation of fibroblast migration / positive regulation of vascular endothelial growth factor receptor signaling pathway / cell migration involved in sprouting angiogenesis / wound healing, spreading of epidermal cells / heterotypic cell-cell adhesion / myoblast differentiation / integrin complex / regulation of spontaneous synaptic transmission / positive regulation of cell-substrate adhesion / dendrite morphogenesis / cellular response to low-density lipoprotein particle stimulus / Molecules associated with elastic fibres / Basigin interactions / muscle organ development / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / lamellipodium assembly / negative regulation of Rho protein signal transduction / cell adhesion mediated by integrin / MET activates PTK2 signaling / Syndecan interactions / negative regulation of vasoconstriction / leukocyte cell-cell adhesion / epidermal growth factor receptor binding / sarcomere organization / positive regulation of wound healing / maintenance of blood-brain barrier / positive regulation of neuroblast proliferation / cell-substrate adhesion / positive regulation of sprouting angiogenesis / endodermal cell differentiation / homophilic cell adhesion via plasma membrane adhesion molecules / TGF-beta receptor signaling activates SMADs / establishment of mitotic spindle orientation / cleavage furrow / glial cell projection / fibronectin binding / negative regulation of anoikis / intercalated disc / RHOG GTPase cycle / negative regulation of neuron differentiation / ECM proteoglycans / neuroblast proliferation / RAC2 GTPase cycle / RAC3 GTPase cycle / Integrin cell surface interactions / cellular defense response / coreceptor activity Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.19 Å | |||||||||||||||
Authors | Werther R / Nguyen A / Estrada Alamo KA / Wang X / Campbell MG | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: To Be Published Title: De Novo Design of Integrin alpha5beta1 Modulating Proteins for Regenerative Medicine Authors: Wang X / Guillem-Marti J / Kumar S / Lee DS / Cabrerizo-Aguado D / Werther R / Estrada Alamo KA / Zhao YT / Nguyen A / Kopyeva I / Huang B / Li J / Hao Y / Li X / Brizuela-Velasco A / Murray ...Authors: Wang X / Guillem-Marti J / Kumar S / Lee DS / Cabrerizo-Aguado D / Werther R / Estrada Alamo KA / Zhao YT / Nguyen A / Kopyeva I / Huang B / Li J / Hao Y / Li X / Brizuela-Velasco A / Murray AN / Gerben S / Roy A / DeForest CA / Springer T / Ruohola-Baker H / Cooper JA / Campbell MG / Maria Manero J / Ginebra M / Baker D | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_45655.map.gz | 86.1 MB | EMDB map data format | |
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Header (meta data) | emd-45655-v30.xml emd-45655.xml | 27.7 KB 27.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_45655_fsc.xml | 11.6 KB | Display | FSC data file |
Images | emd_45655.png | 104 KB | ||
Masks | emd_45655_msk_1.map | 166.4 MB | Mask map | |
Filedesc metadata | emd-45655.cif.gz | 8 KB | ||
Others | emd_45655_additional_1.map.gz emd_45655_additional_2.map.gz emd_45655_additional_3.map.gz emd_45655_half_map_1.map.gz emd_45655_half_map_2.map.gz | 84 MB 85.9 MB 83.9 MB 154.6 MB 154.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-45655 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-45655 | HTTPS FTP |
-Validation report
Summary document | emd_45655_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_45655_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_45655_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | emd_45655_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-45655 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-45655 | HTTPS FTP |
-Related structure data
Related structure data | 9ckvMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_45655.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Sharpened map 3.19Angstrom | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.122 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_45655_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Additional unsharpened map 3.19Angstrom
File | emd_45655_additional_1.map | ||||||||||||
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Annotation | Additional unsharpened map 3.19Angstrom | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Additional sharpened map 3.28Angstrom
File | emd_45655_additional_2.map | ||||||||||||
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Annotation | Additional sharpened map 3.28Angstrom | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Additional unsharpened map 3.28Angstrom
File | emd_45655_additional_3.map | ||||||||||||
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Annotation | Additional unsharpened map 3.28Angstrom | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map B from 3.19Angstrom map
File | emd_45655_half_map_1.map | ||||||||||||
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Annotation | Half Map B from 3.19Angstrom map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map A from 3.19Angstrom map
File | emd_45655_half_map_2.map | ||||||||||||
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Annotation | Half Map A from 3.19Angstrom map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Protein complex of wild type integrin alpha-5 beta-1 with computa...
Entire | Name: Protein complex of wild type integrin alpha-5 beta-1 with computationally designed protein NeoNectin |
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Components |
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-Supramolecule #1: Protein complex of wild type integrin alpha-5 beta-1 with computa...
Supramolecule | Name: 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 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Integrin alpha-5
Macromolecule | Name: Integrin alpha-5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 109.695867 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: 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 |
-Macromolecule #2: Integrin beta-1
Macromolecule | Name: Integrin beta-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 81.743961 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: 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 |
-Macromolecule #3: NeoNectin
Macromolecule | Name: NeoNectin / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 11.270766 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGLNDIFEAQ KIEWHEGGSG GSELIIHGRG DFPSSELERL RERFERLGIK VRVDHKVLTL IGISEEEAER LARELRKRGI WVEIRKGGS LEHHHHHH |
-Macromolecule #7: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 7 / Number of copies: 4 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 2 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #9: MANGANESE (II) ION
Macromolecule | Name: MANGANESE (II) ION / type: ligand / ID: 9 / Number of copies: 3 / Formula: MN |
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Molecular weight | Theoretical: 54.938 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film 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 beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 stage | Cooling holder cryogen: NITROGEN |