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Yorodumi- EMDB-2281: Three-dimensional reconstruction of intact human integrin alphaII... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2281 | |||||||||
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Title | Three-dimensional reconstruction of intact human integrin alphaIIbbeta3 in a phospholipid bilayer nanodisc | |||||||||
Map data | Reconstruction of integrin alphaIIbbeta3 in lipid bilayer nanodisc | |||||||||
Sample |
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Keywords | integrin / alphaIIbbeta3 / nanodisc | |||||||||
Function / homology | Function and homology information tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / positive regulation of glomerular mesangial cell proliferation ...tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / positive regulation of glomerular mesangial cell proliferation / platelet alpha granule membrane / negative regulation of lipoprotein metabolic process / integrin alphav-beta3 complex / negative regulation of low-density lipoprotein receptor activity / fibrinogen binding / alphav-beta3 integrin-PKCalpha complex / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-HMGB1 complex / blood coagulation, fibrin clot formation / mesodermal cell differentiation / vascular endothelial growth factor receptor 2 binding / negative regulation of lipid transport / glycinergic synapse / angiogenesis involved in wound healing / Elastic fibre formation / regulation of release of sequestered calcium ion into cytosol / alphav-beta3 integrin-IGF-1-IGF1R complex / cell-substrate junction assembly / platelet-derived growth factor receptor binding / filopodium membrane / extracellular matrix binding / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of fibroblast migration / regulation of postsynaptic neurotransmitter receptor internalization / apolipoprotein A-I-mediated signaling pathway / regulation of bone resorption / apoptotic cell clearance / wound healing, spreading of epidermal cells / positive regulation of cell adhesion mediated by integrin / heterotypic cell-cell adhesion / integrin complex / positive regulation of leukocyte migration / Molecules associated with elastic fibres / microvillus membrane / smooth muscle cell migration / cell adhesion mediated by integrin / positive regulation of cell-matrix adhesion / negative chemotaxis / Syndecan interactions / cellular response to insulin-like growth factor stimulus / activation of protein kinase activity / p130Cas linkage to MAPK signaling for integrins / protein disulfide isomerase activity / cell-substrate adhesion / positive regulation of smooth muscle cell migration / positive regulation of osteoblast proliferation / cellular response to platelet-derived growth factor stimulus / TGF-beta receptor signaling activates SMADs / PECAM1 interactions / GRB2:SOS provides linkage to MAPK signaling for Integrins / lamellipodium membrane / platelet-derived growth factor receptor signaling pathway / fibronectin binding / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / ECM proteoglycans / positive regulation of bone resorption / positive regulation of T cell migration / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / coreceptor activity / positive regulation of substrate adhesion-dependent cell spreading / cell adhesion molecule binding / positive regulation of endothelial cell proliferation / embryo implantation / Integrin signaling / positive regulation of endothelial cell migration / cell-matrix adhesion / substrate adhesion-dependent cell spreading / platelet aggregation / response to activity / Signal transduction by L1 / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / protein kinase C binding / positive regulation of smooth muscle cell proliferation / wound healing / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / platelet activation / VEGFA-VEGFR2 Pathway / cell-cell adhesion / ruffle membrane / cellular response to mechanical stimulus / positive regulation of angiogenesis / positive regulation of peptidyl-tyrosine phosphorylation / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 20.5 Å | |||||||||
Authors | Choi WS / Rice WJ / Stokes DL / Coller BS | |||||||||
Citation | Journal: Blood / Year: 2013 Title: Three-dimensional reconstruction of intact human integrin αIIbβ3: new implications for activation-dependent ligand binding. Authors: Won-Seok Choi / William J Rice / David L Stokes / Barry S Coller / Abstract: Integrin αIIbβ3 plays a central role in hemostasis and thrombosis. We provide the first 3-dimensional reconstruction of intact purified αIIbβ3 in a nanodisc lipid bilayer. Unlike previous models, ...Integrin αIIbβ3 plays a central role in hemostasis and thrombosis. We provide the first 3-dimensional reconstruction of intact purified αIIbβ3 in a nanodisc lipid bilayer. Unlike previous models, it shows that the ligand-binding head domain is on top, pointing away from the membrane. Moreover, unlike the crystal structure of the recombinant ectodomain, the lower legs are not parallel, straight, and adjacent. Rather, the αIIb lower leg is bent between the calf-1 and calf-2 domains and the β3 Integrin-Epidermal Growth Factor (I-EGF) 2 to 4 domains are freely coiled rather than in a cleft between the β3 headpiece and the αIIb lower leg. Our data indicate an important role for the region that links the distal calf-2 and β-tail domains to their respective transmembrane (TM) domains in transmitting the conformational changes in the TM domains associated with inside-out activation. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2281.map.gz | 8.5 MB | EMDB map data format | |
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Header (meta data) | emd-2281-v30.xml emd-2281.xml | 14.3 KB 14.3 KB | Display Display | EMDB header |
Images | EMD-2281.png | 45.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2281 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2281 | HTTPS FTP |
-Validation report
Summary document | emd_2281_validation.pdf.gz | 206.4 KB | Display | EMDB validaton report |
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Full document | emd_2281_full_validation.pdf.gz | 205.5 KB | Display | |
Data in XML | emd_2281_validation.xml.gz | 5.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2281 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2281 | HTTPS FTP |
-Related structure data
Related structure data | 4cakMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_2281.map.gz / Format: CCP4 / Size: 9.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of integrin alphaIIbbeta3 in lipid bilayer nanodisc | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.96 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Integrin alphaIIbbeta3 in lipid bilayer nanodisc
Entire | Name: Integrin alphaIIbbeta3 in lipid bilayer nanodisc |
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Components |
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-Supramolecule #1000: Integrin alphaIIbbeta3 in lipid bilayer nanodisc
Supramolecule | Name: Integrin alphaIIbbeta3 in lipid bilayer nanodisc / type: sample / ID: 1000 / Details: The sample was monodisperse. / Oligomeric state: monomer / Number unique components: 2 |
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Molecular weight | Experimental: 230 KDa / Theoretical: 230 KDa / Method: SDS-Page |
-Macromolecule #1: integrin alphaIIb
Macromolecule | Name: integrin alphaIIb / type: protein_or_peptide / ID: 1 / Name.synonym: GPIIb Details: Native protein purified from platelet, heterodimer with integrin beta3 subunit Number of copies: 1 / Oligomeric state: hetero dimer / Recombinant expression: No |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Tissue: Blood / Cell: Platelet / Location in cell: Plasma membrane |
Molecular weight | Experimental: 130 KDa / Theoretical: 130 KDa |
Sequence | UniProtKB: Integrin alpha-IIb |
-Macromolecule #2: Integrin beta3
Macromolecule | Name: Integrin beta3 / type: protein_or_peptide / ID: 2 / Name.synonym: GPIIIa Details: Native protein purified from platelet, heterodimer with integrin alphaIIb subunit Number of copies: 1 / Oligomeric state: hetero dimer / Recombinant expression: No |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Tissue: Blood / Cell: Platelet / Location in cell: Plasma membrane |
Molecular weight | Experimental: 100 KDa / Theoretical: 100 KDa |
Sequence | UniProtKB: Integrin beta-3 |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.025 mg/mL |
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Buffer | pH: 7.4 Details: 150 mM NaCl, 10 mM HEPES, pH 7.4, 1 mM CaCl2 and 1 mM MgCl2 |
Staining | Type: NEGATIVE / Details: 2% uranyl acetate |
Grid | Details: 200 mesh copper grid with thin carbon support, glow discharged in H2/O2 atmosphere in plasma cleaner |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy #1
Microscopy ID | 1 |
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Microscope | FEI TECNAI F20 |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 250,000 times magnification |
Details | Low dose package used. CCD magnification is ~1.76 times film magnification |
Date | Feb 1, 2010 |
Image recording | Category: CCD / Film or detector model: GENERIC TVIPS (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 1500 / Average electron dose: 13 e/Å2 / Bits/pixel: 16 |
Tilt angle min | 0 |
Electron beam | Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 50592 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 29000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC / Tilt angle max: 50 |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Electron microscopy #2
Microscopy ID | 2 |
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Microscope | FEI TECNAI F20 |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 250,000 times magnification |
Details | Low dose package used. CCD magnification is ~1.76 times film magnification |
Date | Jul 31, 2010 |
Image recording | Category: CCD / Film or detector model: GENERIC TVIPS (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 1500 / Average electron dose: 13 e/Å2 / Bits/pixel: 16 |
Tilt angle min | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 88249 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 0.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC / Tilt angle max: 50 |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Details | 5 random conical tilt reconstructions were made from class averages, then aligned and merged to make an initial model for reference-based alignment. |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 20.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: spider Details: Initial model was made from aligning and averaging 5 models made by random conical tilt. Number images used: 25008 |
Final angle assignment | Details: SPIDER: theta 45 degrees, phi 45 degrees |
Final two d classification | Number classes: 5 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B |
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Software | Name: Chimera |
Details | The individual alphaIIb and beta3 domains were docked into the anchor graph of the EM map so as to maintain the sequence of domains and the distances between domains in the crystal structure. The locations were then optimized by maximizing the cross-correlation and the atomic inclusion of the domain within the EM map. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross correlation |
Output model | PDB-4cak: |