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- EMDB-2281: Three-dimensional reconstruction of intact human integrin alphaII... -

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Basic information

Entry
Database: EMDB / ID: EMD-2281
TitleThree-dimensional reconstruction of intact human integrin alphaIIbbeta3 in a phospholipid bilayer nanodisc
Map dataReconstruction of integrin alphaIIbbeta3 in lipid bilayer nanodisc
Sample
  • Sample: Integrin alphaIIbbeta3 in lipid bilayer nanodisc
  • Protein or peptide: integrin alphaIIb
  • Protein or peptide: Integrin beta3
Keywordsintegrin / alphaIIbbeta3 / nanodisc
Function / homology
Function and homology information


regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / tube development / 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 / maintenance of postsynaptic specialization structure / regulation of extracellular matrix organization ...regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / tube development / 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 / maintenance of postsynaptic specialization structure / regulation of extracellular matrix organization / platelet alpha granule membrane / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / positive regulation of glomerular mesangial cell proliferation / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / alphav-beta3 integrin-HMGB1 complex / vascular endothelial growth factor receptor 2 binding / negative regulation of lipid transport / positive regulation of vascular endothelial growth factor signaling pathway / Elastic fibre formation / cell-substrate junction assembly / alphav-beta3 integrin-IGF-1-IGF1R complex / positive regulation of bone resorption / platelet-derived growth factor receptor binding / mesodermal cell differentiation / glycinergic synapse / filopodium membrane / extracellular matrix binding / regulation of release of sequestered calcium ion into cytosol / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of cell adhesion mediated by integrin / apolipoprotein A-I-mediated signaling pathway / negative regulation of low-density lipoprotein particle clearance / regulation of bone resorption / angiogenesis involved in wound healing / positive regulation of leukocyte migration / wound healing, spreading of epidermal cells / apoptotic cell clearance / positive regulation of fibroblast migration / integrin complex / cell adhesion mediated by integrin / smooth muscle cell migration / heterotypic cell-cell adhesion / Molecules associated with elastic fibres / positive regulation of smooth muscle cell migration / negative chemotaxis / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / positive regulation of cell-matrix adhesion / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / regulation of postsynaptic neurotransmitter receptor internalization / cellular response to insulin-like growth factor stimulus / positive regulation of osteoblast proliferation / protein disulfide isomerase activity / microvillus membrane / cell-substrate adhesion / platelet-derived growth factor receptor signaling pathway / PECAM1 interactions / GRB2:SOS provides linkage to MAPK signaling for Integrins / TGF-beta receptor signaling activates SMADs / lamellipodium membrane / fibronectin binding / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / blood coagulation, fibrin clot formation / ECM proteoglycans / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / positive regulation of T cell migration / coreceptor activity / cellular response to platelet-derived growth factor stimulus / Integrin signaling / positive regulation of endothelial cell proliferation / positive regulation of substrate adhesion-dependent cell spreading / substrate adhesion-dependent cell spreading / embryo implantation / cell adhesion molecule binding / positive regulation of endothelial cell migration / positive regulation of smooth muscle cell proliferation / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / protein kinase C binding / cell-matrix adhesion / response to activity / Signal transduction by L1 / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / wound healing / cellular response to mechanical stimulus / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / cell-cell adhesion / platelet activation / VEGFA-VEGFR2 Pathway / platelet aggregation / integrin binding / cellular response to xenobiotic stimulus / positive regulation of fibroblast proliferation / ruffle membrane
Similarity search - Function
Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / : / Integrin alpha Ig-like domain 3 / Integrin beta subunit, cytoplasmic domain / Integrin beta tail domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin EGF domain ...Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / : / Integrin alpha Ig-like domain 3 / Integrin beta subunit, cytoplasmic domain / Integrin beta tail domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin EGF domain / EGF-like domain, extracellular / EGF-like domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin alpha cytoplasmic region / : / 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, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor / : / Integrin alpha Ig-like domain 2 / 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. / EGF-like domain signature 2.
Similarity search - Domain/homology
Integrin beta-3 / Integrin alpha-IIb
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 20.5 Å
AuthorsChoi WS / Rice WJ / Stokes DL / Coller BS
CitationJournal: 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
DepositionJan 16, 2013-
Header (metadata) releaseJan 30, 2013-
Map releaseNov 6, 2013-
UpdateJan 8, 2014-
Current statusJan 8, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4cak
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2281.png

Downloads & links

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Map

FileDownload / File: emd_2281.map.gz / Format: CCP4 / Size: 9.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of integrin alphaIIbbeta3 in lipid bilayer nanodisc
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.96 Å/pix.
x 136 pix.
= 402.56 Å		2.96 Å/pix.
x 136 pix.
= 402.56 Å		2.96 Å/pix.
x 136 pix.
= 402.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012 / Movie #1: 0.012
Minimum - Maximum-0.1236376 - 0.2876496
Average (Standard dev.)-0.00056975 (±0.00850065)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions136136136
Spacing136136136
CellA=B=C: 402.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.962.962.96
M x/y/z136136136
origin x/y/z0.0000.0000.000
length x/y/z402.560402.560402.560
α/β/γ90.00090.00090.000
start NX/NY/NZ-36-30-80
NX/NY/NZ7361161
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS136136136
D min/max/mean-0.1240.288-0.001

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Supplemental data

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Sample components

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Entire : Integrin alphaIIbbeta3 in lipid bilayer nanodisc

EntireName: Integrin alphaIIbbeta3 in lipid bilayer nanodisc
Components
  • Sample: Integrin alphaIIbbeta3 in lipid bilayer nanodisc
  • Protein or peptide: integrin alphaIIb
  • Protein or peptide: Integrin beta3

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Supramolecule #1000: Integrin alphaIIbbeta3 in lipid bilayer nanodisc

SupramoleculeName: Integrin alphaIIbbeta3 in lipid bilayer nanodisc / type: sample / ID: 1000 / Details: The sample was monodisperse. / Oligomeric state: monomer / Number unique components: 2
Molecular weightExperimental: 230 KDa / Theoretical: 230 KDa / Method: SDS-Page

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Macromolecule #1: integrin alphaIIb

MacromoleculeName: 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
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Blood / Cell: Platelet / Location in cell: Plasma membrane
Molecular weightExperimental: 130 KDa / Theoretical: 130 KDa
SequenceUniProtKB: Integrin alpha-IIb

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Macromolecule #2: Integrin beta3

MacromoleculeName: 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
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Blood / Cell: Platelet / Location in cell: Plasma membrane
Molecular weightExperimental: 100 KDa / Theoretical: 100 KDa
SequenceUniProtKB: Integrin beta-3

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.025 mg/mL
BufferpH: 7.4
Details: 150 mM NaCl, 10 mM HEPES, pH 7.4, 1 mM CaCl2 and 1 mM MgCl2
StainingType: NEGATIVE / Details: 2% uranyl acetate
GridDetails: 200 mesh copper grid with thin carbon support, glow discharged in H2/O2 atmosphere in plasma cleaner
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy #1

Microscopy ID1
MicroscopeFEI TECNAI F20
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 250,000 times magnification
DetailsLow dose package used. CCD magnification is ~1.76 times film magnification
DateFeb 1, 2010
Image recordingCategory: 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 min0
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated 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 stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Tilt angle max: 50
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Electron microscopy #2

Microscopy ID2
MicroscopeFEI TECNAI F20
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 250,000 times magnification
DetailsLow dose package used. CCD magnification is ~1.76 times film magnification
DateJul 31, 2010
Image recordingCategory: 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 min0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated 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 stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Tilt angle max: 50
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Details5 random conical tilt reconstructions were made from class averages, then aligned and merged to make an initial model for reference-based alignment.
Final reconstructionApplied 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 assignmentDetails: SPIDER: theta 45 degrees, phi 45 degrees
Final two d classificationNumber classes: 5

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Atomic model buiding 1

Initial modelPDB ID:

3fcs


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B
SoftwareName: Chimera
DetailsThe 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.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross correlation
Output model

PDB-4cak:
Three-dimensional reconstruction of intact human integrin alphaIIbbeta3 in a phospholipid bilayer nanodisc

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