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- EMDB-2739: Conformational Snapshots of Inducible Nitric Oxide Synthase (iNOS) -

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Basic information

Entry
Database: EMDB / ID: 2739
TitleConformational Snapshots of Inducible Nitric Oxide Synthase (iNOS)
Map dataSingle-particle reconstruction of iNOS: Group II, Conformation vii
SampleMurine Inducible Nitric Oxide Synthase
  • Inducible Nitric Oxide SynthaseNitric oxide synthase
Keywordsheterogeneity / random conical tilt / nitric oxide synthase / calmodulin / heme / electron transfer / flavin
Function / homologyFAD-binding, type 1 / Flavoprotein-like superfamily / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / Nitric oxide synthase, N-terminal / Oxidoreductase NAD-binding domain / Riboflavin synthase-like beta-barrel / Flavodoxin / Ferredoxin reductase-type FAD-binding domain / FAD binding domain / Nitric-oxide synthase, eukaryote ...FAD-binding, type 1 / Flavoprotein-like superfamily / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / Nitric oxide synthase, N-terminal / Oxidoreductase NAD-binding domain / Riboflavin synthase-like beta-barrel / Flavodoxin / Ferredoxin reductase-type FAD-binding domain / FAD binding domain / Nitric-oxide synthase, eukaryote / Flavodoxin/nitric oxide synthase / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase (NOS) signature. / Flavoprotein pyridine nucleotide cytochrome reductase / Oxidoreductase FAD/NAD(P)-binding / Peroxisomal protein import / Nitric oxide stimulates guanylate cyclase / ROS, RNS production in phagocytes / Ferredoxin reductase-type FAD binding domain profile. / Flavodoxin-like / Flavodoxin-like domain profile. / interleukin-6 secretion / prostaglandin secretion / Ser/Thr protein kinase, TGFB receptor / positive regulation of killing of cells of other organism / tetrahydrobiopterin binding / interleukin-8 secretion / cortical cytoskeleton / arginine binding / superoxide metabolic process / regulation of cytokine production involved in inflammatory response / peptidyl-cysteine S-nitrosylation / cellular response to cytokine stimulus / regulation of insulin secretion / cellular response to organic cyclic compound / nitric-oxide synthase / positive regulation of guanylate cyclase activity / cellular response to interferon-gamma / nitric oxide mediated signal transduction / negative regulation of blood pressure / arginine catabolic process / nitric-oxide synthase activity / NADPH-hemoprotein reductase activity / nitric oxide biosynthetic process / negative regulation of protein catabolic process / cellular response to drug / peroxisome / positive regulation of blood vessel diameter / circadian rhythm / FMN binding / NADP binding / flavin adenine dinucleotide binding / response to lipopolysaccharide / regulation of cell proliferation / calmodulin binding / negative regulation of gene expression / cellular response to lipopolysaccharide / response to hypoxia / inflammatory response / iron ion binding / intracellular / defense response to bacterium / signaling receptor binding / heme binding / perinuclear region of cytoplasm / protein homodimerization activity / metal ion binding / cytosol / cytoplasm / Nitric oxide synthase, inducible
Function and homology information
SourceMus musculus (house mouse)
Methodsingle particle reconstruction / negative staining / 67 Å resolution
AuthorsCampbell MG / Smith BC / Potter CS / Carragher B / Marletta MA
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2014
Title: Molecular architecture of mammalian nitric oxide synthases.
Authors: Melody G Campbell / Brian C Smith / Clinton S Potter / Bridget Carragher / Michael A Marletta
DateDeposition: Jul 29, 2014 / Header (metadata) release: Sep 3, 2014 / Map release: Sep 10, 2014 / Last update: Sep 17, 2014

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.882
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.882
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_2739.map.gz (map file in CCP4 format, 170369 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
352 pix
1.36 Å/pix.
= 478.72 Å
352 pix
1.36 Å/pix.
= 478.72 Å
352 pix
1.36 Å/pix.
= 478.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density
Contour Level:0.882 (by author), 0.882 (movie #1):
Minimum - Maximum-0.84902978 - 2.34935594
Average (Standard dev.)-0.00679095 (0.11729628)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions352352352
Origin-176-176-176
Limit175175175
Spacing352352352
CellA=B=C: 478.72 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.361.361.36
M x/y/z352352352
origin x/y/z0.0000.0000.000
length x/y/z478.720478.720478.720
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ442626
MAP C/R/S123
start NC/NR/NS-176-176-176
NC/NR/NS352352352
D min/max/mean-0.8492.349-0.007

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Supplemental data

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Sample components

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Entire Murine Inducible Nitric Oxide Synthase

EntireName: Murine Inducible Nitric Oxide Synthase / Details: Sample is highly flexible / Number of components: 1 / Oligomeric State: Homodimer
MassTheoretical: 260 kDa

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Component #1: protein, Inducible Nitric Oxide Synthase

ProteinName: Inducible Nitric Oxide SynthaseNitric oxide synthase / a.k.a: iNOSNitric oxide synthase / Oligomeric Details: Homodimer / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 260 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Escherichia coli (E. coli) / Vector: pCWiNOS / Cell of expression system: JM109
Source (natural)Cell: Macrophages
External referencesInterPro: Ser/Thr protein kinase, TGFB receptor / UniProt: Nitric oxide synthase, inducible
Gene Ontology: nitric oxide biosynthetic process, FMN binding, NADP binding, calmodulin binding, flavin adenine dinucleotide binding, heme binding, iron ion binding, nitric-oxide synthase activity

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: negative staining
Sample solutionBuffer solution: 50 mM TEA pH 7.5, 150 mM NaCl, and 5 mM DTT
pH: 7.5
Support filmGlow discharged C-flat grid with 2-micron-diameter holes overlaid by thin 1.5 nm continuous carbon
Staining3 microliters of sample were applied to grid. The specimen was stained twice with 2% uranyl formate, then allowed to air-dry.
VitrificationInstrument: NONE / Cryogen name: NONE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20 / Date: Mar 6, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 37 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 62000 X (nominal), 114705 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 2500 nm
Specimen HolderModel: SIDE ENTRY, EUCENTRIC / Tilt Angle: 0 - 55 deg.
CameraDetector: TVIPS TEMCAM-F416 (4k x 4k)

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Image acquisition

Image acquisition
2226
Image acquisition
Eachareais imagedtwic eonceat55d egreesanda gainwithno tilt

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Image processing

ProcessingMethod: single particle reconstruction / Number of class averages: 1 / Applied symmetry: C1 (asymmetric) / Number of projections: 207 / Details: See publication.
3D reconstructionAlgorithm: RCT / Software: Appion, Spider / CTF correction: Each Image / Details: See publication. / Resolution: 67 Å / Resolution method: FSC 0.5, semi-independent

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