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- EMDB-7065: Cryo-EM structure of human insulin degrading enzyme -

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Basic information

Entry
Database: EMDB / ID: 7065
TitleCryo-EM structure of human insulin degrading enzyme
SampleInsulin degrading enzyme
SourceHomo sapiens / human
Map dataInsulin degrading enzyme in complex with insulin
Methodsingle particle reconstruction, at 6.5 Å resolution
AuthorsZhang Z / Liang WG / Bailey LJ / Tan YZ / Wei H / Kossiakoff AA / Carragher B / Potter SC / Tang WJ
CitationTo Be Published

To Be Published Search PubMed
Ensemble cryo-EM elucidates the mechanism of insulin capture and degradation by human insulin degrading enzyme
Zhang Z / Liang GW / Bailey JL / Tan YZ / Wei H / McCord AL / Woods A / Farcasanu M / Wang A / Lee D / Shang W / Meredith CS / Deprez-Poulain R / Deprez B / Liu D / Koide S / Lissiakoff AA / Li S / Carraghter B / Potter SC / Tang WJ

Validation ReportPDB-ID: 6b7y

SummaryFull reportAbout validation report
DateDeposition: Oct 5, 2017 / Header (metadata) release: Nov 8, 2017 / Map release: Nov 8, 2017 / Last update: Nov 8, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.014
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.014
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-6b7y
  • Surface level: 0.014
  • Imaged by UCSF CHIMERA
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Supplemental images

Downloads & links

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Map

Fileemd_7065.map.gz (map file in CCP4 format, 131073 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
320 pix
1.07 Å/pix.
= 343.36 Å
320 pix
1.07 Å/pix.
= 343.36 Å
320 pix
1.07 Å/pix.
= 343.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.073 Å
Density
Contour Level:0.014 (by author), 0.014 (movie #1):
Minimum - Maximum-0.1315158 - 0.08239051
Average (Standard dev.)0.00026647426 (0.003625321)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions320320320
Origin000
Limit319319319
Spacing320320320
CellA=B=C: 343.36 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0731.0731.073
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z343.360343.360343.360
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.1320.0820.000

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Supplemental data

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Mask #1

Fileemd_7065_msk_1.map ( map file in CCP4 format, 131073 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Annotation detailsInsulin degrading enzyme in complex with insulin
Space group number1

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Mask #1~

Fileemd_7065_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire Insulin degrading enzyme

EntireName: Insulin degrading enzyme
Details: Cryo-EM structure of human Apo insulin degrading enzyme
Number of components: 2
MassExperimental: 100 kDa

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Component #1: protein, Insulin degrading enzyme

ProteinName: Insulin degrading enzyme
Details: Cryo-EM structure of human Apo insulin degrading enzyme
Recombinant expression: No
MassExperimental: 100 kDa
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: BL

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Component #2: protein, Insulin-degrading enzyme

ProteinName: Insulin-degrading enzyme / Recombinant expression: No
MassTheoretical: 111.866484 kDa
Source (engineered)Expression System: Homo sapiens / human

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.3 mg/ml / pH: 7.8
Support filmThe grids are homemade lacey gold nanowire grids
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 85 % / Details: The cryo grids were made using Spotiton

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Details: The image was collected at 20-50 degree tilt
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 6.8 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 22500 X (nominal), 46598 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 940 - 2200 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 70 - 70 K)
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisition #1Number of digital images: 509
Image acquisition #2Number of digital images: 620 / Sampling size: 5 microns

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 24425
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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Atomic model buiding

Output model

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Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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