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- EMDB-0741: cryoEM 3D reconstruction of IGF1R in complex with IGF1 -

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Basic information

Entry
Database: EMDB / ID: EMD-0741
TitlecryoEM 3D reconstruction of IGF1R in complex with IGF1
Map data
SampleIGF1R:
IGF1 receptor
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.7 Å
AuthorsWang T / Sun J
CitationJournal: Structure / Year: 2020
Title: Visualization of Ligand-Bound Ectodomain Assembly in the Full-Length Human IGF-1 Receptor by Cryo-EM Single-Particle Analysis.
Authors: Xi Zhang / Daqi Yu / Jingchuan Sun / Yujie Wu / Junyuan Gong / Xuemei Li / Li Liu / Shan Liu / Jianbo Liu / Yulan Wu / Dongyang Li / Yinping Ma / Xu Han / Yanan Zhu / Zhaolong Wu / Yihua ...Authors: Xi Zhang / Daqi Yu / Jingchuan Sun / Yujie Wu / Junyuan Gong / Xuemei Li / Li Liu / Shan Liu / Jianbo Liu / Yulan Wu / Dongyang Li / Yinping Ma / Xu Han / Yanan Zhu / Zhaolong Wu / Yihua Wang / Qi Ouyang / Tao Wang /
Abstract: Tyrosine kinase receptor of insulin-like growth factor 1 receptor (IGF-1R) and insulin receptor (IR) bind to hormones, such as insulin, IGF-1, and IGF-2, and transduces the signals across the cell ...Tyrosine kinase receptor of insulin-like growth factor 1 receptor (IGF-1R) and insulin receptor (IR) bind to hormones, such as insulin, IGF-1, and IGF-2, and transduces the signals across the cell membrane. However, the complete structure of the receptor and the signal transduction mechanism remains unclear. Here, we report the cryo-EM structure of the ligand-bound ectodomain in the full-length human IGF-1R. We reconstructed the IGF-1R/insulin complex at 4.7 Å and the IGF-1R/IGF-1 complex at 7.7 Å. Our structures reveal that only one insulin or one IGF-1 molecule binds to and activates the full-length human IGF-1R receptor.
History
DepositionAug 14, 2019-
Header (metadata) releaseJul 1, 2020-
Map releaseJul 1, 2020-
UpdateJul 1, 2020-
Current statusJul 1, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00821
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.00821
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0741.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.99 Å/pix.
x 256 pix.
= 253.44 Å
0.99 Å/pix.
x 256 pix.
= 253.44 Å
0.99 Å/pix.
x 256 pix.
= 253.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.99 Å
Density
Contour LevelBy AUTHOR: 0.00821 / Movie #1: 0.00821
Minimum - Maximum-0.034316882 - 0.04214884
Average (Standard dev.)0.00017280868 (±0.0015828972)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 253.44 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.990.990.99
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z253.440253.440253.440
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0340.0420.000

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Supplemental data

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Sample components

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Entire IGF1R

EntireName: IGF1R / Number of components: 2

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Component #1: protein, IGF1R

ProteinName: IGF1R / Recombinant expression: No
MassTheoretical: 300 MDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, IGF1 receptor

ProteinName: IGF1 receptor / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 2 mg/mL / Buffer solution: PBS buffer with 0.05% (w/v) DDM / pH: 7
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 11 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 182734
3D reconstructionSoftware: RELION / Resolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body
Input PDB model: 5U8Q

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