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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 datapostprocess resolution at 7.68A by Relion3.
Sample
  • Complex: IGF1R
    • Protein or peptide: 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
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  • 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

emd_0741.png

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)
Annotationpostprocess resolution at 7.68A by Relion3.
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

Histogram

Histogram (log scale)
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
Components
  • Complex: IGF1R
    • Protein or peptide: IGF1 receptor

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Supramolecule #1: IGF1R

SupramoleculeName: IGF1R / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
Molecular weightTheoretical: 300 kDa/nm

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Macromolecule #1: IGF1 receptor

MacromoleculeName: IGF1 receptor / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKSGSGGGSP TSLWGLLFLS AALSLWPTSG EICGPGIDIR NDYQQLKRLE NCTVIEGYLH ILLISKAEDY RSYRFPKLT VITEYLLLFR VAGLESLGDL FPNLTVIRGW KLFYNYALVI FEMTNLKDIG LYNLRNITRG A IRIEKNAD LCYLSTVDWS LILDAVSNNY ...String:
MKSGSGGGSP TSLWGLLFLS AALSLWPTSG EICGPGIDIR NDYQQLKRLE NCTVIEGYLH ILLISKAEDY RSYRFPKLT VITEYLLLFR VAGLESLGDL FPNLTVIRGW KLFYNYALVI FEMTNLKDIG LYNLRNITRG A IRIEKNAD LCYLSTVDWS LILDAVSNNY IVGNKPPKEC GDLCPGTMEE KPMCEKTTIN NEYNYRCWTT NR CQKMCPS TCGKRACTEN NECCHPECLG SCSAPDNDTA CVACRHYYYA GVCVPACPPN TYRFEGWRCV DRD FCANIL SAESSDSEGF VIHDGECMQE CPSGFIRNGS QSMYCIPCEG PCPKVCEEEK KTKTIDSVTS AQML QGCTI FKGNLLINIR RGNNIASELE NFMGLIEVVT GYVKIRHSHA LVSLSFLKNL RLILGEEQLE GNYSF YVLD NQNLQQLWDW DHRNLTIKAG KMYFAFNPKL CVSEIYRMEE VTGTKGRQSK GDINTRNNGE RASCES DVL HFTSTTTSKN RIIITWHRYR PPDYRDLISF TVYYKEAPFK NVTEYDGQDA CGSNSWNMVD VDLPPNK DV EPGILLHGLK PWTQYAVYVK AVTLTMVEND HIRGAKSEIL YIRTNASVPS IPLDVLSASN SSSQLIVK W NPPSLPNGNL SYYIVRWQRQ PQDGYLYRHN YCSKDKIPIR KYADGTIDIE EVTENPKTEV CGGEKGPCC ACPKTEAEKQ AEKEEAEYRK VFENFLHNSI FVPRPERKRR DVMQVANTTM SSRSRNTTAA DTYNITDPEE LETEYPFFE SRVDNKERTV ISNLRPFTLY RIDIHSCNHE AEKLGCSASN FVFARTMPAE GADDIPGPVT W EPRPENSI FLKWPEPENP NGLILMYEIK YGSQVEDQRE CVSRQEYRKY GGAKLNRLNP GNYTARIQAT SL SGNGSWT DPVFFYVQAK TGYENFIHLI IALPVAVLLI VGGLVIMLYV FHRKRNNSRL GNGVLYASVN PEY FSAADV YVPDEWEVAR EKITMSRELG QGSFGMVYEG VAKGVVKDEP ETRVAIKTVN EAASMRERIE FLNE ASVMK EFNCHHVVRL LGVVSQGQPT LVIMELMTRG DLKSYLRSLR PEMENNPVLA PPSLSKMIQM AGEIA DGMA YLNANKFVHR DLAARNCMVA EDFTVKIGDF GMTRDIYETD YYRKGGKGLL PVRWMSPESL KDGVFT TYS DVWSFGVVLW EIATLAEQPY QGLSNEQVLR FVMEGGLLDK PDNCPDMLFE LMRMCWQYNP KMRPSFL EI ISSIKEEMEP GFREVSFYYS EENKLPEPEE LDLEPENMES VPLDPSASSS SLPLPDRHSG HKAENGPG P GVLVLRASFD ERQPYAHMNG GRKNERALPL PQSSTC

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 7 / Details: PBS buffer with 0.05% (w/v) DDM
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 50.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 11 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.05) / Number images used: 182734
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5u8q

RefinementProtocol: RIGID BODY FIT

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