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- EMDB-20816: Structure of M-6-P/IGFII Receptor and IGFII complex -

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Basic information

Entry
Database: EMDB / ID: EMD-20816
TitleStructure of M-6-P/IGFII Receptor and IGFII complex
Map data
Sample
  • Complex: IGFIIR and IGFII complex
    • Complex: Cation-independent mannose-6-phosphate receptor
      • Protein or peptide: Cation-independent mannose-6-phosphate receptor
    • Complex: Insulin-like growth factor II
      • Protein or peptide: Insulin-like growth factor II
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsM-6-P / IGFII / receptor / SUGAR BINDING PROTEIN
Function / homology
Function and homology information


kringle domain binding / negative regulation of muscle cell differentiation / positive regulation of skeletal muscle tissue growth / embryonic placenta morphogenesis / regulation of muscle cell differentiation / insulin-like growth factor binding / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / IRS-related events triggered by IGF1R / genomic imprinting / positive regulation of organ growth ...kringle domain binding / negative regulation of muscle cell differentiation / positive regulation of skeletal muscle tissue growth / embryonic placenta morphogenesis / regulation of muscle cell differentiation / insulin-like growth factor binding / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / IRS-related events triggered by IGF1R / genomic imprinting / positive regulation of organ growth / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of multicellular organism growth / exocrine pancreas development / positive regulation of vascular endothelial cell proliferation / lysosomal transport / positive regulation of activated T cell proliferation / D-mannose binding / positive regulation of cell division / endocytic vesicle / positive regulation of glycogen biosynthetic process / embryonic placenta development / SHC-related events triggered by IGF1R / positive regulation of insulin receptor signaling pathway / insulin-like growth factor receptor binding / striated muscle cell differentiation / positive regulation of mitotic nuclear division / insulin-like growth factor receptor signaling pathway / protein serine/threonine kinase activator activity / platelet alpha granule lumen / animal organ morphogenesis / phosphoprotein binding / insulin receptor binding / growth factor activity / trans-Golgi network / hormone activity / glucose metabolic process / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / osteoblast differentiation / integrin binding / late endosome / insulin receptor signaling pathway / Platelet degranulation / signaling receptor activity / in utero embryonic development / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / endosome membrane / receptor ligand activity / Golgi membrane / positive regulation of cell population proliferation / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / cell surface / Golgi apparatus / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Insulin-like growth factor II E-peptide, C-terminal / Insulin-like growth factor II / Insulin-like growth factor II E-peptide / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / Insulin-like growth factor / Mannose-6-phosphate receptor binding domain superfamily / MRH domain / MRH domain profile. ...Insulin-like growth factor II E-peptide, C-terminal / Insulin-like growth factor II / Insulin-like growth factor II E-peptide / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / Insulin-like growth factor / Mannose-6-phosphate receptor binding domain superfamily / MRH domain / MRH domain profile. / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily / Kringle-like fold
Similarity search - Domain/homology
Insulin-like growth factor 2 / Cation-independent mannose-6-phosphate receptor
Similarity search - Component
Biological speciesBos taurus (domestic cattle) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.32 Å
AuthorsWang R / Qi X
CitationJournal: Sci Adv / Year: 2020
Title: Marked structural rearrangement of mannose 6-phosphate/IGF2 receptor at different pH environments.
Authors: Rong Wang / Xiaofeng Qi / Philip Schmiege / Elias Coutavas / Xiaochun Li /
Abstract: Many cell surface receptors internalize their ligands and deliver them to endosomes, where the acidic pH causes the ligand to dissociate. The liberated receptor returns to the cell surface in a ...Many cell surface receptors internalize their ligands and deliver them to endosomes, where the acidic pH causes the ligand to dissociate. The liberated receptor returns to the cell surface in a process called receptor cycling. The structural basis for pH-dependent ligand dissociation is not well understood. In some receptors, the ligand binding domain is composed of multiple repeated sequences. The insulin-like growth factor 2 receptor (IGF2R) contains 15 β strand-rich repeat domains. The overall structure and the mechanism by which IGF2R binds IGF2 and releases it are unknown. We used cryo-EM to determine the structures of the IGF2R at pH 7.4 with IGF2 bound and at pH 4.5 in the ligand-dissociated state. The results reveal different arrangements of the receptor in different pH environments mediated by changes in the interactions between the repeated sequences. These results have implications for our understanding of ligand release from receptors in endocytic compartments.
History
DepositionOct 8, 2019-
Header (metadata) releaseOct 30, 2019-
Map releaseFeb 26, 2020-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.005
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.005
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6um2
  • Surface level: 0.005
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6um2
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20816.png

Downloads & links

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Map

FileDownload / File: emd_20816.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 352 pix.
= 302.72 Å		0.86 Å/pix.
x 352 pix.
= 302.72 Å		0.86 Å/pix.
x 352 pix.
= 302.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005 / Movie #1: 0.005
Minimum - Maximum-0.036312383 - 0.059457347
Average (Standard dev.)0.00000037486967 (±0.0014637609)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 302.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.860.860.86
M x/y/z352352352
origin x/y/z0.0000.0000.000
length x/y/z302.720302.720302.720
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS352352352
D min/max/mean-0.0360.0590.000

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Supplemental data

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Sample components

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Entire : IGFIIR and IGFII complex

EntireName: IGFIIR and IGFII complex
Components
  • Complex: IGFIIR and IGFII complex
    • Complex: Cation-independent mannose-6-phosphate receptor
      • Protein or peptide: Cation-independent mannose-6-phosphate receptor
    • Complex: Insulin-like growth factor II
      • Protein or peptide: Insulin-like growth factor II
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: IGFIIR and IGFII complex

SupramoleculeName: IGFIIR and IGFII complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: Cation-independent mannose-6-phosphate receptor

SupramoleculeName: Cation-independent mannose-6-phosphate receptor / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Bos taurus (domestic cattle)

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Supramolecule #3: Insulin-like growth factor II

SupramoleculeName: Insulin-like growth factor II / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cation-independent mannose-6-phosphate receptor

MacromoleculeName: Cation-independent mannose-6-phosphate receptor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 274.830125 KDa
SequenceString: MEAAAGRSSH LGPAPAGRPP RCPLLLQLQL LLLLLLLPPG WVPGAAGTQG AEFPELCSYT WEAVDTKNNM LYKINICGNM GVAQCGPSS AVCMHDLKTD SFHSVGDSLL KTASRSLLEF NTTVNCKQQN HKIQSSITFL CGKTLGTPEF VTATDCVHYF E WRTTAACK ...String:
MEAAAGRSSH LGPAPAGRPP RCPLLLQLQL LLLLLLLPPG WVPGAAGTQG AEFPELCSYT WEAVDTKNNM LYKINICGNM GVAQCGPSS AVCMHDLKTD SFHSVGDSLL KTASRSLLEF NTTVNCKQQN HKIQSSITFL CGKTLGTPEF VTATDCVHYF E WRTTAACK KNIFKANKEV PCYAFDRELK KHDLNPLIKT SGAYLVDDSD PDTSLFINVC RDIEVLRASS PQVRVCPTGA AA CLVRGDR AFDVGRPQEG LKLVSNDRLV LSYVKEGAGQ PDFCDGHSPA VTITFVCPSE RREGTIPKLT AKSNCRFEIE WVT EYACHR DYLESRSCSL SSAQHDVAVD LQPLSRVEAS DSLFYTSEAD EYTYYLSICG GSQAPICNKK DAAVCQVKKA DSTQ VKVAG RPQNLTLRYS DGDLTLIYFG GEECSSGFQR MSVINFECNQ TAGNNGRGAP VFTGEVDCTY FFTWDTKYAC VHEKE ALLC GVSDGKQRFD LSALARHSEL EQNWEAVDGS QREAEKKHFF INICHRVLQT GQARGCPEDA AVCAVDKNGS KNLGRF ISS PTREKGNIQL SYSDGDECGG GQKIITNITL MCKPGDLESA PVLTTSRADG CFYEFEWRTA AACVLSRTEG DNCTVFD SQ AGFSFDLTPL TKKDAYKVET DKYEFHINVC GPVSVGACPP DSGACQVSRS DRKSWNLGRS NAKLSYYDGM IQLTYRDG T PYNNEKRTPR ATLITFLCDR DAGVGFPEYQ EEDNSTYNFR WYTSYACPEE PLECIVTDPV TLDQYDLSRL AKSEGGPGG NWYSLDNGGA RSTWRKYYIN VCRPLNPVPG CDRYASACQM KYQGEQGSYS ETVSISNLGV AKTGPMVEDS GSLLLEYVNG SACTTSDQR RTTYTTRIHL VCSTGSLYTH PIFSLNWECV VSFLWNTAAA CPIRITTDID QVCSIKDPNS GYVFDLNPLN N SRGYVVLG IGKTFLFNVC GDMPACGTLD GKPASGCEAE VQMDDMKTLK PGRLVGLEKS LQLSTEGFIT LNYTGLPSHP NG RADAFII RFVCNDDVYP GTPKFLHQDI DSSLGIRDTF FEFETALACV PSPVDCQVTD PAGNEYDLSG LSKARKPWTA VDT FDEGKK RTFYLSVCTP LPYIPGCHGT AVGCCLVTED SKLNLGVVQI SPQVGANGSL SLVYVNGDKC KNQRFSTRIN LECA HTTGS PTFQLQNDCE YVFLWRTVEA CPVVRAEGDY CEVRDPRHGN LYNLIPLGLN DTVVRAGEYT YYFRVCGELT SGVCP TSDK SKVISSCQEK RGPQGFQKVA GLFNQKLTYE NGVLKMNYTG GDTCHKVYQR STTIFFYCDR STQAPVFLQE TSDCSY LFE WRTQYACPPY DLTECSFKNE AGETYDLSSL SRYSDNWEAV TGTGSTEHYL INVCKSLSPQ AGSDPCPPEA AVCLLGG PK PVNLGRVRDS PQWSQGLTLL KYVDGDLCPD QIRKKSTTIR FTCSESHVNS RPMFISAVED CEYTFSWPTA AACAVKSN V HDDCQVTNPA TGHLFDLSSL SGRAGFTAAY SEKGLVYLSV CGDNENCANG VGACFGQTRI SVGKASKRLT YVDQVLQLV YEGGSPCPSK TGLSYKSVIS FVCRPEVGPT NRPMLISLDK RTCTLFFSWH TPLACEQTTE CSVRNGSSLI DLSPLIHRTG GYEAYDESE DDGSDTSPDF YINICQPLNP MHGLACPAGT AVCKVPVDGP PIDIGRVAGP PILNPIANEV YLNFESSTPC L ADRHFNYT SLITFHCKRG VSMGTPKLLR TSVCDFVFEW ETPLVCPDEV KTDGCSLTDE QLYYSFNLSS LSKSTFKVTR GP HTYSVGV CTAAAGLDEG GCKDGAVCLL SGSKGASFGR LASMKLDYRH QDEAVILSYA NGDTCPPETE DGEPCVFPFV FNG KSYEEC VVESRARLWC ATTANYDRDH EWGFCKHSTS HRTSVIIFKC DEDADVGRPQ VFSEVRGCEV TFEWKTKVVC PPKK MECKF VQKHRTYDLR LLSSLTGSWS FVHNGASYYI NLCQKIYKGP QDCSERASVC KKSTSGEVQV LGLVHTQKLD VVDDR VIVT YSKGHYCGDN KTASAVIELT CAKTVGRPSF TRFDVDSCTY HFSWDSRAAC AVKPQEVQMV NGTITNPANG RSFSLG DIY FKRFSASGDV RTNGDRYIYE IQLSSITGSS SPACSGASIC QRKANDQHFS RKVGTSNQTR YYVQDGDLDV VFTSSSK CG KDKTKSVSST IFFHCDPLVK DGIPEFSHET ADCQYLFSWH TSAVCPLGAG FDEEIAGDDA QEHKGLSERS QAVGAVLS L LLVALTACLL TLLLYKKERR EMVMSRLTNC CRRSANVSYK YSKVNKEEEA DENETEWLME EIQPPAPRPG KEGQENGHV AAKSVRAADT LSALHGDEQD SEDEVLTLPE VKVRPPGRAP GAEGGPPLRP LPRKAPPPLR ADDRVGLVRG EPARRGRPRA AATPISTFH DDSDEDLLHV

UniProtKB: Cation-independent mannose-6-phosphate receptor

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Macromolecule #2: Insulin-like growth factor II

MacromoleculeName: Insulin-like growth factor II / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.615667 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MAYRPSETLC GGELVDTLQF VCGDRGFYFS RPASRVSRRS RGIVEECCFR SCDLALLETY CATPAKSE

UniProtKB: Insulin-like growth factor 2

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 7 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 100.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.32 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 75821
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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