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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 IIInsulin-like growth factor 2
      • Protein or peptide: Insulin-like growth factor IIInsulin-like growth factor 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


kringle domain binding / spongiotrophoblast cell proliferation / positive regulation of skeletal muscle tissue growth / negative regulation of muscle cell differentiation / embryonic placenta morphogenesis / regulation of muscle cell differentiation / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / IRS-related events triggered by IGF1R / insulin-like growth factor binding / genomic imprinting ...kringle domain binding / spongiotrophoblast cell proliferation / positive regulation of skeletal muscle tissue growth / negative regulation of muscle cell differentiation / embryonic placenta morphogenesis / regulation of muscle cell differentiation / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / IRS-related events triggered by IGF1R / insulin-like growth factor binding / genomic imprinting / positive regulation of organ growth / exocrine pancreas development / positive regulation of multicellular organism growth / lysosomal transport / positive regulation of vascular endothelial cell proliferation / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of activated T cell proliferation / D-mannose binding / positive regulation of cell division / endocytic vesicle / embryonic placenta development / positive regulation of glycogen biosynthetic process / SHC-related events triggered by IGF1R / positive regulation of insulin receptor signaling pathway / striated muscle cell differentiation / insulin-like growth factor receptor binding / protein serine/threonine kinase activator activity / positive regulation of mitotic nuclear division / insulin-like growth factor receptor signaling pathway / platelet alpha granule lumen / phosphoprotein binding / animal organ morphogenesis / growth factor activity / insulin receptor binding / trans-Golgi network / hormone activity / osteoblast differentiation / glucose metabolic process / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of peptidyl-tyrosine phosphorylation / integrin binding / late endosome / Platelet degranulation / insulin receptor signaling pathway / signaling receptor activity / in utero embryonic development / positive regulation of MAPK cascade / receptor ligand activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endosome membrane / Golgi membrane / positive regulation of cell population proliferation / regulation of DNA-templated transcription / Golgi apparatus / negative regulation of transcription by RNA polymerase II / cell surface / 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 / MRH domain / MRH domain profile. / Mannose-6-phosphate receptor binding domain superfamily ...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 / MRH domain / MRH domain profile. / Mannose-6-phosphate receptor binding domain superfamily / 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/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin-like superfamily / Kringle-like fold
Similarity search - Domain/homology
Insulin-like growth factor II / Cation-independent mannose-6-phosphate receptor
Similarity search - Component
Biological speciesBos taurus (cattle) / Homo sapiens (human) / Bovine (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.32 Å
AuthorsWang R / Qi X / Li 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-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing 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)
Voxel sizeX=Y=Z: 0.86 Å
Density
Contour LevelBy AUTHOR: 0.005 / Movie #1: 0.005
Minimum - Maximum-0.036312383 - 0.059457347
Average (Standard dev.)0.00000037487 (±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 IIInsulin-like growth factor 2
      • Protein or peptide: Insulin-like growth factor IIInsulin-like growth factor 2
  • 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 (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)
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)

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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: Bovine (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

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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

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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 / N-Acetylglucosamine

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

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Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.32 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 75821

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