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- PDB-6um2: Structure of M-6-P/IGFII Receptor and IGFII complex -

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Basic information

Entry
Database: PDB / ID: 6um2
TitleStructure of M-6-P/IGFII Receptor and IGFII complex
Components
  • Cation-independent mannose-6-phosphate receptor
  • Insulin-like growth factor II
KeywordsSUGAR BINDING PROTEIN / M-6-P / IGFII / receptor
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 / positive regulation of glycogen biosynthetic process / embryonic placenta development / SHC-related events triggered by IGF1R / positive regulation of insulin receptor signaling pathway / striated muscle cell differentiation / 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 / insulin-like growth factor receptor binding / 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 / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor ligand activity / endosome membrane / Golgi membrane / positive regulation of cell population proliferation / regulation of DNA-templated transcription / Golgi apparatus / cell surface / negative regulation of transcription by RNA polymerase II / 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 speciesHomo sapiens (human)
Bos taurus (cattle)
MethodELECTRON MICROSCOPY / single 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, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Assembly

Deposited unit
A: Cation-independent mannose-6-phosphate receptor
B: Insulin-like growth factor II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)283,9949
Polymers282,4462
Non-polymers1,5487
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Cation-independent mannose-6-phosphate receptor / M6PR / 300 kDa mannose 6-phosphate receptor / MPR 300 / Insulin-like growth factor 2 receptor / ...M6PR / 300 kDa mannose 6-phosphate receptor / MPR 300 / Insulin-like growth factor 2 receptor / Insulin-like growth factor II receptor / IGF-II receptor


Mass: 274830.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P08169
#2: Protein Insulin-like growth factor II / IGF-II / Somatomedin-A / T3M-11-derived growth factor


Mass: 7615.667 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGF2, PP1446 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P01344
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1IGFIIR and IGFII complexCOMPLEX#1-#20MULTIPLE SOURCES
2Cation-independent mannose-6-phosphate receptorCOMPLEX#11NATURAL
3Insulin-like growth factor IICOMPLEX#21RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Bos taurus (cattle)9913
23Homo sapiens (human)9606
Source (recombinant)Organism: Escherichia coli K-12 (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DARK FIELD
Image recordingElectron dose: 100 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0238 / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 4.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 75821 / Symmetry type: POINT
RefinementResolution: 4.32→302.72 Å / Cor.coef. Fo:Fc: 0.76 / SU B: 65.401 / SU ML: 0.813 / ESU R: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.47977 --
obs0.47977 720745 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.059 Å2
Baniso -1Baniso -2Baniso -3
1--1.31 Å22.35 Å2-1.07 Å2
2--0.09 Å2-0.65 Å2
3---1.21 Å2
Refinement stepCycle: 1 / Total: 13094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0040.01313447
ELECTRON MICROSCOPYr_bond_other_d0.0180.01711853
ELECTRON MICROSCOPYr_angle_refined_deg1.6021.65918306
ELECTRON MICROSCOPYr_angle_other_deg1.5751.58327633
ELECTRON MICROSCOPYr_dihedral_angle_1_deg10.79851681
ELECTRON MICROSCOPYr_dihedral_angle_2_deg30.55922.301678
ELECTRON MICROSCOPYr_dihedral_angle_3_deg16.908152113
ELECTRON MICROSCOPYr_dihedral_angle_4_deg15.8131581
ELECTRON MICROSCOPYr_chiral_restr0.0790.21758
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.0215169
ELECTRON MICROSCOPYr_gen_planes_other0.0020.022856
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it1.3772.0736739
ELECTRON MICROSCOPYr_mcbond_other1.3772.0746738
ELECTRON MICROSCOPYr_mcangle_it2.6273.1038415
ELECTRON MICROSCOPYr_mcangle_other2.6273.1038416
ELECTRON MICROSCOPYr_scbond_it0.5632.0636708
ELECTRON MICROSCOPYr_scbond_other0.5632.0636709
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other1.2993.0629892
ELECTRON MICROSCOPYr_long_range_B_refined4.13523.43114448
ELECTRON MICROSCOPYr_long_range_B_other4.13523.4314449
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 4.32→4.432 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.581 53437 -
obs--100 %

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