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- PDB-2v5p: COMPLEX STRUCTURE OF HUMAN IGF2R DOMAINS 11-13 BOUND TO IGF-II -

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Basic information

Entry
Database: PDB / ID: 2v5p
TitleCOMPLEX STRUCTURE OF HUMAN IGF2R DOMAINS 11-13 BOUND TO IGF-II
Components
  • CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR
  • INSULIN-LIKE GROWTH FACTOR II
KeywordsRECEPTOR/GLYCOPROTEIN / CATION INDEPENDENT MANNOSE 6-PHOSPHATE / MEMBRANE / RECEPTOR / LYSOSOME / TRANSPORT / BETA BARREL / PHOSPHORYLATION / FIBRONECTIN TYPE II / INSULIN-LIKE GROWTH FACTOR / RECEPTOR-GLYCOPROTEIN COMPLEX / POLYMORPHISM / GLYCOPROTEIN / TRANSMEMBRANE
Function / homology
Function and homology information


embryonic placenta morphogenesis / positive regulation of skeletal muscle tissue growth / clathrin coat / Retrograde transport at the Trans-Golgi-Network / negative regulation of muscle cell differentiation / response to tetrachloromethane / insulin-like growth factor receptor activity / retromer complex binding / insulin-like growth factor binding / regulation of muscle cell differentiation ...embryonic placenta morphogenesis / positive regulation of skeletal muscle tissue growth / clathrin coat / Retrograde transport at the Trans-Golgi-Network / negative regulation of muscle cell differentiation / response to tetrachloromethane / insulin-like growth factor receptor activity / retromer complex binding / insulin-like growth factor binding / regulation of muscle cell differentiation / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / IRS-related events triggered by IGF1R / positive regulation of organ growth / insulin-like growth factor II binding / trans-Golgi network transport vesicle / genomic imprinting / transmembrane receptor protein tyrosine kinase activator activity / host-mediated activation of viral process / retinoic acid binding / positive regulation of multicellular organism growth / exocrine pancreas development / positive regulation of vascular endothelial cell proliferation / lysosomal transport / Golgi Associated Vesicle Biogenesis / nuclear envelope lumen / D-mannose binding / positive regulation of activated T cell proliferation / positive regulation of cell division / endocytic vesicle / G-protein alpha-subunit binding / animal organ regeneration / positive regulation of insulin receptor signaling pathway / positive regulation of glycogen biosynthetic process / response to retinoic acid / embryonic placenta development / SHC-related events triggered by IGF1R / transport vesicle / insulin-like growth factor receptor binding / striated muscle cell differentiation / positive regulation of mitotic nuclear division / insulin-like growth factor receptor signaling pathway / receptor-mediated endocytosis / platelet alpha granule lumen / secretory granule membrane / animal organ morphogenesis / protein serine/threonine kinase activator activity / trans-Golgi network membrane / post-embryonic development / insulin receptor binding / growth factor activity / phosphoprotein binding / trans-Golgi network / clathrin-coated endocytic vesicle membrane / liver development / hormone activity / integrin binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / glucose metabolic process / osteoblast differentiation / insulin receptor signaling pathway / late endosome / Platelet degranulation / Cargo recognition for clathrin-mediated endocytosis / signaling receptor activity / Clathrin-mediated endocytosis / spermatogenesis / in utero embryonic development / early endosome / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endosome / endosome membrane / positive regulation of MAPK cascade / positive regulation of apoptotic process / G protein-coupled receptor signaling pathway / receptor ligand activity / Golgi membrane / focal adhesion / positive regulation of cell population proliferation / Neutrophil degranulation / regulation of DNA-templated transcription / perinuclear region of cytoplasm / enzyme binding / cell surface / negative regulation of transcription by RNA polymerase II / Golgi apparatus / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1 Å
AuthorsBrown, J. / Delaine, C. / Zaccheo, O.J. / Siebold, C. / Gilbert, R.J. / van Boxel, G. / Denley, A. / Wallace, J.C. / Hassan, A.B. / Forbes, B.E. / Jones, E.Y.
CitationJournal: Embo J. / Year: 2008
Title: Structure and Functional Analysis of the Igf-II/Igf2R Interaction
Authors: Brown, J. / Delaine, C. / Zaccheo, O.J. / Siebold, C. / Gilbert, R.J. / Van Boxel, G. / Denley, A. / Wallace, J.C. / Hassan, A.B. / Forbes, B.E. / Jones, E.Y.
History
DepositionJul 6, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name ..._entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR
B: CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR
C: INSULIN-LIKE GROWTH FACTOR II
D: INSULIN-LIKE GROWTH FACTOR II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,49010
Polymers123,7974
Non-polymers1,6936
Water00
1
A: CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR
D: INSULIN-LIKE GROWTH FACTOR II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9285
Polymers61,8992
Non-polymers1,0293
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-16.7 kcal/mol
Surface area31860 Å2
MethodPQS
2
B: CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR
C: INSULIN-LIKE GROWTH FACTOR II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5625
Polymers61,8992
Non-polymers6643
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-15.7 kcal/mol
Surface area31950 Å2
MethodPQS
Unit cell
Length a, b, c (Å)165.979, 117.312, 116.668
Angle α, β, γ (deg.)90.00, 123.41, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.95658, 0.03012, 0.28992), (-0.041, 0.99866, 0.03152), (-0.28858, 0.04204, 0.95653)-12.637, -51.03441, 16.99037
2given(0.94785, 0.06043, 0.31293), (-0.04775, 0.9977, -0.04804), (-0.31512, 0.03059, 0.94856)-12.73361, -48.40027, 18.56183

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Components

#1: Protein CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR / INSULIN-LIKE GROWTH FACTOR II RECEPTOR / CI MAN-6-P RECEPTOR / CI-MPR / M6PR / INSULIN-LIKE GROWTH ...INSULIN-LIKE GROWTH FACTOR II RECEPTOR / CI MAN-6-P RECEPTOR / CI-MPR / M6PR / INSULIN-LIKE GROWTH FACTOR 2 RECEPTOR / IGF-II RECEPTOR / M6P/IGF2 RECEPTOR / M6P/IGF2R / 300 KDA MANNOSE 6-PHOSPHATE RECEPTOR / MPR 300 / MPR300 / CD222 ANTIGEN


Mass: 54414.172 Da / Num. of mol.: 2 / Fragment: DOMAINS 11-13, RESIDUES 1508-1992
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: PLACENTA / Plasmid: PEE14 / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / Variant (production host): LECR 3.2.8.1 / References: UniProt: P11717
#2: Protein INSULIN-LIKE GROWTH FACTOR II / IGF-II / SOMATOMEDIN A


Mass: 7484.472 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEM-TEASY / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P01344
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
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 protein modificationY
Sequence detailsTHE CONFLICT INDICATED IN THE SEQADV RECORDS BELOW HAS BEEN DESCRIBED IN UNIPROT ENTRY P11717 UNDER ...THE CONFLICT INDICATED IN THE SEQADV RECORDS BELOW HAS BEEN DESCRIBED IN UNIPROT ENTRY P11717 UNDER REFERENCE WITH PUBMEDID: 2957598.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.8 Å3/Da / Density % sol: 68 %
Crystal growpH: 9 / Details: 0.1 M TRIS-HCL PH 9.0, 15% (V/V) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 13, 2003 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 4.1→20 Å / Num. obs: 14662 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.29 / Net I/σ(I): 5.4
Reflection shellResolution: 4.1→4.2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V5O

2v5o


Resolution: 4.1→47.51 Å / Cor.coef. Fo:Fc: 0.791 / Cor.coef. Fo:Fc free: 0.746 / SU B: 175.868 / SU ML: 1.024 / Cross valid method: THROUGHOUT / ESU R Free: 1.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.327 741 5.1 %RANDOM
Rwork0.291 ---
obs0.293 13919 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 90.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20.09 Å2
2---0.44 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 4.1→47.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7880 0 109 0 7989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0228215
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9061.98111186
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.58651018
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2523.678348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.843151278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5371552
X-RAY DIFFRACTIONr_chiral_restr0.060.21240
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.026300
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1740.23047
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.25424
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1050.2182
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 4.1→4.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 43 -
Rwork0.347 1030 -
obs--100 %

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