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- PDB-5iei: X-ray crystallographic structure of a high affinity IGF2 antagoni... -

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Basic information

Entry
Database: PDB / ID: 5iei
TitleX-ray crystallographic structure of a high affinity IGF2 antagonist (Domain11 AB5 RHH) based on human IGF2R domain 11
ComponentsCation-independent mannose-6-phosphate receptor
KeywordsTRANSPORT PROTEIN / IGF2 / IGF2R / domain 11
Function / homology
Function and homology information


clathrin coat / Retrograde transport at the Trans-Golgi-Network / response to tetrachloromethane / insulin-like growth factor receptor activity / retromer complex binding / insulin-like growth factor binding / insulin-like growth factor II binding / trans-Golgi network transport vesicle / host-mediated activation of viral process / retinoic acid binding ...clathrin coat / Retrograde transport at the Trans-Golgi-Network / response to tetrachloromethane / insulin-like growth factor receptor activity / retromer complex binding / insulin-like growth factor binding / insulin-like growth factor II binding / trans-Golgi network transport vesicle / host-mediated activation of viral process / retinoic acid binding / lysosomal transport / Golgi Associated Vesicle Biogenesis / nuclear envelope lumen / D-mannose binding / G-protein alpha-subunit binding / endocytic vesicle / animal organ regeneration / response to retinoic acid / transport vesicle / receptor-mediated endocytosis / secretory granule membrane / trans-Golgi network membrane / post-embryonic development / phosphoprotein binding / clathrin-coated endocytic vesicle membrane / trans-Golgi network / liver development / late endosome / Cargo recognition for clathrin-mediated endocytosis / signaling receptor activity / Clathrin-mediated endocytosis / spermatogenesis / early endosome / endosome membrane / endosome / positive regulation of apoptotic process / G protein-coupled receptor signaling pathway / Golgi membrane / focal adhesion / Neutrophil degranulation / perinuclear region of cytoplasm / enzyme binding / cell surface / Golgi apparatus / signal transduction / extracellular exosome / identical protein binding / membrane / plasma membrane
Similarity search - Function
Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / Cation-dependent Mannose-6-phosphate Receptor; Chain A / Mannose-6-phosphate receptor binding domain / Mannose-6-phosphate receptor binding domain superfamily / MRH domain / MRH domain profile. / Fibronectin type II domain / Fibronectin type II domain superfamily ...Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / Cation-dependent Mannose-6-phosphate Receptor; Chain A / Mannose-6-phosphate receptor binding domain / 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 / Kringle-like fold / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Cation-independent mannose-6-phosphate receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsNicholls, R.D. / Williams, C. / Strickland, M. / Frago, S. / Hassan, A.B. / Crump, M.P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC429/A9891 United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Functional evolution of IGF2:IGF2R domain 11 binding generates novel structural interactions and a specific IGF2 antagonist.
Authors: Frago, S. / Nicholls, R.D. / Strickland, M. / Hughes, J. / Williams, C. / Garner, L. / Surakhy, M. / Maclean, R. / Rezgui, D. / Prince, S.N. / Zaccheo, O.J. / Ebner, D. / Sanegre, S. / Yu, S. ...Authors: Frago, S. / Nicholls, R.D. / Strickland, M. / Hughes, J. / Williams, C. / Garner, L. / Surakhy, M. / Maclean, R. / Rezgui, D. / Prince, S.N. / Zaccheo, O.J. / Ebner, D. / Sanegre, S. / Yu, S. / Buffa, F.M. / Crump, M.P. / Hassan, A.B.
History
DepositionFeb 25, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Aug 30, 2017Group: Advisory / Author supporting evidence
Category: pdbx_audit_support / pdbx_unobs_or_zero_occ_residues
Item: _pdbx_audit_support.funding_organization
Revision 1.3Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_data_processing_status ...diffrn_source / pdbx_data_processing_status / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Jan 10, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9636
Polymers15,5551
Non-polymers4085
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-24 kcal/mol
Surface area7490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.120, 48.560, 62.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 / M6P/IGF2 receptor / M6P/IGF2R


Mass: 15554.753 Da / Num. of mol.: 1 / Fragment: UNP residues 1508-1649 / Mutation: Q1569R, P1597H, S1602H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGF2R, MPRI / Plasmid: pET26a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P11717
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
Has protein modificationY

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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: 2.06 Å3/Da / Density % sol: 40.43 %
Description: Elongated clear bars, normally crystalise from droplet edge inward.
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.0 M Ammonium Sulphate, 0.1M Bis-(2-hydroxyethyl)imino-tris(hydroxymethyl methane, pH 7.0.
PH range: 6.5-8.0
Temp details: Crystal growth at 277K and 298 led to precipitation or small needles. Optimal growth conditions were at 291K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jan 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→38.36 Å / Num. obs: 3414 / % possible obs: 99.8 % / Redundancy: 6.2 % / Biso Wilson estimate: 26.5 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.2 / Net I/σ(I): 6.4
Reflection shellResolution: 2.8→2.86 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.2 / Mean I/σ(I) obs: 1.35 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GP0

1gp0


Resolution: 2.8→38.36 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.885 / SU B: 13.074 / SU ML: 0.26 / Cross valid method: THROUGHOUT / ESU R Free: 0.417 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24908 351 10.3 %RANDOM
Rwork0.22198 ---
obs0.22479 3063 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.441 Å2
Baniso -1Baniso -2Baniso -3
1-3.52 Å20 Å2-0 Å2
2---2.92 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 2.8→38.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1018 0 24 0 1042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191047
X-RAY DIFFRACTIONr_bond_other_d0.0060.02964
X-RAY DIFFRACTIONr_angle_refined_deg1.7451.9431418
X-RAY DIFFRACTIONr_angle_other_deg1.02932222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5465130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.87222.88945
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.97715168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.755157
X-RAY DIFFRACTIONr_chiral_restr0.0880.2151
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211184
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02253
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2832.632526
X-RAY DIFFRACTIONr_mcbond_other1.2832.63525
X-RAY DIFFRACTIONr_mcangle_it2.2423.937654
X-RAY DIFFRACTIONr_mcangle_other2.2413.94655
X-RAY DIFFRACTIONr_scbond_it1.6012.827521
X-RAY DIFFRACTIONr_scbond_other1.6022.821519
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7164.166764
X-RAY DIFFRACTIONr_long_range_B_refined3.98620.8291104
X-RAY DIFFRACTIONr_long_range_B_other3.98820.8441105
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 25 -
Rwork0.282 220 -
obs--99.19 %

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