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- PDB-1gp0: Human IGF2R domain 11 -

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Basic information

Entry
Database: PDB / ID: 1gp0
TitleHuman IGF2R domain 11
ComponentsCATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR
KeywordsRECEPTOR / INSULIN-LIKE GROWTH FACTOR / CATION INDEPENDENT MANNOSE 6-PHOSPHATE / TRANSPORT / BETA BARREL
Function / homology
Function and homology information


Retrograde transport at the Trans-Golgi-Network / retromer complex binding / clathrin coat / response to tetrachloromethane / insulin-like growth factor receptor activity / insulin-like growth factor binding / positive regulation by host of viral process / insulin-like growth factor II binding / trans-Golgi network transport vesicle / retinoic acid binding ...Retrograde transport at the Trans-Golgi-Network / retromer complex binding / clathrin coat / response to tetrachloromethane / insulin-like growth factor receptor activity / insulin-like growth factor binding / positive regulation by host of viral process / insulin-like growth factor II binding / trans-Golgi network transport vesicle / retinoic acid binding / lysosomal transport / Golgi Associated Vesicle Biogenesis / nuclear envelope lumen / mannose binding / endocytic vesicle / G-protein alpha-subunit binding / animal organ regeneration / response to retinoic acid / transport vesicle / receptor-mediated endocytosis / post-embryonic development / secretory granule membrane / trans-Golgi network membrane / liver development / phosphoprotein binding / clathrin-coated endocytic vesicle membrane / trans-Golgi network / 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 / Golgi apparatus / enzyme binding / cell surface / signal transduction / extracellular exosome / membrane / identical protein binding / plasma membrane
Similarity search - Function
Cation-independent mannose-6-phosphate receptor repeat / Cation-dependent Mannose-6-phosphate Receptor; Chain A / Mannose-6-phosphate receptor binding domain / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / MRH domain / MRH domain profile. / Mannose-6-phosphate receptor binding domain superfamily / Fibronectin type II domain / Fibronectin type II domain superfamily ...Cation-independent mannose-6-phosphate receptor repeat / Cation-dependent Mannose-6-phosphate Receptor; Chain A / Mannose-6-phosphate receptor binding domain / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / 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 / 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 / OTHER / Resolution: 1.4 Å
AuthorsBrown, J. / Esnouf, R.M. / Jones, M.A. / Linnell, J. / Harlos, K. / Hassan, A.B. / Jones, E.Y.
CitationJournal: Embo J. / Year: 2002
Title: Structure of a Functional Igf2R Fragment Determined from the Anomalous Scattering of Sulfur
Authors: Brown, J. / Esnouf, R.M. / Jones, M.A. / Linnell, J. / Harlos, K. / Hassan, A.B. / Jones, E.Y.
History
DepositionOct 29, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Apr 10, 2019Group: Data collection / Source and taxonomy
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / entity_src_gen / struct_biol
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6612
Polymers15,5651
Non-polymers961
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)49.405, 49.405, 118.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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 / 300 KDA MANNOSE 6- ...INSULIN-LIKE GROWTH FACTOR II RECEPTOR / CI MAN-6-P / RECEPTOR / CI-MPR / 300 KDA MANNOSE 6-PHOSPHATE RECEPTOR / MPR 300 / MPR300


Mass: 15564.672 Da / Num. of mol.: 1
Fragment: IGF-II-BINDING DOMAIN, REPEAT 11 RESIDUES 1508-1650
Source method: isolated from a genetically manipulated source
Details: RESIDUES VISIBLE IN THE ELECTRON DENSITY MAP CORRESPOND TO MATURE IGF2R RESIDUE NUMBERS 1515 -1647
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: PLACENTA / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): Origami / References: UniProt: P11717
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTRANSPORT OF PHOSPHORYLATED LYSOSOMAL ENZYMES FROM THE GOLGI COMPLEX AND THE CELL SURFACE TO ...TRANSPORT OF PHOSPHORYLATED LYSOSOMAL ENZYMES FROM THE GOLGI COMPLEX AND THE CELL SURFACE TO LYSOSOMES. LYSOSOMAL ENZYMES BEARING PHOSPHOMANNOSYL RESIDUES BIND SPECIFICALLY TO MANNOSE-6-PHOSPHATE RECEPTORS IN THE GOLGI APPARATUS AND THE RESULTING RECEPTOR-LIGAND COMPLEX IS TRANSPORTED TO AN ACIDIC PRELYOSOMAL COMPARTMENT WHERE THE LOW PH MEDIATES THE DISSOCIATION OF THE COMPLEX. THIS RECEPTOR ALSO BINDS INSULIN GROWTH FACTOR II.

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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: 2.18 Å3/Da / Density % sol: 42 %
Description: SULFUR PHASING DATA COLLECTED AT 1.77122 A ON ESRF BM14
Crystal growpH: 8.5
Details: PROTEIN WAS CRYSTALLIZED FROM 0.2 M LITHIUM SULFATE, 0.1 M TRIS HCL PH 8.5, 30 % PEG 4000
Crystal grow
*PLUS
pH: 3 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112 mg/mlprotein1drop
2100 mMTris-HCl1droppH3.0
3100 mM1dropNaCl
40.2 Mlithium sulfate1reservoir
50.1 MTris-HCl1reservoirpH8.5
630 %PEG40001reservoir

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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: Nov 15, 2000 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.4→20 Å / Num. obs: 29550 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 25.8 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 35.7
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 9.4 / % possible all: 95.6
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 761896
Reflection shell
*PLUS
% possible obs: 95.6 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: OTHER / Resolution: 1.4→19.62 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 764785.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1402 4.9 %RANDOM
Rwork0.209 ---
obs0.209 28735 96.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.7082 Å2 / ksol: 0.387586 e/Å3
Displacement parametersBiso mean: 22.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å20 Å20 Å2
2---1.36 Å20 Å2
3---2.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.02 Å0.04 Å
Refinement stepCycle: LAST / Resolution: 1.4→19.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1006 0 5 179 1190
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.21
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.731.5
X-RAY DIFFRACTIONc_mcangle_it3.62
X-RAY DIFFRACTIONc_scbond_it4.772
X-RAY DIFFRACTIONc_scangle_it5.912.5
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.261 230 5.2 %
Rwork0.227 4227 -
obs--91.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.49 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.662
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.21

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