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- PDB-1gp3: Human IGF2R domain 11 -

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Basic information

Entry
Database: PDB / ID: 1gp3
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


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 / endocytic vesicle / G-protein alpha-subunit binding / animal organ regeneration / response to retinoic acid / transport vesicle / receptor-mediated endocytosis / secretory granule membrane / trans-Golgi network membrane / post-embryonic development / phosphoprotein binding / trans-Golgi network / clathrin-coated endocytic vesicle membrane / liver development / late endosome / Cargo recognition for clathrin-mediated endocytosis / signaling receptor activity / Clathrin-mediated endocytosis / spermatogenesis / early endosome / endosome / endosome membrane / 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: 1.95 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 1.3Apr 10, 2019Group: Data collection / Other / Source and taxonomy
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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


Theoretical massNumber of molelcules
Total (without water)15,5651
Polymers15,5651
Non-polymers00
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)31.373, 49.843, 83.030
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 / 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, WITH THE EXCEPTION OF RESIDUES 1618 - 1621 WHERE THE DENSITY IS NOT CONTINUOUS
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: PLACENTA / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): Origami / References: UniProt: P11717
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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.
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: 1.95 Å3/Da / Density % sol: 36 %
Crystal growpH: 8.5
Details: PROTEIN WAS CRYSTALLIZED FROM 0.2 M SODIUM ACETATE, 0.1 M TRIS HCL PH 8.5, 30 % W/V 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 Msodium acetate1reservoir
50.1 MTris-HCl1reservoirpH8.5
630 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 15, 2000 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 9752 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 21.9
Reflection shellResolution: 1.95→2.02 Å / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 2.4 / % possible all: 92.9
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 75027 / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
% possible obs: 92.9 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GP0

1gp0


Resolution: 1.95→29.35 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 397551.98 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.255 492 5.2 %RANDOM
Rwork0.206 ---
obs0.206 9427 94.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.4069 Å2 / ksol: 0.363344 e/Å3
Displacement parametersBiso mean: 35.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.75 Å20 Å20 Å2
2---2.17 Å20 Å2
3---3.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.95→29.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms983 0 0 78 1061
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.631.5
X-RAY DIFFRACTIONc_mcangle_it2.72
X-RAY DIFFRACTIONc_scbond_it2.582
X-RAY DIFFRACTIONc_scangle_it3.92.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.303 68 4.9 %
Rwork0.232 1313 -
obs--84.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 35.31 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.33
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.72

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