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2v5o

STRUCTURE OF HUMAN IGF2R DOMAINS 11-14

Method: X-RAY DIFFRACTION Dmax: 120.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR

Homo sapiens

UniProt P11717

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1508–2128 Fragment：DOMAINS 11-14, RESIDUES 1508-2128 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CL CHLORIDE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.4；0.1 M MES PH6.4, 2.5% (W/V) PEG 3000 Resolution 2.91 Å R-free 0.304

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 2V5O Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1E6F Human MIR-receptor, repeat 11 Deposited 2000-08-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1508–1650（143 aa） Fragment：IGF-II-BINDING DOMAIN, REPEAT 11, RESIDUES 1508-1650
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；PRECIPITANT: 0.2 M AMMONIUM ACETATE, 0.1 M CACODYLATE PH 5 28% PEG 4000. PROTEIN SOLUTION: 8 MG/ML IN 10 MM TRIS-HCL PH7.5, 150 MM N VAPOUR DIFFUSION, HANGING DROPS,1:1 RATIO.
Resolution 1.75 Å R-free 0.273
1E6F Human MIR-receptor, repeat 11 Deposited 2000-08-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1508–1650（143 aa） Fragment：IGF-II-BINDING DOMAIN, REPEAT 11, RESIDUES 1508-1650
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；PRECIPITANT: 0.2 M AMMONIUM ACETATE, 0.1 M CACODYLATE PH 5 28% PEG 4000. PROTEIN SOLUTION: 8 MG/ML IN 10 MM TRIS-HCL PH7.5, 150 MM N VAPOUR DIFFUSION, HANGING DROPS,1:1 RATIO.
Resolution 1.75 Å R-free 0.273
1GP0 Human IGF2R domain 11 Deposited 2001-10-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1508–1650（143 aa） Fragment：IGF-II-BINDING DOMAIN, REPEAT 11 RESIDUES 1508-1650
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；PROTEIN WAS CRYSTALLIZED FROM 0.2 M LITHIUM SULFATE, 0.1 M TRIS HCL PH 8.5, 30 % PEG 4000
Resolution 1.40 Å R-free 0.237
1GP3 Human IGF2R domain 11 Deposited 2001-10-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1508–1650（143 aa） Fragment：IGF-II BINDING DOMAIN REPEAT 11 RESIDUES 1508-1650
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；PROTEIN WAS CRYSTALLIZED FROM 0.2 M SODIUM ACETATE, 0.1 M TRIS HCL PH 8.5, 30 % W/V PEG 4000
Resolution 1.95 Å R-free 0.255
1GQB HUMAN MIR-RECEPTOR, REPEAT 11 Deposited 2001-11-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1508–1650（143 aa） Fragment：IGF-II-BINDING DOMAIN, REPEAT 11, RESIDUES 1508-1650
Not recorded BR BROMIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；PRECIPITANT: 0.2 M AMMONIUM ACETATE, 0.1 M CACODYLATE PH 5, 28% PEG 4000. PROTEIN SOLUTION: 8 MG/ML IN 10 MM TRIS-HCL PH7.5, 150 MM VAPOUR DIFFUSION, HANGING DROPS,1:1 RATIO.
Resolution 1.80 Å R-free 0.253
1GQB HUMAN MIR-RECEPTOR, REPEAT 11 Deposited 2001-11-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1508–1650（143 aa） Fragment：IGF-II-BINDING DOMAIN, REPEAT 11, RESIDUES 1508-1650
Not recorded BR BROMIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；PRECIPITANT: 0.2 M AMMONIUM ACETATE, 0.1 M CACODYLATE PH 5, 28% PEG 4000. PROTEIN SOLUTION: 8 MG/ML IN 10 MM TRIS-HCL PH7.5, 150 MM VAPOUR DIFFUSION, HANGING DROPS,1:1 RATIO.
Resolution 1.80 Å R-free 0.253
1JPL GGA3 VHS domain complexed with C-terminal peptide from cation-independent mannose 6-phosphate receptor Deposited 2001-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 2480–2491（12 aa） Fragment：C-terminal peptide
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.6；293 K；1.5M Sodium/Potassium Phosphate, 200mM Lithium Sulfate, pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.40 Å R-free 0.257
1JPL GGA3 VHS domain complexed with C-terminal peptide from cation-independent mannose 6-phosphate receptor Deposited 2001-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 10 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 2480–2491（12 aa） Fragment：C-terminal peptide
Chain F 2480–2491（12 aa） Fragment：C-terminal peptide
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.6；293 K；1.5M Sodium/Potassium Phosphate, 200mM Lithium Sulfate, pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.40 Å R-free 0.257
1JPL GGA3 VHS domain complexed with C-terminal peptide from cation-independent mannose 6-phosphate receptor Deposited 2001-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 2480–2491（12 aa） Fragment：C-terminal peptide
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.6；293 K；1.5M Sodium/Potassium Phosphate, 200mM Lithium Sulfate, pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.40 Å R-free 0.257
1JPL GGA3 VHS domain complexed with C-terminal peptide from cation-independent mannose 6-phosphate receptor Deposited 2001-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 2480–2491（12 aa） Fragment：C-terminal peptide
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.6；293 K；1.5M Sodium/Potassium Phosphate, 200mM Lithium Sulfate, pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.40 Å R-free 0.257
1JPL GGA3 VHS domain complexed with C-terminal peptide from cation-independent mannose 6-phosphate receptor Deposited 2001-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 2480–2491（12 aa） Fragment：C-terminal peptide
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.6；293 K；1.5M Sodium/Potassium Phosphate, 200mM Lithium Sulfate, pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.40 Å R-free 0.257
1JPL GGA3 VHS domain complexed with C-terminal peptide from cation-independent mannose 6-phosphate receptor Deposited 2001-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain E 2480–2491（12 aa） Fragment：C-terminal peptide
Chain F 2480–2491（12 aa） Fragment：C-terminal peptide
Chain G 2480–2491（12 aa） Fragment：C-terminal peptide
Chain H 2480–2491（12 aa） Fragment：C-terminal peptide
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.6；293 K；1.5M Sodium/Potassium Phosphate, 200mM Lithium Sulfate, pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.40 Å R-free 0.257
1JPL GGA3 VHS domain complexed with C-terminal peptide from cation-independent mannose 6-phosphate receptor Deposited 2001-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain E 2480–2491（12 aa） Fragment：C-terminal peptide
Chain F 2480–2491（12 aa） Fragment：C-terminal peptide
Chain G 2480–2491（12 aa） Fragment：C-terminal peptide
Chain H 2480–2491（12 aa） Fragment：C-terminal peptide
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.6；293 K；1.5M Sodium/Potassium Phosphate, 200mM Lithium Sulfate, pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.40 Å R-free 0.257
1JPL GGA3 VHS domain complexed with C-terminal peptide from cation-independent mannose 6-phosphate receptor Deposited 2001-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain E 2480–2491（12 aa） Fragment：C-terminal peptide
Chain F 2480–2491（12 aa） Fragment：C-terminal peptide
Chain G 2480–2491（12 aa） Fragment：C-terminal peptide
Chain H 2480–2491（12 aa） Fragment：C-terminal peptide
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.6；293 K；1.5M Sodium/Potassium Phosphate, 200mM Lithium Sulfate, pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.40 Å R-free 0.257
1JPL GGA3 VHS domain complexed with C-terminal peptide from cation-independent mannose 6-phosphate receptor Deposited 2001-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain E 2480–2491（12 aa） Fragment：C-terminal peptide
Chain F 2480–2491（12 aa） Fragment：C-terminal peptide
Chain G 2480–2491（12 aa） Fragment：C-terminal peptide
Chain H 2480–2491（12 aa） Fragment：C-terminal peptide
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.6；293 K；1.5M Sodium/Potassium Phosphate, 200mM Lithium Sulfate, pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.40 Å R-free 0.257
1JPL GGA3 VHS domain complexed with C-terminal peptide from cation-independent mannose 6-phosphate receptor Deposited 2001-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 9 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain G 2480–2491（12 aa） Fragment：C-terminal peptide
Chain H 2480–2491（12 aa） Fragment：C-terminal peptide
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.6；293 K；1.5M Sodium/Potassium Phosphate, 200mM Lithium Sulfate, pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.40 Å R-free 0.257
1JWG VHS Domain of human GGA1 complexed with cation-independent M6PR C-terminal Peptide Deposited 2001-09-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2479–2491（13 aa） Fragment：C-terminal fragment
Not recorded IOD IODIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG 3350, ammonium iodide, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.00 Å R-free 0.261
1JWG VHS Domain of human GGA1 complexed with cation-independent M6PR C-terminal Peptide Deposited 2001-09-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2479–2491（13 aa） Fragment：C-terminal fragment
Not recorded IOD IODIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG 3350, ammonium iodide, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.00 Å R-free 0.261
1LF8 Complex of GGA3-VHS Domain and CI-MPR C-terminal Phosphopeptide Deposited 2002-04-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 2480–2491（12 aa） Fragment：C-terminus (residues 2480-2491)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100mM CAPS 10.2-11.0, 200 mM Lithium Sulfate, 1.3-2M Sodium/Potassium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.255
1LF8 Complex of GGA3-VHS Domain and CI-MPR C-terminal Phosphopeptide Deposited 2002-04-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 2480–2491（12 aa） Fragment：C-terminus (residues 2480-2491)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100mM CAPS 10.2-11.0, 200 mM Lithium Sulfate, 1.3-2M Sodium/Potassium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.255
1LF8 Complex of GGA3-VHS Domain and CI-MPR C-terminal Phosphopeptide Deposited 2002-04-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 2480–2491（12 aa） Fragment：C-terminus (residues 2480-2491)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100mM CAPS 10.2-11.0, 200 mM Lithium Sulfate, 1.3-2M Sodium/Potassium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.255
1LF8 Complex of GGA3-VHS Domain and CI-MPR C-terminal Phosphopeptide Deposited 2002-04-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 2480–2491（12 aa） Fragment：C-terminus (residues 2480-2491)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100mM CAPS 10.2-11.0, 200 mM Lithium Sulfate, 1.3-2M Sodium/Potassium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.255
2CNJ NMR studies on the interaction of Insulin-Growth Factor II (IGF-II) with IGF2R domain 11 Deposited 2006-05-22 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1508–1650（143 aa） Fragment：DOMAIN 11, RESIDUES 1508-1650
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.5；298 K；Pressure 1.0
NMR sample composition 5% D2O/ 95% H2O
Resolution not provided
2V5N STRUCTURE OF HUMAN IGF2R DOMAINS 11-12 Deposited 2007-07-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1508–1799（292 aa） Fragment：DOMAINS 11 AND 12, RESIDUES 1508-1799
Non-standard monomer：Yes (specific site not provided by mmCIF) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.2 M POTASSIUM SODIUM TARTRATE, 20% (W/V) PEG 3350, pH 7.5
Resolution 3.20 Å R-free 0.317
2V5P COMPLEX STRUCTURE OF HUMAN IGF2R DOMAINS 11-13 BOUND TO IGF-II Deposited 2007-07-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1508–1992（485 aa） Fragment：DOMAINS 11-13, RESIDUES 1508-1992
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；0.1 M TRIS-HCL PH 9.0, 15% (V/V) MPD
Resolution 4.10 Å R-free 0.327
2V5P COMPLEX STRUCTURE OF HUMAN IGF2R DOMAINS 11-13 BOUND TO IGF-II Deposited 2007-07-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1508–1992（485 aa） Fragment：DOMAINS 11-13, RESIDUES 1508-1992
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；0.1 M TRIS-HCL PH 9.0, 15% (V/V) MPD
Resolution 4.10 Å R-free 0.327
5IEI X-ray crystallographic structure of a high affinity IGF2 antagonist (Domain11 AB5 RHH) based on human IGF2R domain 11 Deposited 2016-02-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1508–1649（142 aa） Fragment：UNP residues 1508-1649
Mutation：Q1569R, P1597H, S1602H GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.0 M Ammonium Sulphate, 0.1M Bis-(2-hydroxyethyl)imino-tris(hydroxymethyl methane, pH 7.0.
Resolution 2.80 Å R-free 0.249
6N5X Crystal structure of the SNX5 PX domain in complex with the CI-MPR (space group P212121 - Form 1) Deposited 2018-11-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2347–2377（31 aa）
Not recorded GOL GLYCEROL × 1 JEF O-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE GLYCOL 500) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；75% of 0.2 M (NH4)SO4, 0.1 M MES pH 6.5, 30% (w/v) PEG5000 MME + 15% glycerol + 40% v/v Polypropylene glycol P400
Resolution 2.05 Å R-free 0.234
6N5Y Crystal structure of the SNX5 PX domain in complex with the CI-MPR (space group P212121 - Form 1) Deposited 2018-11-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2347–2377（31 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；75% of 0.2 M (NH4)SO4, 0.1 M MES pH 6.5, 30% (w/v) PEG5000 MME + 15% glycerol + 30% v/v (+/-)-2-Methyl-2,4-pentanediol
Resolution 2.26 Å R-free 0.235
6P8I N-terminal 5 domains of IGFIIR Deposited 2019-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–763（728 aa） Fragment：N-terminal 5 domains
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；292.15 K；100mM ammonium citrate dibasic, 20% PEG 3350
Resolution 2.54 Å R-free 0.282
6V02 N-terminal 5 domains of CI-MPR Deposited 2019-11-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–763（721 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292.15 K；100 mM HEPES pH 7.0, 30% Jeffamine ED-2003
Resolution 2.46 Å R-free 0.308
6Z30 Human cation-independent mannose 6-phosphate/ IGF2 receptor domains 9-10 Deposited 2020-05-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1222–1510（289 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；298 K；0.1 M SPG buffer (succinic acid, sodium dihydrogen phosphate monohydrate, glycine) pH 9, 25 % PEG 1500
Resolution 1.50 Å R-free 0.228
6Z31 Human cation-independent mannose 6-phosphate/ IGF2 receptor domain 8 Deposited 2020-05-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1082–1220（139 aa）
Not recorded CL CHLORIDE ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；1.5 M Ammonium sulphate, 0.1 M Tris pH 8.5, 12 % glycerol
Resolution 2.56 Å R-free 0.251
6Z31 Human cation-independent mannose 6-phosphate/ IGF2 receptor domain 8 Deposited 2020-05-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1082–1220（139 aa）
Not recorded CL CHLORIDE ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；1.5 M Ammonium sulphate, 0.1 M Tris pH 8.5, 12 % glycerol
Resolution 2.56 Å R-free 0.251
6Z32 Human cation-independent mannose 6-phosphate/IGF2 receptor domains 7-11 Deposited 2020-05-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 927–1649（723 aa）
Not recorded SO4 SULFATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.1 M MES pH 6.5, 1.6 M MgSO4, 10 mM mannose 6-phosphate
Resolution 3.47 Å R-free 0.300
6Z32 Human cation-independent mannose 6-phosphate/IGF2 receptor domains 7-11 Deposited 2020-05-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain B 927–1649（723 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.1 M MES pH 6.5, 1.6 M MgSO4, 10 mM mannose 6-phosphate
Resolution 3.47 Å R-free 0.300
8AFZ Architecture of the ESCPE-1 membrane coat Deposited 2022-07-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 2347–2377（31 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Incubation time 30s Blotting time 2s
Resolution 10.00 Å

19 other PDB entries and 37 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MPRI_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–621； UniProt 1508–2128

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 2v5o

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2v5o
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2v5o
Deposition date deposition_date2007-07-06
Structure title titleSTRUCTURE OF HUMAN IGF2R DOMAINS 11-14
Keywords keywords;CATION INDEPENDENT MANNOSE 6-PHOSPHATE, MEMBRANE, RECEPTOR, LYSOSOME, TRANSPORT, BETA BARREL, PHOSPHORYLATION, FIBRONECTIN TYPE II, INSULIN-LIKE GROWTH FACTOR, GLYCOPROTEIN, TRANSMEMBRANE ;; RECEPTOR
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier34.05 Å
Radius of gyration Rg (electron density) rg_electron34.43 Å
Forward intensity I(0) i074253600.00
Molecular weight molecular_weight66972.0 kDa
Excluded volume excluded_volume83191 ų
Envelope volume envelope_volume116670 ų
Hydration-shell volume shell_volume30824 ų
Envelope diameter envelope_diameter124.0 Å
Shell Rg shell_rg37.28 Å
Envelope Rg envelope_rg34.30 Å
Shape Rg shape_rg34.41 Å
Total Rg total_rg34.72 Å
Total atoms total_atoms4686
Residues n_residues604
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax120.0 Å
Rg (real space) rg_real34.43 Å
Rg uncertainty (real space) rg_real_error1.32 Å
I(0) (real space) i0_real7.4250e+07
I(0) uncertainty (real space) i0_real_error1.2000e+06
Rg (reciprocal space) rg_reciprocal34.19 Å
I(0) (reciprocal space) i0_reciprocal74240000.0000
Solution quality estimate total_estimate0.8022
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary28.7 Å
Skewness Skewness skewness0.588
Kurtosis Kurtosis kurtosis-0.338
Angular range angular_range— – 0.2300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10420000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.651; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.647; Smooth: 0.826
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id2v5oA01
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology130 — Cation-dependent Mannose-6-phosphate Receptor; Chain A
Homologous superfamily homologous superfamily10 — Mannose-6-phosphate receptor binding domain
Domain ID domain_id2v5oA02
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology130 — Cation-dependent Mannose-6-phosphate Receptor; Chain A
Homologous superfamily homologous superfamily10 — Mannose-6-phosphate receptor binding domain
Domain ID domain_id2v5oA03
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology130 — Cation-dependent Mannose-6-phosphate Receptor; Chain A
Homologous superfamily homologous superfamily10 — Mannose-6-phosphate receptor binding domain
Domain ID domain_id2v5oA04
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology10 — Seminal Fluid Protein PDC-109 (Domain B)
Homologous superfamily homologous superfamily10 — Fibronectin, type II, collagen-binding
Domain ID domain_id2v5oA05
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology130 — Cation-dependent Mannose-6-phosphate Receptor; Chain A
Homologous superfamily homologous superfamily10 — Mannose-6-phosphate receptor binding domain
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8. Citations (1)

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9. Files and Curves (10)