6z30

Human cation-independent mannose 6-phosphate/ IGF2 receptor domains 9-10

Method: X-RAY DIFFRACTION D_max: 77.9 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

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1222–1510	Not recorded	;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1	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

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 6Z30	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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 oligomeric state 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 oligomeric state 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
2V5O STRUCTURE OF HUMAN IGF2R DOMAINS 11-14 Deposited 2007-07-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1508–2128（621 aa） Fragment：DOMAINS 11-14, RESIDUES 1508-2128	Not recorded	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
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 oligomeric state 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 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 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 oligomeric state 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
6Z31 Human cation-independent mannose 6-phosphate/ IGF2 receptor domain 8 Deposited 2020-05-19	Different construct Different oligomeric state 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 oligomeric state 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 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 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 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 6–294； UniProt 1222–1510

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6z30
Deposition date deposition_date	2020-05-19
Structure title title	Human cation-independent mannose 6-phosphate/ IGF2 receptor domains 9-10
Keywords keywords	;Mannose 6-phosphate, Cation-independent mannose 6-phosphate receptor, Insulin-like growth factor 2 receptor, P-type lectin, SUGAR BINDING PROTEIN ;; SUGAR BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	24.02 Å
Radius of gyration Rg (electron density) rg_electron	23.28 Å
Forward intensity I(0) i0	19671600.00
Molecular weight molecular_weight	32747.0 kDa
Excluded volume excluded_volume	40539 Å³
Envelope volume envelope_volume	50525 Å³
Hydration-shell volume shell_volume	19060 Å³
Envelope diameter envelope_diameter	80.8 Å
Shell Rg shell_rg	29.15 Å
Envelope Rg envelope_rg	23.37 Å
Shape Rg shape_rg	23.24 Å
Total Rg total_rg	24.18 Å
Total atoms total_atoms	2293
Residues n_residues	285
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	77.9 Å
Rg (real space) rg_real	24.13 Å
Rg uncertainty (real space) rg_real_error	0.59 Å
I(0) (real space) i0_real	1.9670e+07
I(0) uncertainty (real space) i0_real_error	2.7550e+05
Rg (reciprocal space) rg_reciprocal	24.10 Å
I(0) (reciprocal space) i0_reciprocal	19670000.0000
Solution quality estimate total_estimate	0.8820
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.9 Å
Skewness Skewness skewness	0.373
Kurtosis Kurtosis kurtosis	-0.577
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3203000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.878; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.855; Smooth: 0.972

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Cation-independent mannose-6-phosphate receptor
Molecular weight formula_weight	33646.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2732

ETGASVEGDNCEVKDPRHGNLYDLKPLGLNDTIVSAGEYTYYFRVCGKLSSDVCPTSDKSKVVSSCQEKREPQGFHKVAGLLTQKLTYENGLLKMNFTGGDTCHKVYQRSTAIFFYCDRGTQRPVFLKETSDCSYLFEWRTQYACPPFDLTECSFKDGAGNSFDLSSLSRYSDNWEAITGTGDPEHYLINVCKSLAPQAGTEPCPPEAAACLLGGSKPVNLGRVRDGPQWRDGIIVLKYVDGDLCPDGIRKKSTTIRFTCSESQVNSRPMFISAVEDCEYTFAWPTATACPMKSTRHHHHHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 branched

Description description	;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	1073.0 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	439

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6z30A01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	130 — Cation-dependent Mannose-6-phosphate Receptor; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-6-phosphate receptor binding domain

Domain ID domain_id	6z30A02
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	130 — Cation-dependent Mannose-6-phosphate Receptor; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-6-phosphate receptor binding domain

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8. Citations (1)

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Unit-cell length a length_a	40.360 Å
Unit-cell length b length_b	55.830 Å
Unit-cell length c length_c	132.660 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	51.460 Å
R factor r_factor	0.1977
R_work r_work	0.1991
R_free r_free	0.2284

fit	/app/data/saxs_computation/z3/6z30/6z30.fit
pddf	/app/data/pr_computation/z3/6z30/6z30.pr.out
profile	/app/data/saxs_computation/z3/6z30/6z30.dat