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1jpl

GGA3 VHS domain complexed with C-terminal peptide from cation-independent mannose 6-phosphate receptor

Method: X-RAY DIFFRACTION Dmax: 107.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3

Homo sapiens

UniProt Q9NZ52

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–166 Fragment：VHS domain Non-standard monomer：Yes (specific site not provided by mmCIF) Cation-Independent Mannose 6-phosphate receptor × 1 （P11717） 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
10 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1–166 Chain B； UniProt 1–166 Fragment：VHS domain Non-standard monomer：Yes (specific site not provided by mmCIF) Cation-Independent Mannose 6-phosphate receptor × 2 （P11717） 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 1–166 Fragment：VHS domain Non-standard monomer：Yes (specific site not provided by mmCIF) Cation-Independent Mannose 6-phosphate receptor × 1 （P11717） 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
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 1–166 Fragment：VHS domain Non-standard monomer：Yes (specific site not provided by mmCIF) Cation-Independent Mannose 6-phosphate receptor × 1 （P11717） 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
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 1–166 Fragment：VHS domain Non-standard monomer：Yes (specific site not provided by mmCIF) Cation-Independent Mannose 6-phosphate receptor × 1 （P11717） 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
5 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain A； UniProt 1–166 Chain B； UniProt 1–166 Chain C； UniProt 1–166 Chain D； UniProt 1–166 Fragment：VHS domain Non-standard monomer：Yes (specific site not provided by mmCIF) Cation-Independent Mannose 6-phosphate receptor × 4 （P11717） 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
6 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain A； UniProt 1–166 Chain B； UniProt 1–166 Chain C； UniProt 1–166 Chain D； UniProt 1–166 Fragment：VHS domain Non-standard monomer：Yes (specific site not provided by mmCIF) Cation-Independent Mannose 6-phosphate receptor × 4 （P11717） 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
7 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain A； UniProt 1–166 Chain B； UniProt 1–166 Chain C； UniProt 1–166 Chain D； UniProt 1–166 Fragment：VHS domain Non-standard monomer：Yes (specific site not provided by mmCIF) Cation-Independent Mannose 6-phosphate receptor × 4 （P11717） 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
8 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain A； UniProt 1–166 Chain B； UniProt 1–166 Chain C； UniProt 1–166 Chain D； UniProt 1–166 Fragment：VHS domain Non-standard monomer：Yes (specific site not provided by mmCIF) Cation-Independent Mannose 6-phosphate receptor × 4 （P11717） 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
9 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain C； UniProt 1–166 Chain D； UniProt 1–166 Fragment：VHS domain Non-standard monomer：Yes (specific site not provided by mmCIF) Cation-Independent Mannose 6-phosphate receptor × 2 （P11717） 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

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 1JPL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1JUQ GGA3 VHS domain complexed with C-terminal peptide from cation-dependent Mannose 6-phosphate receptor Deposited 2001-08-26 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–166（166 aa） Fragment：VHS domain
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；Sodium/Potassium phosphate, Lithium Sulfate, CAPS, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.20 Å R-free 0.254
1JUQ GGA3 VHS domain complexed with C-terminal peptide from cation-dependent Mannose 6-phosphate receptor Deposited 2001-08-26 Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–166（166 aa） Fragment：VHS domain
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；Sodium/Potassium phosphate, Lithium Sulfate, CAPS, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.20 Å R-free 0.254
1JUQ GGA3 VHS domain complexed with C-terminal peptide from cation-dependent Mannose 6-phosphate receptor Deposited 2001-08-26 Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–166（166 aa） Fragment：VHS domain
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；Sodium/Potassium phosphate, Lithium Sulfate, CAPS, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.20 Å R-free 0.254
1JUQ GGA3 VHS domain complexed with C-terminal peptide from cation-dependent Mannose 6-phosphate receptor Deposited 2001-08-26 Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–166（166 aa） Fragment：VHS domain
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；Sodium/Potassium phosphate, Lithium Sulfate, CAPS, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.20 Å R-free 0.254
1JUQ GGA3 VHS domain complexed with C-terminal peptide from cation-dependent Mannose 6-phosphate receptor Deposited 2001-08-26 Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–166（166 aa） Fragment：VHS domain
Chain B 1–166（166 aa） Fragment：VHS domain
Chain C 1–166（166 aa） Fragment：VHS domain
Chain D 1–166（166 aa） Fragment：VHS domain
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) 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；Sodium/Potassium phosphate, Lithium Sulfate, CAPS, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.20 Å R-free 0.254
1JUQ GGA3 VHS domain complexed with C-terminal peptide from cation-dependent Mannose 6-phosphate receptor Deposited 2001-08-26 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–166（166 aa） Fragment：VHS domain
Chain B 1–166（166 aa） Fragment：VHS domain
Chain C 1–166（166 aa） Fragment：VHS domain
Chain D 1–166（166 aa） Fragment：VHS domain
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) 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；Sodium/Potassium phosphate, Lithium Sulfate, CAPS, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.20 Å R-free 0.254
1LF8 Complex of GGA3-VHS Domain and CI-MPR C-terminal Phosphopeptide Deposited 2002-04-10 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–166（166 aa） Fragment：VHS domain (residues 1-166)
Not recorded 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 experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–166（166 aa） Fragment：VHS domain (residues 1-166)
Not recorded 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 experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–166（166 aa） Fragment：VHS domain (residues 1-166)
Not recorded 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 experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–166（166 aa） Fragment：VHS domain (residues 1-166)
Not recorded 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
1P4U CRYSTAL STRUCTURE OF GGA3 GAE DOMAIN IN COMPLEX WITH RABAPTIN-5 PEPTIDE Deposited 2003-04-24 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 571–723（153 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；1.6M sodium citrate, pH 6.5
Resolution 2.20 Å R-free 0.255
1P4U CRYSTAL STRUCTURE OF GGA3 GAE DOMAIN IN COMPLEX WITH RABAPTIN-5 PEPTIDE Deposited 2003-04-24 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 571–723（153 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；1.6M sodium citrate, pH 6.5
Resolution 2.20 Å R-free 0.255
1WR6 Crystal structure of GGA3 GAT domain in complex with ubiquitin Deposited 2004-10-12 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 209–319（111 aa） Fragment：C-GAT domain(RESIDUES 209-319)
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；pH 6.5；293 K；PEG3350, Ammonium formate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.290
1WR6 Crystal structure of GGA3 GAT domain in complex with ubiquitin Deposited 2004-10-12 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 209–319（111 aa） Fragment：C-GAT domain(RESIDUES 209-319)
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；pH 6.5；293 K；PEG3350, Ammonium formate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.290
1WR6 Crystal structure of GGA3 GAT domain in complex with ubiquitin Deposited 2004-10-12 Different construct Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 209–319（111 aa） Fragment：C-GAT domain(RESIDUES 209-319)
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；pH 6.5；293 K；PEG3350, Ammonium formate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.290
1WR6 Crystal structure of GGA3 GAT domain in complex with ubiquitin Deposited 2004-10-12 Different construct Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 209–319（111 aa） Fragment：C-GAT domain(RESIDUES 209-319)
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；pH 6.5；293 K；PEG3350, Ammonium formate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.290
1YD8 COMPLEX OF HUMAN GGA3 GAT DOMAIN AND UBIQUITIN Deposited 2004-12-23 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 208–301（94 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.80 Å R-free 0.297
1YD8 COMPLEX OF HUMAN GGA3 GAT DOMAIN AND UBIQUITIN Deposited 2004-12-23 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 208–301（94 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.80 Å R-free 0.297

5 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GGA3_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 6–171； UniProt 1–166 Author chain B； PDBConstruct 6–171； UniProt 1–166 Author chain C； PDBConstruct 6–171； UniProt 1–166 Author chain D； PDBConstruct 6–171； UniProt 1–166

Cation-Independent Mannose 6-phosphate receptor

OrganismNot specified

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain E； UniProt 2480–2491 Fragment：C-terminal peptide ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3 × 1 （Q9NZ52） 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
10 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain E； UniProt 2480–2491 Chain F； UniProt 2480–2491 Fragment：C-terminal peptide ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3 × 2 （Q9NZ52） 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain F； UniProt 2480–2491 Fragment：C-terminal peptide ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3 × 1 （Q9NZ52） 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
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain G； UniProt 2480–2491 Fragment：C-terminal peptide ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3 × 1 （Q9NZ52） 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
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain H； UniProt 2480–2491 Fragment：C-terminal peptide ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3 × 1 （Q9NZ52） 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
5 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain E； UniProt 2480–2491 Chain F； UniProt 2480–2491 Chain G； UniProt 2480–2491 Chain H； UniProt 2480–2491 Fragment：C-terminal peptide ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3 × 4 （Q9NZ52） 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
6 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain E； UniProt 2480–2491 Chain F； UniProt 2480–2491 Chain G； UniProt 2480–2491 Chain H； UniProt 2480–2491 Fragment：C-terminal peptide ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3 × 4 （Q9NZ52） 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
7 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain E； UniProt 2480–2491 Chain F； UniProt 2480–2491 Chain G； UniProt 2480–2491 Chain H； UniProt 2480–2491 Fragment：C-terminal peptide ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3 × 4 （Q9NZ52） 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
8 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain E； UniProt 2480–2491 Chain F； UniProt 2480–2491 Chain G； UniProt 2480–2491 Chain H； UniProt 2480–2491 Fragment：C-terminal peptide ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3 × 4 （Q9NZ52） 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
9 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain G； UniProt 2480–2491 Chain H； UniProt 2480–2491 Fragment：C-terminal peptide ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3 × 2 （Q9NZ52） 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

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 1JPL 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
1JWG VHS Domain of human GGA1 complexed with cation-independent M6PR C-terminal Peptide Deposited 2001-09-04 Different construct 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 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 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 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 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 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 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 oligomeric state 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
6Z30 Human cation-independent mannose 6-phosphate/ IGF2 receptor domains 9-10 Deposited 2020-05-19 Different construct Different oligomeric state 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 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 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 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 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MPRI_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain E； PDBConstruct 1–12； UniProt 2480–2491 Author chain F； PDBConstruct 1–12； UniProt 2480–2491 Author chain G； PDBConstruct 1–12； UniProt 2480–2491 Author chain H； PDBConstruct 1–12； UniProt 2480–2491

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 1jpl

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1jpl
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1jpl
Deposition date deposition_date2001-08-02
Structure title titleGGA3 VHS domain complexed with C-terminal peptide from cation-independent mannose 6-phosphate receptor
Keywords keywordsProtein-peptide complex; VHS domain; DXXLL sorting signal, SIGNALING PROTEIN; SIGNALING PROTEIN
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_guinier33.84 Å
Radius of gyration Rg (electron density) rg_electron33.53 Å
Forward intensity I(0) i098282000.00
Molecular weight molecular_weight78091.0 kDa
Excluded volume excluded_volume97080 ų
Envelope volume envelope_volume124750 ų
Hydration-shell volume shell_volume32133 ų
Envelope diameter envelope_diameter115.0 Å
Shell Rg shell_rg38.79 Å
Envelope Rg envelope_rg33.04 Å
Shape Rg shape_rg33.52 Å
Total Rg total_rg33.96 Å
Total atoms total_atoms5418
Residues n_residues653
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 dmax107.8 Å
Rg (real space) rg_real33.99 Å
Rg uncertainty (real space) rg_real_error0.94 Å
I(0) (real space) i0_real9.8280e+07
I(0) uncertainty (real space) i0_real_error1.6670e+06
Rg (reciprocal space) rg_reciprocal33.90 Å
I(0) (reciprocal space) i0_reciprocal98270000.0000
Solution quality estimate total_estimate0.8378
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.5 Å
Skewness Skewness skewness0.344
Kurtosis Kurtosis kurtosis-0.807
Angular range angular_range— – 0.2350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha35650000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.759; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.746; Smooth: 0.865
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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) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd1jpla1
Class classa — All alpha proteins
Fold Fold folda.118 — alpha-alpha superhelix
Superfamily Superfamily superfamilya.118.9 — ENTH/VHS domain
Family Family familya.118.9.2 — VHS domain
Domain ID domain_idd1jpla2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1jplb1
Class classa — All alpha proteins
Fold Fold folda.118 — alpha-alpha superhelix
Superfamily Superfamily superfamilya.118.9 — ENTH/VHS domain
Family Family familya.118.9.2 — VHS domain
Domain ID domain_idd1jplb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1jplc1
Class classa — All alpha proteins
Fold Fold folda.118 — alpha-alpha superhelix
Superfamily Superfamily superfamilya.118.9 — ENTH/VHS domain
Family Family familya.118.9.2 — VHS domain
Domain ID domain_idd1jplc2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1jpld1
Class classa — All alpha proteins
Fold Fold folda.118 — alpha-alpha superhelix
Superfamily Superfamily superfamilya.118.9 — ENTH/VHS domain
Family Family familya.118.9.2 — VHS domain
Domain ID domain_idd1jpld2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id1jplA00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily90 —
Domain ID domain_id1jplB00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily90 —
Domain ID domain_id1jplC00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily90 —
Domain ID domain_id1jplD00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily90 —
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8. Citations (1)

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9. Files and Curves (10)