2dwx

Co-crystal Structure Analysis of GGA1-GAE with the WNSF motif

Method: X-RAY DIFFRACTION D_max: 97.7 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

ADP-ribosylation factor-binding protein GGA1

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	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 507–639 Chain P； UniProt 376–388	Fragment：GAE DOMAIN, RESIDUES 507-639	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, DI-AMMONIUM TARTRATE, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.55 Å R-free 0.287
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 507–639	Fragment：GAE DOMAIN, RESIDUES 507-639	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, DI-AMMONIUM TARTRATE, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.55 Å R-free 0.287
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 507–639 Chain Q； UniProt 376–388	Fragment：GAE DOMAIN, RESIDUES 507-639	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, DI-AMMONIUM TARTRATE, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.55 Å R-free 0.287
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 507–639	Fragment：GAE DOMAIN, RESIDUES 507-639	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, DI-AMMONIUM TARTRATE, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.55 Å R-free 0.287

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 2DWX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1J2J Crystal structure of GGA1 GAT N-terminal region in complex with ARF1 GTP form Deposited 2003-01-05	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 B 166–210（45 aa） Fragment：GAT N-terminal region	Not recorded	MG MAGNESIUM ION × 1 IOD IODIDE ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, KI, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.227
1JWF Crystal Structure of human GGA1 VHS domain. Deposited 2001-09-04	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–147（147 aa） Fragment：VHS DOMAIN(N-terminal domain)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG 3350, potassium dihydrogen phosphate, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 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 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–147（147 aa） Fragment：VHS DOMAIN(N-terminal domain)	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 B 1–147（147 aa） Fragment：VHS DOMAIN(N-terminal domain)	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
1NA8 Crystal structure of ADP-ribosylation factor binding protein GGA1 Deposited 2002-11-27	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 494–639（146 aa） Fragment：appendage domain, Residues 494-639 of SWS Q9UJY5 Chain B 494–639（146 aa） Fragment：appendage domain, Residues 494-639 of SWS Q9UJY5	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；289 K；sodium citrate, ammonium sulphate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K	Resolution 2.30 Å R-free 0.279
1NAF Crystal structure of the human GGA1 GAT domain Deposited 2002-11-27	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 165–314（150 aa） Fragment：GAT domain, Residues 165-314 of SWS Q9UJY5	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 4.5；289 K；sodium acetate, lithium sulphate, NaH2PO4/K2HPO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.80 Å R-free 0.283
1NWM GAT domain of human GGA1 Deposited 2003-02-06	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 166–302（137 aa） Fragment：GAT domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；298.15 K；polyethylene glycol 4000, iso-propanol, sodium citrate, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K	Resolution 2.40 Å R-free 0.286
1O3X Crystal structure of human GGA1 GAT domain Deposited 2003-05-08	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 166–305（140 aa） Fragment：Gat domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；MPD, PEG6000, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.290
1OM9 Structure of the GGA1-appendage in complex with the p56 binding peptide Deposited 2003-02-25	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 494–639（146 aa） Fragment：appendage domain, Residues 494-639 of SWS Q9UJY5	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；288 K；100 mM sodium citrate, 100 mM MgCl2 and 35% PEG 400, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K	Resolution 2.50 Å R-free 0.262
1OM9 Structure of the GGA1-appendage in complex with the p56 binding peptide Deposited 2003-02-25	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 494–639（146 aa） Fragment：appendage domain, Residues 494-639 of SWS Q9UJY5	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；288 K；100 mM sodium citrate, 100 mM MgCl2 and 35% PEG 400, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K	Resolution 2.50 Å R-free 0.262
1OM9 Structure of the GGA1-appendage in complex with the p56 binding peptide Deposited 2003-02-25	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 494–639（146 aa） Fragment：appendage domain, Residues 494-639 of SWS Q9UJY5 Chain B 494–639（146 aa） Fragment：appendage domain, Residues 494-639 of SWS Q9UJY5	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；288 K；100 mM sodium citrate, 100 mM MgCl2 and 35% PEG 400, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K	Resolution 2.50 Å R-free 0.262
1OXZ Crystal Structure of the Human GGA1 GAT domain Deposited 2003-04-03	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 141–326（186 aa） Fragment：GAT domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；lithium sulfate, MES, ethylene glycol , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.285
1PY1 Complex of GGA1-VHS domain and beta-secretase C-terminal phosphopeptide Deposited 2003-07-07	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 2–157（156 aa） Fragment：VHS Domain (Residues 2-157) Chain B 2–157（156 aa） Fragment：VHS Domain (Residues 2-157)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；PEG 3350, AMMONIUM SULFATE, CACODYLATE, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.288
1PY1 Complex of GGA1-VHS domain and beta-secretase C-terminal phosphopeptide Deposited 2003-07-07	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 2–157（156 aa） Fragment：VHS Domain (Residues 2-157) Chain D 2–157（156 aa） Fragment：VHS Domain (Residues 2-157)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；PEG 3350, AMMONIUM SULFATE, CACODYLATE, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.288
1UJJ VHS domain of human GGA1 complexed with C-terminal peptide from BACE Deposited 2003-08-05	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–147（147 aa） Fragment：VHS domain, N-terminal domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.6；293 K；PEG 5000MME, di-Ammonium hydrogen phosphate, Tris-HCl, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.295
1UJJ VHS domain of human GGA1 complexed with C-terminal peptide from BACE Deposited 2003-08-05	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–147（147 aa） Fragment：VHS domain, N-terminal domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.6；293 K；PEG 5000MME, di-Ammonium hydrogen phosphate, Tris-HCl, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.295
1UJK VHS domain of human GGA1 complexed with C-terminal phosphopeptide from BACE Deposited 2003-08-05	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 A 1–147（147 aa） Fragment：VHS domain, N-terminal domain	Not recorded	IOD IODIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG5000MME, Ammonium Iodide, 1,6-hexanediol, MES-NaOH, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.245
1UJK VHS domain of human GGA1 complexed with C-terminal phosphopeptide from BACE Deposited 2003-08-05	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 1–147（147 aa） Fragment：VHS domain, N-terminal domain	Not recorded	IOD IODIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG5000MME, Ammonium Iodide, 1,6-hexanediol, MES-NaOH, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.245
1UJK VHS domain of human GGA1 complexed with C-terminal phosphopeptide from BACE Deposited 2003-08-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–147（147 aa） Fragment：VHS domain, N-terminal domain Chain B 1–147（147 aa） Fragment：VHS domain, N-terminal domain	Not recorded	IOD IODIDE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG5000MME, Ammonium Iodide, 1,6-hexanediol, MES-NaOH, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.245
1X79 Crystal structure of human GGA1 GAT domain complexed with the GAT-binding domain of Rabaptin5 Deposited 2004-08-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 210–302（93 aa）	Not recorded	SO4 SULFATE ION × 2 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；AMMONIUM SULFATE, TRIS, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.41 Å R-free 0.283
2DWY Crystal Structure Analysis of GGA1-GAE Deposited 2006-08-21	Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 507–639（133 aa） Fragment：GAE DOMAIN, RESIDUES 507-639	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, DI-AMMONIUM TARTRATE, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.257
2DWY Crystal Structure Analysis of GGA1-GAE Deposited 2006-08-21	Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 507–639（133 aa） Fragment：GAE DOMAIN, RESIDUES 507-639	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, DI-AMMONIUM TARTRATE, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.257
2DWY Crystal Structure Analysis of GGA1-GAE Deposited 2006-08-21	Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 507–639（133 aa） Fragment：GAE DOMAIN, RESIDUES 507-639	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, DI-AMMONIUM TARTRATE, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.257
2DWY Crystal Structure Analysis of GGA1-GAE Deposited 2006-08-21	Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 507–639（133 aa） Fragment：GAE DOMAIN, RESIDUES 507-639	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, DI-AMMONIUM TARTRATE, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.257
2DWY Crystal Structure Analysis of GGA1-GAE Deposited 2006-08-21	Different construct Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 507–639（133 aa） Fragment：GAE DOMAIN, RESIDUES 507-639 Chain D 507–639（133 aa） Fragment：GAE DOMAIN, RESIDUES 507-639	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, DI-AMMONIUM TARTRATE, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.257
2DWY Crystal Structure Analysis of GGA1-GAE Deposited 2006-08-21	Different construct Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 507–639（133 aa） Fragment：GAE DOMAIN, RESIDUES 507-639 Chain B 507–639（133 aa） Fragment：GAE DOMAIN, RESIDUES 507-639	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, DI-AMMONIUM TARTRATE, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.257
3G2S VHS Domain of human GGA1 complexed with SorLA C-terminal Peptide Deposited 2009-02-01	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–147（147 aa） Fragment：VHS Domain (N-terminal domain)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；15%(w/v) PEG 5000 mmE, 0.2M NH4I, 0.3M 1,6-hexanediol, 0.1M MES-NaOH, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 1.70 Å R-free 0.226
3G2S VHS Domain of human GGA1 complexed with SorLA C-terminal Peptide Deposited 2009-02-01	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 1–147（147 aa） Fragment：VHS Domain (N-terminal domain)	Not recorded	HEZ HEXANE-1,6-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；15%(w/v) PEG 5000 mmE, 0.2M NH4I, 0.3M 1,6-hexanediol, 0.1M MES-NaOH, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 1.70 Å R-free 0.226
3G2T VHS Domain of human GGA1 complexed with SorLA C-terminal Phosphopeptide Deposited 2009-02-01	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 A 1–147（147 aa） Fragment：VHS Domain (N-terminal domain)	Not recorded	IOD IODIDE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；18%(w/v) PEG 5000 MME, 0.2M NH4I, 0.1M TRIS-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.00 Å R-free 0.233
3G2T VHS Domain of human GGA1 complexed with SorLA C-terminal Phosphopeptide Deposited 2009-02-01	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 1–147（147 aa） Fragment：VHS Domain (N-terminal domain)	Not recorded	IOD IODIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；18%(w/v) PEG 5000 MME, 0.2M NH4I, 0.1M TRIS-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.00 Å R-free 0.233
3G2U VHS Domain of human GGA1 complexed with Sotilin C-terminal Peptide Deposited 2009-02-01	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 A 1–147（147 aa） Fragment：VHS Domain (N-terminal domain)	Not recorded	IOD IODIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；15%(w/v) PEG 5000 mmE, 0.2M NH4I, 0.3M 1,6-hexanediol, 0.1M MES-NaOH, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.30 Å R-free 0.246
3G2U VHS Domain of human GGA1 complexed with Sotilin C-terminal Peptide Deposited 2009-02-01	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 1–147（147 aa） Fragment：VHS Domain (N-terminal domain)	Not recorded	IOD IODIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；15%(w/v) PEG 5000 mmE, 0.2M NH4I, 0.3M 1,6-hexanediol, 0.1M MES-NaOH, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.30 Å R-free 0.246
3G2V VHS Domain of human GGA1 complexed with Sotilin C-terminal Phosphopeptide Deposited 2009-02-01	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 A 1–147（147 aa） Fragment：VHS Domain (N-terminal domain)	Not recorded	IOD IODIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；16%(w/v) PEG 5000 mmE, 0.2M NH4I, 0.3M 1,6-hexanediol, 0.1M MES-NaOH, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.10 Å R-free 0.244
3G2V VHS Domain of human GGA1 complexed with Sotilin C-terminal Phosphopeptide Deposited 2009-02-01	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 1–147（147 aa） Fragment：VHS Domain (N-terminal domain)	Not recorded	IOD IODIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；16%(w/v) PEG 5000 mmE, 0.2M NH4I, 0.3M 1,6-hexanediol, 0.1M MES-NaOH, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.10 Å R-free 0.244
3G2W VHS Domain of human GGA1 complexed with a DXXLL hinge peptide Deposited 2009-02-01	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–147（147 aa） Fragment：VHS Domain (N-terminal domain) Chain C 351–364（14 aa）	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, SITTING DROP；pH 6；292 K；15%(w/v) PEG 5000 mmE, 0.2M NH4I, 0.3M 1,6-hexanediol, 0.1M MES-NaOH, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.40 Å R-free 0.259
3G2W VHS Domain of human GGA1 complexed with a DXXLL hinge peptide Deposited 2009-02-01	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–147（147 aa） Fragment：VHS Domain (N-terminal domain) Chain D 351–364（14 aa）	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, SITTING DROP；pH 6；292 K；15%(w/v) PEG 5000 mmE, 0.2M NH4I, 0.3M 1,6-hexanediol, 0.1M MES-NaOH, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.40 Å R-free 0.259

19 other PDB entries and 36 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GGA1_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–133； UniProt 507–639 Author chain B； PDBConstruct 1–133； UniProt 507–639 Author chain C； PDBConstruct 1–133； UniProt 507–639 Author chain D； PDBConstruct 1–133； UniProt 507–639 Author chain P； PDBConstruct 1–13； UniProt 376–388 Author chain Q； PDBConstruct 1–13； UniProt 376–388

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	2dwx
Deposition date deposition_date	2006-08-21
Structure title title	Co-crystal Structure Analysis of GGA1-GAE with the WNSF motif
Keywords keywords	IG FOLD, ADAPTIN, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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	28.14 Å
Radius of gyration Rg (electron density) rg_electron	27.26 Å
Forward intensity I(0) i0	50569000.00
Molecular weight molecular_weight	58232.0 kDa
Excluded volume excluded_volume	74142 Å³
Envelope volume envelope_volume	91965 Å³
Hydration-shell volume shell_volume	28822 Å³
Envelope diameter envelope_diameter	101.2 Å
Shell Rg shell_rg	33.64 Å
Envelope Rg envelope_rg	27.28 Å
Shape Rg shape_rg	27.25 Å
Total Rg total_rg	28.00 Å
Total atoms total_atoms	4113
Residues n_residues	520
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	97.7 Å
Rg (real space) rg_real	28.24 Å
Rg uncertainty (real space) rg_real_error	0.80 Å
I(0) (real space) i0_real	5.0570e+07
I(0) uncertainty (real space) i0_real_error	7.2240e+05
Rg (reciprocal space) rg_reciprocal	28.21 Å
I(0) (reciprocal space) i0_reciprocal	50570000.0000
Solution quality estimate total_estimate	0.8572
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.4 Å
Skewness Skewness skewness	0.424
Kurtosis Kurtosis kurtosis	-0.323
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12240000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.777; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.896; Smooth: 0.912

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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	ADP-ribosylation factor-binding protein GGA1
Molecular weight formula_weight	14891.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4235

IKPSNILPVTVYDQHGFRILFHFARDPLPGRSDVLVVVVSMLSTAPQPIRNIVFQSAVPKVMKVKLQPPSGTELPAFNPIVHPSAITQVLLLANPQKEKVRLRYKLTFTMGDQTYNEMGDVDQFPPPETWGSL

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	Escherichia coli

Entity 2 Entity 2 polymer

Description description	hinge peptide from ADP-ribosylation factor binding protein GGA1
Molecular weight formula_weight	1385.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P,Q

SLDGTGWNSFQSS

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	122

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2dwxa_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.10 — Clathrin adaptor appendage domain
Family Family family	b.1.10.2 — gamma-adaptin C-terminal appendage domain-like

Domain ID domain_id	d2dwxb_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.10 — Clathrin adaptor appendage domain
Family Family family	b.1.10.2 — gamma-adaptin C-terminal appendage domain-like

Domain ID domain_id	d2dwxc_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.10 — Clathrin adaptor appendage domain
Family Family family	b.1.10.2 — gamma-adaptin C-terminal appendage domain-like

Domain ID domain_id	d2dwxd_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.10 — Clathrin adaptor appendage domain
Family Family family	b.1.10.2 — gamma-adaptin C-terminal appendage domain-like

CATH v4.4 (4 domains)

Domain ID domain_id	2dwxA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1230 — Gamma-adaptin ear (GAE) domain

Domain ID domain_id	2dwxB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1230 — Gamma-adaptin ear (GAE) domain

Domain ID domain_id	2dwxC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1230 — Gamma-adaptin ear (GAE) domain

Domain ID domain_id	2dwxD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1230 — Gamma-adaptin ear (GAE) domain

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8. Citations (1)

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Unit-cell length a length_a	48.220 Å
Unit-cell length b length_b	69.620 Å
Unit-cell length c length_c	184.967 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	16

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

Resolution resolution	2.550 Å
Low-resolution limit resolution_low	38.630 Å
R factor r_factor	0.2410
R_work r_work	0.2380
R_free r_free	0.2870

fit	/app/data/saxs_computation/dw/2dwx/2dwx.fit
pddf	/app/data/pr_computation/dw/2dwx/2dwx.pr.out
profile	/app/data/saxs_computation/dw/2dwx/2dwx.dat

Co-crystal Structure Analysis of GGA1-GAE with the WNSF motif

1. Protein Identity and Related Structures Protein Identity & Related Structures

ADP-ribosylation factor-binding protein GGA1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)