SAXSdb — 2f6m

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

Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease

Saccharomyces cerevisiae

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 322–385	Fragment：Vps23C-terminal domain (322-385) Mutation：C344A	Vacuolar protein sorting-associated protein VPS28 × 1 （Q02767） MG MAGNESIUM ION × 1 DDQ DECYLAMINE-N,N-DIMETHYL-N-OXIDE × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；277 K；5mg/ml protein solution containing 40 mM TRIS pH 7.4, 120 mM NaCl, and 20 mM DDAO was mixed with equal volume of crystallant containing 13% PEG 3350, 200 mM MgCl2 and 20% glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.10 Å R-free 0.261
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 322–385	Fragment：Vps23C-terminal domain (322-385) Mutation：C344A	Vacuolar protein sorting-associated protein VPS28 × 1 （Q02767） DDQ DECYLAMINE-N,N-DIMETHYL-N-OXIDE × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；277 K；5mg/ml protein solution containing 40 mM TRIS pH 7.4, 120 mM NaCl, and 20 mM DDAO was mixed with equal volume of crystallant containing 13% PEG 3350, 200 mM MgCl2 and 20% glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.10 Å R-free 0.261

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 2F6M	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1UZX A complex of the Vps23 UEV with ubiquitin Deposited 2004-03-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–161（161 aa） Fragment：UEV DOMAIN, RESIDUES 1-161	Non-standard monomer：Yes (specific site not provided by mmCIF)	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；22% PEG 8000, 0.1M MES PH 6.5, 0.2M (NH4)2SO4	Resolution 1.85 Å R-free 0.274
2CAZ ESCRT-I core Deposited 2005-12-23	Different construct Different mutation/modification 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 305–385（81 aa） Fragment：RESIDUES 305-385	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；290 K；8-10% PEG 8000, 8-9% ETHYLENE GLYCOL, 0.1 M HEPES (PH 7.0- 8.0), 17 DEG C	Resolution 3.60 Å R-free 0.357
2CAZ ESCRT-I core Deposited 2005-12-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 305–385（81 aa） Fragment：RESIDUES 305-385	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；290 K；8-10% PEG 8000, 8-9% ETHYLENE GLYCOL, 0.1 M HEPES (PH 7.0- 8.0), 17 DEG C	Resolution 3.60 Å R-free 0.357
2F66 Structure of the ESCRT-I endosomal trafficking complex Deposited 2005-11-28	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 322–385（64 aa） Fragment：Vps23C-Terminal Domain (322-385)	Mutation：C344A	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；100mM trisodium citrate (pH 5.6), 900mM lithium sulfate, 500mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.256
2F66 Structure of the ESCRT-I endosomal trafficking complex Deposited 2005-11-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 322–385（64 aa） Fragment：Vps23C-Terminal Domain (322-385)	Mutation：C344A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；100mM trisodium citrate (pH 5.6), 900mM lithium sulfate, 500mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.256
2F66 Structure of the ESCRT-I endosomal trafficking complex Deposited 2005-11-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 322–385（64 aa） Fragment：Vps23C-Terminal Domain (322-385) Chain D 322–385（64 aa） Fragment：Vps23C-Terminal Domain (322-385)	Mutation：C344A Mutation：C344A	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；100mM trisodium citrate (pH 5.6), 900mM lithium sulfate, 500mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.256
2P22 Structure of the Yeast ESCRT-I Heterotetramer Core Deposited 2007-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 215–385（171 aa） Fragment：Vps23 (215-385)	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；294 K；Crystals were grown by mixing 2 microL of 4 mg/mL protein in 50 mM Tris (pH 7.4), 150 mM NaCl, 5 mM DTT with an equal volume of 100 mM citric acid (pH 4.0), 800 mM ammonium sulfate., VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.70 Å R-free 0.315
2P22 Structure of the Yeast ESCRT-I Heterotetramer Core Deposited 2007-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain A 215–385（171 aa） Fragment：Vps23 (215-385)	Not recorded	SO4 SULFATE ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；294 K；Crystals were grown by mixing 2 microL of 4 mg/mL protein in 50 mM Tris (pH 7.4), 150 mM NaCl, 5 mM DTT with an equal volume of 100 mM citric acid (pH 4.0), 800 mM ammonium sulfate., VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.70 Å R-free 0.315
2P22 Structure of the Yeast ESCRT-I Heterotetramer Core Deposited 2007-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 215–385（171 aa） Fragment：Vps23 (215-385)	Not recorded	SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；294 K；Crystals were grown by mixing 2 microL of 4 mg/mL protein in 50 mM Tris (pH 7.4), 150 mM NaCl, 5 mM DTT with an equal volume of 100 mM citric acid (pH 4.0), 800 mM ammonium sulfate., VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.70 Å R-free 0.315
2P22 Structure of the Yeast ESCRT-I Heterotetramer Core Deposited 2007-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 215–385（171 aa） Fragment：Vps23 (215-385)	Not recorded	SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；294 K；Crystals were grown by mixing 2 microL of 4 mg/mL protein in 50 mM Tris (pH 7.4), 150 mM NaCl, 5 mM DTT with an equal volume of 100 mM citric acid (pH 4.0), 800 mM ammonium sulfate., VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.70 Å R-free 0.315
2P22 Structure of the Yeast ESCRT-I Heterotetramer Core Deposited 2007-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 215–385（171 aa） Fragment：Vps23 (215-385)	Not recorded	SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；294 K；Crystals were grown by mixing 2 microL of 4 mg/mL protein in 50 mM Tris (pH 7.4), 150 mM NaCl, 5 mM DTT with an equal volume of 100 mM citric acid (pH 4.0), 800 mM ammonium sulfate., VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.70 Å R-free 0.315
2P22 Structure of the Yeast ESCRT-I Heterotetramer Core Deposited 2007-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 215–385（171 aa） Fragment：Vps23 (215-385)	Not recorded	SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；294 K；Crystals were grown by mixing 2 microL of 4 mg/mL protein in 50 mM Tris (pH 7.4), 150 mM NaCl, 5 mM DTT with an equal volume of 100 mM citric acid (pH 4.0), 800 mM ammonium sulfate., VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.70 Å R-free 0.315
3R3Q Crystal structure of the yeast Vps23 UEV domain Deposited 2011-03-16	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 1–160（160 aa） Fragment：N-terminal UEV domain (UNP residues 1-160)	Mutation：C133A	ZN ZINC ION × 9 CL CHLORIDE ION × 1 IMD IMIDAZOLE × 7 ACT ACETATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；288 K；0.2 M zinc acetate, 0.1 M imidazole, 25% 1,2-propanediol, 10% glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 1.45 Å R-free 0.184
3R42 Crystal structure of the yeast vps23 UEV domain in complex with a vps27 PSDP peptide Deposited 2011-03-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–160（160 aa） Fragment：N-terminal UEV domain (UNP residues 1-160)	Mutation：C133A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；288 K；0.2 M sodium phosphate monobasic, 20% PEG3350, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 1.87 Å R-free 0.203
3R42 Crystal structure of the yeast vps23 UEV domain in complex with a vps27 PSDP peptide Deposited 2011-03-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–160（160 aa） Fragment：N-terminal UEV domain (UNP residues 1-160)	Mutation：C133A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；288 K；0.2 M sodium phosphate monobasic, 20% PEG3350, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 1.87 Å R-free 0.203

6 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	STP22_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–65； UniProt 322–385 Author chain C； PDBConstruct 2–65； UniProt 322–385

Vacuolar protein sorting-associated protein VPS28

Saccharomyces cerevisiae

UniProt Q02767

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 B； UniProt 13–118	Fragment：Vps28N-terminal domain (13-118) Mutation：C101A	Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease × 1 （P25604） MG MAGNESIUM ION × 1 DDQ DECYLAMINE-N,N-DIMETHYL-N-OXIDE × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；277 K；5mg/ml protein solution containing 40 mM TRIS pH 7.4, 120 mM NaCl, and 20 mM DDAO was mixed with equal volume of crystallant containing 13% PEG 3350, 200 mM MgCl2 and 20% glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.10 Å R-free 0.261
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 13–118	Fragment：Vps28N-terminal domain (13-118) Mutation：C101A	Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease × 1 （P25604） DDQ DECYLAMINE-N,N-DIMETHYL-N-OXIDE × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；277 K；5mg/ml protein solution containing 40 mM TRIS pH 7.4, 120 mM NaCl, and 20 mM DDAO was mixed with equal volume of crystallant containing 13% PEG 3350, 200 mM MgCl2 and 20% glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.10 Å R-free 0.261

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 2F6M	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2CAZ ESCRT-I core Deposited 2005-12-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–147（147 aa） Fragment：RESIDUES 1-147	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；290 K；8-10% PEG 8000, 8-9% ETHYLENE GLYCOL, 0.1 M HEPES (PH 7.0- 8.0), 17 DEG C	Resolution 3.60 Å R-free 0.357
2CAZ ESCRT-I core Deposited 2005-12-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 1–147（147 aa） Fragment：RESIDUES 1-147	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；290 K；8-10% PEG 8000, 8-9% ETHYLENE GLYCOL, 0.1 M HEPES (PH 7.0- 8.0), 17 DEG C	Resolution 3.60 Å R-free 0.357
2F66 Structure of the ESCRT-I endosomal trafficking complex Deposited 2005-11-28	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 B 13–125（113 aa） Fragment：Vps28N-Terminal Domain (13-125)	Mutation：C101A	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；100mM trisodium citrate (pH 5.6), 900mM lithium sulfate, 500mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.256
2F66 Structure of the ESCRT-I endosomal trafficking complex Deposited 2005-11-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 13–125（113 aa） Fragment：Vps28N-Terminal Domain (13-125)	Mutation：C101A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；100mM trisodium citrate (pH 5.6), 900mM lithium sulfate, 500mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.256
2F66 Structure of the ESCRT-I endosomal trafficking complex Deposited 2005-11-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 13–125（113 aa） Fragment：Vps28N-Terminal Domain (13-125) Chain E 13–125（113 aa） Fragment：Vps28N-Terminal Domain (13-125)	Mutation：C101A Mutation：C101A	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；100mM trisodium citrate (pH 5.6), 900mM lithium sulfate, 500mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.256
2G3K Crystal structure of the C-terminal domain of Vps28 Deposited 2006-02-20	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 148–241（94 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, HANGING DROP；pH 4.6；293 K；1 M AS 100 mM sodium acetate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.05 Å R-free 0.273
2G3K Crystal structure of the C-terminal domain of Vps28 Deposited 2006-02-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 10 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 148–241（94 aa） Chain G 148–241（94 aa）	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；pH 4.6；293 K；1 M AS 100 mM sodium acetate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.05 Å R-free 0.273
2G3K Crystal structure of the C-terminal domain of Vps28 Deposited 2006-02-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 11 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 148–241（94 aa） Chain F 148–241（94 aa）	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；pH 4.6；293 K；1 M AS 100 mM sodium acetate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.05 Å R-free 0.273
2G3K Crystal structure of the C-terminal domain of Vps28 Deposited 2006-02-20	Different construct Different mutation/modification 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 148–241（94 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, HANGING DROP；pH 4.6；293 K；1 M AS 100 mM sodium acetate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.05 Å R-free 0.273
2G3K Crystal structure of the C-terminal domain of Vps28 Deposited 2006-02-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 148–241（94 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, HANGING DROP；pH 4.6；293 K；1 M AS 100 mM sodium acetate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.05 Å R-free 0.273
2G3K Crystal structure of the C-terminal domain of Vps28 Deposited 2006-02-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 148–241（94 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, HANGING DROP；pH 4.6；293 K；1 M AS 100 mM sodium acetate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.05 Å R-free 0.273
2G3K Crystal structure of the C-terminal domain of Vps28 Deposited 2006-02-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 148–241（94 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, HANGING DROP；pH 4.6；293 K；1 M AS 100 mM sodium acetate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.05 Å R-free 0.273
2G3K Crystal structure of the C-terminal domain of Vps28 Deposited 2006-02-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 148–241（94 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, HANGING DROP；pH 4.6；293 K；1 M AS 100 mM sodium acetate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.05 Å R-free 0.273
2G3K Crystal structure of the C-terminal domain of Vps28 Deposited 2006-02-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 148–241（94 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, HANGING DROP；pH 4.6；293 K；1 M AS 100 mM sodium acetate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.05 Å R-free 0.273
2G3K Crystal structure of the C-terminal domain of Vps28 Deposited 2006-02-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 148–241（94 aa） Chain B 148–241（94 aa）	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；pH 4.6；293 K；1 M AS 100 mM sodium acetate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.05 Å R-free 0.273
2G3K Crystal structure of the C-terminal domain of Vps28 Deposited 2006-02-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 9 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 148–241（94 aa） Chain B 148–241（94 aa） Chain F 148–241（94 aa）	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；pH 4.6；293 K；1 M AS 100 mM sodium acetate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.05 Å R-free 0.273
2J9U 2 Angstrom X-ray structure of the yeast ESCRT-I Vps28 C-terminus in complex with the NZF-N domain from ESCRT-II Deposited 2006-11-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 148–242（95 aa） Fragment：RESIDUES 148-242	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；20% ETHANOL, 0.1M KCL, pH 7.40	Resolution 2.00 Å R-free 0.260
2J9U 2 Angstrom X-ray structure of the yeast ESCRT-I Vps28 C-terminus in complex with the NZF-N domain from ESCRT-II Deposited 2006-11-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 148–242（95 aa） Fragment：RESIDUES 148-242	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；20% ETHANOL, 0.1M KCL, pH 7.40	Resolution 2.00 Å R-free 0.260
2J9V 2 Angstrom X-ray structure of the yeast ESCRT-I Vps28 C-terminus Deposited 2006-11-16	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 148–242（95 aa） Fragment：RESIDUES 148-242	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；4% PEG 400, 0.1M LITHIUM SULPHATE, 0.1M SODIUM CITRATE (PH5.6), pH 5.60	Resolution 2.00 Å R-free 0.255
2P22 Structure of the Yeast ESCRT-I Heterotetramer Core Deposited 2007-03-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–118（118 aa） Fragment：Vps28N-Terminal Domain (1-118)	Mutation：C101A	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；294 K；Crystals were grown by mixing 2 microL of 4 mg/mL protein in 50 mM Tris (pH 7.4), 150 mM NaCl, 5 mM DTT with an equal volume of 100 mM citric acid (pH 4.0), 800 mM ammonium sulfate., VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.70 Å R-free 0.315
2P22 Structure of the Yeast ESCRT-I Heterotetramer Core Deposited 2007-03-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain B 1–118（118 aa） Fragment：Vps28N-Terminal Domain (1-118)	Mutation：C101A	SO4 SULFATE ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；294 K；Crystals were grown by mixing 2 microL of 4 mg/mL protein in 50 mM Tris (pH 7.4), 150 mM NaCl, 5 mM DTT with an equal volume of 100 mM citric acid (pH 4.0), 800 mM ammonium sulfate., VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.70 Å R-free 0.315
2P22 Structure of the Yeast ESCRT-I Heterotetramer Core Deposited 2007-03-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 1–118（118 aa） Fragment：Vps28N-Terminal Domain (1-118)	Mutation：C101A	SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；294 K；Crystals were grown by mixing 2 microL of 4 mg/mL protein in 50 mM Tris (pH 7.4), 150 mM NaCl, 5 mM DTT with an equal volume of 100 mM citric acid (pH 4.0), 800 mM ammonium sulfate., VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.70 Å R-free 0.315
2P22 Structure of the Yeast ESCRT-I Heterotetramer Core Deposited 2007-03-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 1–118（118 aa） Fragment：Vps28N-Terminal Domain (1-118)	Mutation：C101A	SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；294 K；Crystals were grown by mixing 2 microL of 4 mg/mL protein in 50 mM Tris (pH 7.4), 150 mM NaCl, 5 mM DTT with an equal volume of 100 mM citric acid (pH 4.0), 800 mM ammonium sulfate., VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.70 Å R-free 0.315
2P22 Structure of the Yeast ESCRT-I Heterotetramer Core Deposited 2007-03-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 1–118（118 aa） Fragment：Vps28N-Terminal Domain (1-118)	Mutation：C101A	SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；294 K；Crystals were grown by mixing 2 microL of 4 mg/mL protein in 50 mM Tris (pH 7.4), 150 mM NaCl, 5 mM DTT with an equal volume of 100 mM citric acid (pH 4.0), 800 mM ammonium sulfate., VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.70 Å R-free 0.315
2P22 Structure of the Yeast ESCRT-I Heterotetramer Core Deposited 2007-03-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 1–118（118 aa） Fragment：Vps28N-Terminal Domain (1-118)	Mutation：C101A	SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；294 K；Crystals were grown by mixing 2 microL of 4 mg/mL protein in 50 mM Tris (pH 7.4), 150 mM NaCl, 5 mM DTT with an equal volume of 100 mM citric acid (pH 4.0), 800 mM ammonium sulfate., VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.70 Å R-free 0.315

6 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VPS28_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–109； UniProt 13–118 Author chain D； PDBConstruct 4–109； UniProt 13–118

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2f6m
Deposition date deposition_date	2005-11-29
Structure title title	Structure of a Vps23-C:Vps28-N subcomplex
Keywords keywords	;endosomes, trafficking complex, Vps23, Vps28, Vacuole Protein Sorting, ESCRT protein complexes, Endosomal Sorting Complex Required for Transport, ESCRT-I, Ubiquitin, TSG101, TRANSPORT PROTEIN ;; TRANSPORT 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	24.08 Å
Radius of gyration Rg (electron density) rg_electron	22.84 Å
Forward intensity I(0) i0	26098000.00
Molecular weight molecular_weight	40751.0 kDa
Excluded volume excluded_volume	51889 Å³
Envelope volume envelope_volume	66020 Å³
Hydration-shell volume shell_volume	23930 Å³
Envelope diameter envelope_diameter	80.1 Å
Shell Rg shell_rg	29.78 Å
Envelope Rg envelope_rg	22.96 Å
Shape Rg shape_rg	22.83 Å
Total Rg total_rg	23.82 Å
Total atoms total_atoms	2873
Residues n_residues	337
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	76.1 Å
Rg (real space) rg_real	23.98 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	2.6100e+07
I(0) uncertainty (real space) i0_real_error	3.8560e+05
Rg (reciprocal space) rg_reciprocal	24.00 Å
I(0) (reciprocal space) i0_reciprocal	26100000.0000
Solution quality estimate total_estimate	0.9059
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.9 Å
Skewness Skewness skewness	0.163
Kurtosis Kurtosis kurtosis	-0.543
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5715000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.981

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease
Molecular weight formula_weight	7550.7 kDa
Mutation mutation	C344A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	2913

MTDGLNQLYNLVAQDYALTDTIEALSRMLHRGTIPLDTFVKQGRELARQQFLVRWHIQRITSPLS

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	Vacuolar protein sorting-associated protein VPS28
Molecular weight formula_weight	12533.9 kDa
Mutation mutation	C101A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

GAMDISQLFHDEVPLFDNSITSKDKEVIETLSEIYSIVITLDHVEKAYLKDSIDDTQYTNTVDKLLKQFKVYLNSQNKEEINKHFQSIEAFADTYNITASNAITRLERG

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli BL21

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	DECYLAMINE-N,N-DIMETHYL-N-OXIDE
Molecular weight formula_weight	201.3 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	40

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7. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d2f6ma2
Class class	a — All alpha proteins
Fold Fold fold	a.2 — Long alpha-hairpin
Superfamily Superfamily superfamily	a.2.17 — Endosomal sorting complex assembly domain
Family Family family	a.2.17.1 — VPS23 C-terminal domain

Domain ID domain_id	d2f6ma3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2f6mb2
Class class	a — All alpha proteins
Fold Fold fold	a.2 — Long alpha-hairpin
Superfamily Superfamily superfamily	a.2.17 — Endosomal sorting complex assembly domain
Family Family family	a.2.17.2 — VPS28 N-terminal domain

Domain ID domain_id	d2f6mb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2f6mc2
Class class	a — All alpha proteins
Fold Fold fold	a.2 — Long alpha-hairpin
Superfamily Superfamily superfamily	a.2.17 — Endosomal sorting complex assembly domain
Family Family family	a.2.17.1 — VPS23 C-terminal domain

Domain ID domain_id	d2f6mc3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2f6md_
Class class	a — All alpha proteins
Fold Fold fold	a.2 — Long alpha-hairpin
Superfamily Superfamily superfamily	a.2.17 — Endosomal sorting complex assembly domain
Family Family family	a.2.17.2 — VPS28 N-terminal domain

CATH v4.4 (4 domains)

Domain ID domain_id	2f6mA00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	820 —

Domain ID domain_id	2f6mB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1440 — de novo design (two linked rop proteins)
Homologous superfamily homologous superfamily	200 — Vps28 N-terminal domain

Domain ID domain_id	2f6mC00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	820 —

Domain ID domain_id	2f6mD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1440 — de novo design (two linked rop proteins)
Homologous superfamily homologous superfamily	200 — Vps28 N-terminal domain

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8. Citations (1)

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Unit-cell length a length_a	61.239 Å
Unit-cell length b length_b	119.252 Å
Unit-cell length c length_c	125.391 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	I 21 21 21
Space-group number int_tables_number	24
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	19.510 Å
R factor r_factor	0.2417
R_work r_work	0.2407
R_free r_free	0.2610

fit	/app/data/saxs_computation/f6/2f6m/2f6m.fit
pddf	/app/data/pr_computation/f6/2f6m/2f6m.pr.out
profile	/app/data/saxs_computation/f6/2f6m/2f6m.dat

Structure of a Vps23-C:Vps28-N subcomplex

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

Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease

State in the Current Structure

Other States of the Same Protein in the Database

Vacuolar protein sorting-associated protein VPS28

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

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (7 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)