SAXSdb — 2j9u

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

VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 28

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 148–242	Fragment：RESIDUES 148-242	VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 36 × 1 （Q06696） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 148–242	Fragment：RESIDUES 148-242	VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 36 × 1 （Q06696） 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

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 2J9U	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 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 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 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 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 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 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
2F6M Structure of a Vps23-C:Vps28-N subcomplex Deposited 2005-11-29	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 B 13–118（106 aa） Fragment：Vps28N-terminal domain (13-118)	Mutation：C101A	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
2F6M Structure of a Vps23-C:Vps28-N subcomplex Deposited 2005-11-29	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 D 13–118（106 aa） Fragment：Vps28N-terminal domain (13-118)	Mutation：C101A	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
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
2J9V 2 Angstrom X-ray structure of the yeast ESCRT-I Vps28 C-terminus Deposited 2006-11-16	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 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 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 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 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 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 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 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 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 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 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 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 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	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–96； UniProt 148–242 Author chain C； PDBConstruct 2–96； UniProt 148–242

VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 36

SACCHAROMYCES CEREVISIAE

UniProt Q06696

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 110–171	Fragment：RESIDUES 110-176	VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 28 × 1 （Q02767） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 110–171	Fragment：RESIDUES 110-176	VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 28 × 1 （Q02767） 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

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 2J9U	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1U5T Structure of the ESCRT-II endosomal trafficking complex Deposited 2004-07-28	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 396–564（169 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；298 K；Naacetate, hepes, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 3.60 Å R-free 0.288
1W7P The crystal structure of endosomal complex ESCRT-II (VPS22/VPS25/VPS36) Deposited 2004-09-07	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 D 1–566（566 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；3.1% PEG35000, 0.1 M TRIS ACETATE PH 8.5, 1.36 M SODIUM FORMIATE, 19% GLYCEROL	Resolution 3.60 Å R-free 0.330
2CAY Vps36 N-terminal PH domain 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 homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–99（99 aa） Fragment：PH DOMAIN, RESIDUES 1-99 AND 252-289 Chain A 252–289（38 aa） Fragment：PH DOMAIN, RESIDUES 1-99 AND 252-289 Chain B 1–99（99 aa） Fragment：PH DOMAIN, RESIDUES 1-99 AND 252-289 Chain B 252–289（38 aa） Fragment：PH DOMAIN, RESIDUES 1-99 AND 252-289	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 9.5；1M AMSO4, 0.2M NACL, 6% GLYCEROL 0.1M TRIS PH 9.5	Resolution 1.90 Å R-free 0.228

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VPS36_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 10–71； UniProt 110–171 Author chain D； PDBConstruct 10–71； UniProt 110–171

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	2j9u
Deposition date deposition_date	2006-11-16
Structure title title	2 Angstrom X-ray structure of the yeast ESCRT-I Vps28 C-terminus in complex with the NZF-N domain from ESCRT-II
Keywords keywords	ZINC-FINGER, METAL-BINDING, 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	22.76 Å
Radius of gyration Rg (electron density) rg_electron	21.71 Å
Forward intensity I(0) i0	17124900.00
Molecular weight molecular_weight	32060.0 kDa
Excluded volume excluded_volume	40481 Å³
Envelope volume envelope_volume	50316 Å³
Hydration-shell volume shell_volume	20086 Å³
Envelope diameter envelope_diameter	74.3 Å
Shell Rg shell_rg	27.59 Å
Envelope Rg envelope_rg	21.75 Å
Shape Rg shape_rg	21.70 Å
Total Rg total_rg	22.58 Å
Total atoms total_atoms	2244
Residues n_residues	282
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	73.4 Å
Rg (real space) rg_real	22.74 Å
Rg uncertainty (real space) rg_real_error	0.51 Å
I(0) (real space) i0_real	1.7120e+07
I(0) uncertainty (real space) i0_real_error	2.6130e+05
Rg (reciprocal space) rg_reciprocal	22.75 Å
I(0) (reciprocal space) i0_reciprocal	17120000.0000
Solution quality estimate total_estimate	0.9068
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.6 Å
Skewness Skewness skewness	0.284
Kurtosis Kurtosis kurtosis	-0.460
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3023000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.992

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 28
Molecular weight formula_weight	11151.8 kDa
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	2295

MFNAKYVAEATGNFITVMDALKLNYNAKDQLHPLLAELLISINRVTRDDFENRSKLIDWIVRINKLSIGDTLTETQIRELLFDLELAYKSFYALLD

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(DE3)

Entity 2 Entity 2 polymer

Description description	VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 36
Molecular weight formula_weight	8315.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MAHHHHHHMASADVVSTWVCPICMVSNETQGEFTKDTLPTPICINCGVPADYELTKSSINCSNAIDPNANPRNQFG

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(DE3)

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	51

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2j9ua_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.28 — VPS28 C-terminal domain-like
Family Family family	a.24.28.1 — VPS28 C-terminal domain-like

Domain ID domain_id	d2j9ub1
Class class	g — Small proteins
Fold Fold fold	g.41 — Rubredoxin-like
Superfamily Superfamily superfamily	g.41.11 — Ran binding protein zinc finger-like
Family Family family	g.41.11.1 — Ran binding protein zinc finger-like

Domain ID domain_id	d2j9uc_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.28 — VPS28 C-terminal domain-like
Family Family family	a.24.28.1 — VPS28 C-terminal domain-like

Domain ID domain_id	d2j9ud_
Class class	g — Small proteins
Fold Fold fold	g.41 — Rubredoxin-like
Superfamily Superfamily superfamily	g.41.11 — Ran binding protein zinc finger-like
Family Family family	g.41.11.1 — Ran binding protein zinc finger-like

CATH v4.4 (4 domains)

Domain ID domain_id	2j9uA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1130 — Vps28 C-terminal domain

Domain ID domain_id	2j9uB00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	380 — Zn-finger domain of Sec23/24

Domain ID domain_id	2j9uC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1130 — Vps28 C-terminal domain

Domain ID domain_id	2j9uD00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	380 — Zn-finger domain of Sec23/24

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8. Citations (1)

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Unit-cell length a length_a	66.645 Å
Unit-cell length b length_b	99.961 Å
Unit-cell length c length_c	115.619 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	32.030 Å
R factor r_factor	0.2240
R_work r_work	0.2230
R_free r_free	0.2600

fit	/app/data/saxs_computation/j9/2j9u/2j9u.fit
pddf	/app/data/pr_computation/j9/2j9u/2j9u.pr.out
profile	/app/data/saxs_computation/j9/2j9u/2j9u.dat

2 Angstrom X-ray structure of the yeast ESCRT-I Vps28 C-terminus in complex with the NZF-N domain from ESCRT-II

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

VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 28

State in the Current Structure

Other States of the Same Protein in the Database

VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 36

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 (4)

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 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)