SAXSdb — 1q0w

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

Vacuolar protein sorting-associated protein VPS27

OrganismNot specified

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 256–279	Fragment：Amino-terminal UIM, residues 256 to 278	Ubiquitin × 1 （P61864）	SOLUTION NMR NMR measurement conditions：pH 6；298 K；Ionic strength (raw mmCIF value) 20 mM sodium phosphate, pH 6.0, 0.2% NaN3；Pressure 1 NMR sample composition：1 mM U-15N,13C Ubiquitin + 1 mM Vps27 amino-terminal UIM \| 90% H2O/10% D2O NMR sample composition：1 mM U-15N,13C Ubiquitin + 1 mM Vps27 amino-terminal UIM \| 100% D2O	Resolution not provided

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 1Q0W	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1O06 Crystal structure of the Vps27p Ubiquitin Interacting Motif (UIM) Deposited 2003-02-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 301–320（20 aa） Fragment：Residues 301-320	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.08M sodium cacodylate, 0.16M zinc acetate, 10.4% PEG-8000, 20% glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K	Resolution 1.45 Å R-free 0.224
1O06 Crystal structure of the Vps27p Ubiquitin Interacting Motif (UIM) Deposited 2003-02-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 301–320（20 aa） Fragment：Residues 301-320	Not recorded	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.08M sodium cacodylate, 0.16M zinc acetate, 10.4% PEG-8000, 20% glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K	Resolution 1.45 Å R-free 0.224
1O06 Crystal structure of the Vps27p Ubiquitin Interacting Motif (UIM) Deposited 2003-02-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 301–320（20 aa） Fragment：Residues 301-320	Not recorded	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.08M sodium cacodylate, 0.16M zinc acetate, 10.4% PEG-8000, 20% glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K	Resolution 1.45 Å R-free 0.224
1Q0V Solution Structure of Tandem UIMs of Vps27 Deposited 2003-07-17	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 249–329（81 aa） Fragment：Tandem UIM	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 20 mM sodium phosphate, pH 6.0, 0.2% NaN3；Pressure 1 NMR sample composition 1 mM Vps27 UIM U-15N \| 90% H2O/10% D2O NMR sample composition 1 mM Vps27 UIM U-15N,U-13C \| 100% D2O	Resolution not provided
1VFY PHOSPHATIDYLINOSITOL-3-PHOSPHATE BINDING FYVE DOMAIN OF VPS27P PROTEIN FROM SACCHAROMYCES CEREVISIAE Deposited 1999-04-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 163–230（68 aa） Fragment：163-229, FYVE DOMAIN	Mutation：6 RESIDUES (EFIVTD) INSERTED AT C-TERMINUS	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；0.2 M AMMONIUM ACETATE, 0.1 M SODIUM ACETATE PH 4.6, 15% PEG 4000, pH 5.6	Resolution 1.15 Å R-free 0.181
2KDI Solution structure of a Ubiquitin/UIM fusion protein Deposited 2009-01-09	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 258–277（20 aa） Fragment：UIM 1	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；300 K；Ionic strength (raw mmCIF value) 0.103；Pressure ambient NMR sample composition 1.24 mM [U-100% 13C; U-100% 15N] Ubiquitin/UIM fusion protein-1, 3 mM sodium azide-2, 20 mM sodium phosphate-3, 50 mM sodium chloride-4, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1.1 mM [U-100% 15N] Ubiquitin/UIM fusion protein-5, 3 mM sodium azide-6, 20 mM sodium phosphate-7, 50 mM sodium chloride-8, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.5 mM [U-100% 15N] Ubiquitin/UIM fusion protein-9, 3 mM sodium azide-10, 20 mM sodium phosphate-11, 50 mM sodium chloride-12, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2PJW The Vps27/Hse1 complex is a GAT domain-based scaffold for ubiquitin-dependent sorting Deposited 2007-04-16	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain V 348–438（91 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 8.85；288 K；1.1-1.4 M ammonium sulfate, 0.1 M Tris-HCl. Then micro-seeding into 1.25 M ammonium sulfate, 0.1 M Tris-HCl, pH 8.85, VAPOR DIFFUSION, SITTING DROP, temperature 288K	Resolution 3.01 Å R-free 0.285
2PJW The Vps27/Hse1 complex is a GAT domain-based scaffold for ubiquitin-dependent sorting Deposited 2007-04-16	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain V 348–438（91 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 8.85；288 K；1.1-1.4 M ammonium sulfate, 0.1 M Tris-HCl. Then micro-seeding into 1.25 M ammonium sulfate, 0.1 M Tris-HCl, pH 8.85, VAPOR DIFFUSION, SITTING DROP, temperature 288K	Resolution 3.01 Å R-free 0.285
3R42 Crystal structure of the yeast vps23 UEV domain in complex with a vps27 PSDP peptide Deposited 2011-03-17	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 445–453（9 aa） Fragment：PSDP peptide (UNP residues 445-453)	Not recorded	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 oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 445–453（9 aa） Fragment：PSDP peptide (UNP residues 445-453)	Not recorded	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
6NJG Ubiquitin Variant in Complex with Ubiquitin Interacting Motif Deposited 2019-01-03	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 256–278（23 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.1 M DL-Malic acid	Resolution 2.35 Å R-free 0.244

7 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VPS27_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–24； UniProt 256–279

Ubiquitin

Saccharomyces cerevisiae

UniProt P61864

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 1–76	Not recorded	Vacuolar protein sorting-associated protein VPS27 × 1 （P40343）	SOLUTION NMR NMR measurement conditions：pH 6；298 K；Ionic strength (raw mmCIF value) 20 mM sodium phosphate, pH 6.0, 0.2% NaN3；Pressure 1 NMR sample composition：1 mM U-15N,13C Ubiquitin + 1 mM Vps27 amino-terminal UIM \| 90% H2O/10% D2O NMR sample composition：1 mM U-15N,13C Ubiquitin + 1 mM Vps27 amino-terminal UIM \| 100% D2O	Resolution not provided

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 1Q0W	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1OTR Solution Structure of a CUE-Ubiquitin Complex Deposited 2003-03-22	Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 20 mM sodium phosphate, pH 7.0, 0.2% NaN3；Pressure 1 NMR sample composition 1 mM U-15N,13C Cue2 + 1 mM Ubiquitin; 20 mM sodium phosphate buffer, pH 7.0, 0.2% NaN3 \| 90% H2O/10% D2O NMR sample composition 1 mM U-15N,13C Cue2 + 1 mM Ubiquitin; 20 mM sodium phosphate buffer, pH 7.0, 0.2% NaN3 \| 99.996% D2O NMR sample composition 1 mM Cue2 + 1 mM U-15N,13C Ubiquitin; 20 mM sodium phosphate buffer, pH 7.0, 0.2% NaN3 \| 90% H2O/10% D2O NMR sample composition 1 mM Cue2 + 1 mM U-15N,13C Ubiquitin; 20 mM sodium phosphate buffer, pH 7.0, 0.2% NaN3 \| 99.996% D2O	Resolution not provided
1WR1 The complex structure of Dsk2p UBA with ubiquitin Deposited 2004-10-08	Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–76（76 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 20mM potassium phosphate, 5mM potassium chloride NMR sample composition U-15N, 13C ubiquitin + DSK2-UBA complex (0.9mM) \| 20mM Phosphate buffer (pH 6.8); 5mM potassium chloride; 1mM EDTA; 5% D2O NMR sample composition U-15N, 13C DSK2-UBA + ubiquitin complex (1.0mM) \| 20mM Phosphate buffer (pH 6.8); 5mM potassium chloride; 1mM EDTA; 5% D2O	Resolution not provided
1ZGU Solution structure of the human Mms2-Ubiquitin complex Deposited 2005-04-22	Different mutation/modification Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Mutation：K48R	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；293 K；Ionic strength (raw mmCIF value) 150 mM NaCl；Pressure 1 NMR measurement conditions pH 7.5；303 K；Ionic strength (raw mmCIF value) 150 mM NaCl；Pressure 1 NMR sample composition [U-15N; U-10% 13C]-hMms2 + Ubiquitin (1:4 ratio) 90% H20 : 10% D20 \| 90% H20 : 10% D20 NMR sample composition [U-13C; U-15N]-Ubiquitin + hMms2 (4:1 ratio) 90% H20 : 10% D20 \| 90% H20 : 10% D20 NMR sample composition [U-13C; U-15N]-hMms2 + Ubiquitin (1:4 ratio) 90% H20 : 10% D20 \| 90% H20 : 10% D20	Resolution not provided
1ZW7 Elimination of the C-cap in Ubiquitin Structure, Dynamics and Thermodynamic Consequences Deposited 2005-06-03	Different mutation/modification Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–76（76 aa）	Mutation：R42E, E34P	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；298 K；Ionic strength (raw mmCIF value) 30 mM actate；Pressure Ambient NMR sample composition 1-2 mM of appropriately labeled mutant ubiquitin \| 30 mM acetate buffer, pH 5.0	Resolution not provided
2G3Q Solution Structure of Ede1 UBA-ubiquitin complex Deposited 2006-02-20	Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 20mM Sodium Phosphate；Pressure 1 NMR sample composition 1mM 15N,13C-labeled Ede1 UBA; 1mM Ubiquitin; 20mM phosphate buffer (pH 6.0), 2mM DTT, 0.2% NaN3, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1mM 15N,13C-labeled Ede1 UBA; 1mM Ubiquitin; 20mM phosphate buffer (pH 6.0), 2mM DTT, 0.2% NaN3, 100% D2O \| 100% D2O NMR sample composition 1mM Ede1 UBA; 1mM 15N,13C-labeled Ubiquitin; 20mM phosphate buffer (pH 6.0), 2mM DTT, 0.2% NaN3, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1mM Ede1 UBA; 1mM 15N,13C-labeled Ubiquitin; 20mM phosphate buffer (pH 6.0), 2mM DTT, 0.2% NaN3, 100% D2O \| 100% D2O	Resolution not provided
2JT4 Solution Structure of the Sla1 SH3-3-Ubiquitin Complex Deposited 2007-07-18	Different construct Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa） Fragment：SH3 domain sequence database residues 350-420	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；318 K；Ionic strength (raw mmCIF value) 20；Pressure ambient NMR sample composition 0.9 mM [U-98% 13C; U-98% 15N] SH3, 0.9 mM ubiquitin, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.9 mM [U-98% 13C; U-98% 15N] ubiquitin, 0.9 mM SH3, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.9 mM [U-98% 13C; U-98% 15N] SH3, 0.9 mM ubiquitin, 100% D2O \| 100% D2O NMR sample composition 0.9 mM [U-98% 13C; U-98% 15N] ubiquitin, 0.9 mM SH3, 100% D2O \| 100% D2O	Resolution not provided
2JWZ Mutations in the hydrophobic core of ubiquitin differentially affect its recognition by receptor proteins Deposited 2007-10-31	Different mutation/modification Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–76（76 aa）	Mutation：L69S	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；296 K；Ionic strength (raw mmCIF value) 20 mM；Pressure AMBIENT NMR sample composition 2 mM [U-100% 15N] L69S UBIQUITIN, 2 mM L69S UBIQUITIN, 93% H2O/7% D2O \| 93% H2O/7% D2O	Resolution not provided
2L00 Solution structure of the non-covalent complex of the ZNF216 A20 domain with ubiquitin Deposited 2010-06-29	Different construct Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa） Fragment：ubiquitin core domain	Not recorded	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 4 mM ZNF216-A20-1, 50 uM Zinc-2, 0.1 mM DSS-3, 5 mM TRIS-4, 50 mM sodium chloride-5, 1 mM [U-100% 15N] ubiquitin-6, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1.0 mM [U-100% 15N] ZNF216-A20-7, 50 uM Zinc-8, 4 mM MTSL-9, 5 mM TRIS-10, 50 mM sodium chloride-11, 4 mM ubiquitin-12, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] ZNF216-A20-13, 50 uM Zinc-14, 0.1 mM DSS-15, 5 mM TRIS-16, 50 mM sodium chloride-17, 2 mM ubiquitin-18, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1.0 mM [U-100% 15N] ZNF216-A20-19, 50 uM Zinc-20, 0.1 mM DSS-21, 5 mM TRIS-22, 50 mM sodium chloride-23, 5 % Polyacrylamide gel-24, 4 mM ubiquitin-25, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 4 mM ZNF216-A20-26, 50 uM Zinc-27, 0.1 mM DSS-28, 5 mM TRIS-29, 50 mM sodium chloride-30, 5 % Polyacrylamide gel-31, 1 mM [U-100% 15N] ubiquitin-32, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 2 mM ZNF216-A20-33, 50 uM Zinc-34, 0.1 mM DSS-35, 5 mM TRIS-36, 50 mM sodium chloride-37, 1 mM [U-100% 13C; U-100% 15N] ubiquitin-38, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 15N] ZNF216-A20-39, 50 uM Zinc-40, 0.1 mM DSS-41, 5 mM TRIS-42, 50 mM sodium chloride-43, 4 mM ubiquitin-44, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3CMM Crystal Structure of the Uba1-Ubiquitin Complex Deposited 2008-03-23	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Not recorded	PRO PROLINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；298 K；L-proline, PEG 5000 MME, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.247
3CMM Crystal Structure of the Uba1-Ubiquitin Complex Deposited 2008-03-23	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–76（76 aa）	Not recorded	PRO PROLINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；298 K；L-proline, PEG 5000 MME, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.247
3L0W Structure of split monoubiquitinated PCNA with ubiquitin in position two Deposited 2009-12-10	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa） Fragment：ubi-C fragment	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；291 K；2.04 M ammonium sulfate, 0.1 M sodium citrate, 3% ethanol, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.80 Å R-free 0.314
3L10 Structure of split monoubiquitinated PCNA with ubiquitin in position one Deposited 2009-12-10	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa） Fragment：Ubi-C fragment	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；291 K；2.04M ammonium sulfate, 0.1M sodium citrate, 3% ethanol, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.80 Å R-free 0.314

11 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UBIQ_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–76； UniProt 1–76

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	1q0w
Deposition date deposition_date	2003-07-17
Structure title title	Solution structure of Vps27 amino-terminal UIM-ubiquitin complex
Keywords keywords	PROTEIN-PROTEIN COMPLEX, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	14.11 Å
Radius of gyration Rg (electron density) rg_electron	13.49 Å
Forward intensity I(0) i0	732636000.00
Molecular weight molecular_weight	227480.0 kDa
Excluded volume excluded_volume	284950 Å³
Envelope volume envelope_volume	36942 Å³
Hydration-shell volume shell_volume	17915 Å³
Envelope diameter envelope_diameter	62.6 Å
Shell Rg shell_rg	23.66 Å
Envelope Rg envelope_rg	17.47 Å
Shape Rg shape_rg	13.49 Å
Total Rg total_rg	13.75 Å
Total atoms total_atoms	32420
Residues n_residues	2000
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	55.5 Å
Rg (real space) rg_real	14.04 Å
Rg uncertainty (real space) rg_real_error	0.51 Å
I(0) (real space) i0_real	7.3260e+08
I(0) uncertainty (real space) i0_real_error	9.2800e+06
Rg (reciprocal space) rg_reciprocal	14.04 Å
I(0) (reciprocal space) i0_reciprocal	732600000.0000
Solution quality estimate total_estimate	0.7819
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	17.6 Å
Skewness Skewness skewness	0.261
Kurtosis Kurtosis kurtosis	-0.094
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	912800.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.435; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.858; Smooth: 0.998

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1q0wa_
Class class	j — Peptides
Fold Fold fold	j.105 — Ubiquitin interacting motif (UIM)
Superfamily Superfamily superfamily	j.105.1 — Ubiquitin interacting motif (UIM)
Family Family family	j.105.1.1 — Ubiquitin interacting motif (UIM)

Domain ID domain_id	d1q0wb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

CATH v4.4 (1 domains)

Domain ID domain_id	1q0wB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Description description	Vacuolar protein sorting-associated protein VPS27
Molecular weight formula_weight	2824.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	32420

Description description	Ubiquitin
Molecular weight formula_weight	8568.8 kDa
Source method src_method	man
Copy count entity_count	1

Solution structure of Vps27 amino-terminal UIM-ubiquitin complex

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

Vacuolar protein sorting-associated protein VPS27

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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)

fit	/app/data/saxs_computation/q0/1q0w/1q0w.fit
pddf	/app/data/pr_computation/q0/1q0w/1q0w.pr.out
profile	/app/data/saxs_computation/q0/1q0w/1q0w.dat