6och

Crystal structure of VASH1-SVBP complex bound with parthenolide

Method: X-RAY DIFFRACTION D_max: 97.1 Å Quality: GOOD

▼

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

Tubulinyl-Tyr carboxypeptidase 1

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 61–302	Not recorded	Small vasohibin-binding protein × 1 （Q8N300） M4Y parthenolide × 1 GOL GLYCEROL × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M ammonium sulfate, 0.1 M Bis-tris, pH 5.5, and 25 % (w/v) PEG 3350	Resolution 2.00 Å R-free 0.229
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 61–302	Not recorded	Small vasohibin-binding protein × 1 （Q8N300） M4Y parthenolide × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M ammonium sulfate, 0.1 M Bis-tris, pH 5.5, and 25 % (w/v) PEG 3350	Resolution 2.00 Å R-free 0.229

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 6OCH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6J4U Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications Deposited 2019-01-10	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 57–307（251 aa）	Mutation：E71S/A72H/K79M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5；293 K；by introducing three mutations E71S/A72H/K79M into V1c allowed us to solve the V1c-SVBP to high resolution. Well diffracting crystals of the mutant V1c-SVBP complex were obtained in 1.0 M lithium chloride, 0.1 M citric acid, pH 5.0, 20% PEG 6000.	Resolution 2.00 Å R-free 0.204
6J7B Crystal structure of VASH1-SVBP in complex with epoY Deposited 2019-01-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 57–306（250 aa）	Not recorded	BJL N-[(3R)-4-ethoxy-3-hydroxy-4-oxobutanoyl]-L-tyrosine × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6；293 K；20%PEG6000, 1M lithium chloride, 0.1M MES pH6.0	Resolution 1.62 Å R-free 0.197
6J8F Crystal structure of SVBP-VASH1 with peptide mimic the C-terminal of alpha-tubulin Deposited 2019-01-18	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 70–306（237 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M Na citrate tribasic dihydrate pH 5.0, 18% PEG 20000	Resolution 2.28 Å R-free 0.237
6J8N Crystal structure of SVBP-VASH1 complex, mutation C169A of VASH1 Deposited 2019-01-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 70–306（237 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；6% v/v Tacsimate pH6.0, 0.1M MES monohydrate pH 6.0, 25% PEG 4000	Resolution 1.95 Å R-free 0.210
6J8N Crystal structure of SVBP-VASH1 complex, mutation C169A of VASH1 Deposited 2019-01-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 70–306（237 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；6% v/v Tacsimate pH6.0, 0.1M MES monohydrate pH 6.0, 25% PEG 4000	Resolution 1.95 Å R-free 0.210
6J8O Structure of a hypothetical protease Deposited 2019-01-20	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 70–306（237 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M BIS-TRIS pH 6.5, 16% polyethylene glycol 10000	Resolution 1.85 Å R-free 0.195
6J91 Structure of a hypothetical protease Deposited 2019-01-21	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 70–306（237 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；291 K；0.1M Na citrate tribasic dihydrate pH 5.5, 16% PEG 8000, 0.01M Cadmium chloride hydrate	Resolution 3.50 Å R-free 0.258
6J9H Crystal structure of SVBP-VASH1 complex Deposited 2019-01-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 70–306（237 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M Na citrate tribasic dihydrate pH 5.5, 16% PEG 8000, 0.01M Cadmium chloride hydrate	Resolution 2.31 Å R-free 0.271
6J9H Crystal structure of SVBP-VASH1 complex Deposited 2019-01-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 70–306（237 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M Na citrate tribasic dihydrate pH 5.5, 16% PEG 8000, 0.01M Cadmium chloride hydrate	Resolution 2.31 Å R-free 0.271
6K81 Crystal structure of human VASH1-SVBP complex Deposited 2019-06-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–365（365 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；Calcium acetate, PEG 3000	Resolution 2.28 Å R-free 0.242
6LPG human VASH1-SVBP complex Deposited 2020-01-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 56–310（255 aa）	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.16 M ammonium sulfate, 0.08 M Sodium acetate pH4.6, 20%(w/v) PEG4000, 20%(v/v) glycerol	Resolution 2.30 Å R-free 0.236
6NVQ Crystal structure of the VASH1-SVBP complex Deposited 2019-02-05	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 C 1–315（315 aa）	Mutation：C169A	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；293 K；19% PEG 3000, 0.1M Tris-HCl, 0.2M calcium chloride	Resolution 2.10 Å R-free 0.214
6OCF The crystal structure of VASH1-SVBP complex Deposited 2019-03-23	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 58–305（248 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293.15 K；0.1 M sodium citrate tribasic dihydrate, pH 5.0, and 18% (w/v) PEG20000	Resolution 2.10 Å R-free 0.222
6OCG Crystal structure of VASH1-SVBP complex bound with EpoY Deposited 2019-03-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 59–305（247 aa）	Not recorded	CL CHLORIDE ION × 1 GOL GLYCEROL × 1 BJL N-[(3R)-4-ethoxy-3-hydroxy-4-oxobutanoyl]-L-tyrosine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293.15 K；5% (v/v) TacsimateTM, 0.1 M HEPES, pH 7.0, and 10% (w/v) polyethylene glycol monomethyl ether 5,000	Resolution 1.83 Å R-free 0.219
6WSL Cryo-EM structure of VASH1-SVBP bound to microtubules Deposited 2020-05-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain C 52–310（259 aa） Chain G 52–310（259 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å

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

View Construct and Data Evidence

UniProt name	VASH1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–242； UniProt 61–302 Author chain C； PDBConstruct 1–242； UniProt 61–302

Small vasohibin-binding protein

Homo sapiens

UniProt Q8N300

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 25–52	Not recorded	Tubulinyl-Tyr carboxypeptidase 1 × 1 （Q7L8A9） M4Y parthenolide × 1 GOL GLYCEROL × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M ammonium sulfate, 0.1 M Bis-tris, pH 5.5, and 25 % (w/v) PEG 3350	Resolution 2.00 Å R-free 0.229
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 25–52	Not recorded	Tubulinyl-Tyr carboxypeptidase 1 × 1 （Q7L8A9） M4Y parthenolide × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M ammonium sulfate, 0.1 M Bis-tris, pH 5.5, and 25 % (w/v) PEG 3350	Resolution 2.00 Å R-free 0.229

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6OCH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6J4O Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications Deposited 2019-01-10	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 1–66（66 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 5 PO4 PHOSPHATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.2；293 K；1.6 M sodium/potassium phosphate, pH 8.2	Resolution 2.30 Å R-free 0.224
6J4P Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications Deposited 2019-01-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–66（66 aa）	Not recorded	BJL N-[(3R)-4-ethoxy-3-hydroxy-4-oxobutanoyl]-L-tyrosine × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；293 K；V2c-SVBP was mixed with the inhibitor epoY at a mole ratio of 1:5 and incubated on ice for 30 min. Then, the resulting co-complex of V2c-SVBP-epoY was crystallized in 1.0 M lithium chloride, 0.1 M HEPES, pH 7.0, 20% PEG 6000.	Resolution 1.60 Å R-free 0.188
6J4Q Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications Deposited 2019-01-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–66（66 aa）	Not recorded	TQ8 N-[(2S)-4-chloro-3-oxo-1-phenyl-butan-2-yl]-4-methyl-benzenesulfonamide × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；293 K；V2c-SVBP was mixed with the inhibitor TPCK at a mole ratio of 1:5 and incubated on ice for 30 min. Then, the resulting co-complex of V2c-SVBP-TPCK was crystallized in 1.0 M sodium malonate, pH 7.0.	Resolution 2.70 Å R-free 0.247
6J4Q Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications Deposited 2019-01-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–66（66 aa）	Not recorded	TQ8 N-[(2S)-4-chloro-3-oxo-1-phenyl-butan-2-yl]-4-methyl-benzenesulfonamide × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；293 K；V2c-SVBP was mixed with the inhibitor TPCK at a mole ratio of 1:5 and incubated on ice for 30 min. Then, the resulting co-complex of V2c-SVBP-TPCK was crystallized in 1.0 M sodium malonate, pH 7.0.	Resolution 2.70 Å R-free 0.247
6J4Q Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications Deposited 2019-01-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 1–66（66 aa）	Not recorded	TQ8 N-[(2S)-4-chloro-3-oxo-1-phenyl-butan-2-yl]-4-methyl-benzenesulfonamide × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；293 K；V2c-SVBP was mixed with the inhibitor TPCK at a mole ratio of 1:5 and incubated on ice for 30 min. Then, the resulting co-complex of V2c-SVBP-TPCK was crystallized in 1.0 M sodium malonate, pH 7.0.	Resolution 2.70 Å R-free 0.247
6J4Q Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications Deposited 2019-01-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 1–66（66 aa）	Not recorded	TQ8 N-[(2S)-4-chloro-3-oxo-1-phenyl-butan-2-yl]-4-methyl-benzenesulfonamide × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；293 K；V2c-SVBP was mixed with the inhibitor TPCK at a mole ratio of 1:5 and incubated on ice for 30 min. Then, the resulting co-complex of V2c-SVBP-TPCK was crystallized in 1.0 M sodium malonate, pH 7.0.	Resolution 2.70 Å R-free 0.247
6J4S Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications Deposited 2019-01-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–66（66 aa）	Not recorded	GOL GLYCEROL × 3 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.8；293 K；full-length V2-SVBP complex at a concentration of 15 mg/mL was crystallized in 1.8 M sodium/potassium phosphate, pH 6.8	Resolution 2.80 Å R-free 0.227
6J4U Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications Deposited 2019-01-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–66（66 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5；293 K；by introducing three mutations E71S/A72H/K79M into V1c allowed us to solve the V1c-SVBP to high resolution. Well diffracting crystals of the mutant V1c-SVBP complex were obtained in 1.0 M lithium chloride, 0.1 M citric acid, pH 5.0, 20% PEG 6000.	Resolution 2.00 Å R-free 0.204
6J4V Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications Deposited 2019-01-10	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 1–66（66 aa）	Mutation：C58S	PO4 PHOSPHATE ION × 2 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.2；293 K；For crystallization of V2c-SVBP C58S in complex with the maTail peptide the components were mixed in a 1:3 molar ratio and incubated at room temperature for 24 h before setting up crystallization trials. The resulting V2c-SVBP S58C-maTail complex was crystallized in 1.4 M sodium/potassium phosphate, pH 8.2.	Resolution 2.10 Å R-free 0.200
6J7B Crystal structure of VASH1-SVBP in complex with epoY Deposited 2019-01-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–52（52 aa）	Not recorded	BJL N-[(3R)-4-ethoxy-3-hydroxy-4-oxobutanoyl]-L-tyrosine × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6；293 K；20%PEG6000, 1M lithium chloride, 0.1M MES pH6.0	Resolution 1.62 Å R-free 0.197
6J8F Crystal structure of SVBP-VASH1 with peptide mimic the C-terminal of alpha-tubulin Deposited 2019-01-18	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 3–48（46 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M Na citrate tribasic dihydrate pH 5.0, 18% PEG 20000	Resolution 2.28 Å R-free 0.237
6J8N Crystal structure of SVBP-VASH1 complex, mutation C169A of VASH1 Deposited 2019-01-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–66（66 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；6% v/v Tacsimate pH6.0, 0.1M MES monohydrate pH 6.0, 25% PEG 4000	Resolution 1.95 Å R-free 0.210
6J8N Crystal structure of SVBP-VASH1 complex, mutation C169A of VASH1 Deposited 2019-01-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–66（66 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；6% v/v Tacsimate pH6.0, 0.1M MES monohydrate pH 6.0, 25% PEG 4000	Resolution 1.95 Å R-free 0.210
6J8O Structure of a hypothetical protease Deposited 2019-01-20	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 3–49（47 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M BIS-TRIS pH 6.5, 16% polyethylene glycol 10000	Resolution 1.85 Å R-free 0.195
6J91 Structure of a hypothetical protease Deposited 2019-01-21	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 1–66（66 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；291 K；0.1M Na citrate tribasic dihydrate pH 5.5, 16% PEG 8000, 0.01M Cadmium chloride hydrate	Resolution 3.50 Å R-free 0.258
6J9H Crystal structure of SVBP-VASH1 complex Deposited 2019-01-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–66（66 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M Na citrate tribasic dihydrate pH 5.5, 16% PEG 8000, 0.01M Cadmium chloride hydrate	Resolution 2.31 Å R-free 0.271
6J9H Crystal structure of SVBP-VASH1 complex Deposited 2019-01-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–66（66 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M Na citrate tribasic dihydrate pH 5.5, 16% PEG 8000, 0.01M Cadmium chloride hydrate	Resolution 2.31 Å R-free 0.271
6JZC Structural basis of tubulin detyrosination Deposited 2019-05-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–66（66 aa）	Not recorded	GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291.15 K；HEPES, Ammonium sulphate, potassium chloride	Resolution 2.20 Å R-free 0.215
6JZC Structural basis of tubulin detyrosination Deposited 2019-05-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–66（66 aa）	Not recorded	GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291.15 K；HEPES, Ammonium sulphate, potassium chloride	Resolution 2.20 Å R-free 0.215
6JZD Crystal structure of peptide-bound VASH2-SVBP complex Deposited 2019-05-01	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 1–66（66 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291.15 K；HEPES, potassium chloride, Ammonium sulphate	Resolution 2.48 Å R-free 0.230
6JZE Crystal structure of VASH2-SVBP complex with the magic triangle I3C Deposited 2019-05-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–66（66 aa）	Not recorded	I3C 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；BIS-TRIS propane, Sodium formate	Resolution 2.51 Å R-free 0.266
6K81 Crystal structure of human VASH1-SVBP complex Deposited 2019-06-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–66（66 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；Calcium acetate, PEG 3000	Resolution 2.28 Å R-free 0.242
6LPG human VASH1-SVBP complex Deposited 2020-01-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–66（65 aa）	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.16 M ammonium sulfate, 0.08 M Sodium acetate pH4.6, 20%(w/v) PEG4000, 20%(v/v) glycerol	Resolution 2.30 Å R-free 0.236
6NVQ Crystal structure of the VASH1-SVBP complex Deposited 2019-02-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–66（66 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；293 K；19% PEG 3000, 0.1M Tris-HCl, 0.2M calcium chloride	Resolution 2.10 Å R-free 0.214
6OCF The crystal structure of VASH1-SVBP complex Deposited 2019-03-23	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 18–66（49 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293.15 K；0.1 M sodium citrate tribasic dihydrate, pH 5.0, and 18% (w/v) PEG20000	Resolution 2.10 Å R-free 0.222
6OCG Crystal structure of VASH1-SVBP complex bound with EpoY Deposited 2019-03-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 26–51（26 aa）	Not recorded	CL CHLORIDE ION × 1 GOL GLYCEROL × 1 BJL N-[(3R)-4-ethoxy-3-hydroxy-4-oxobutanoyl]-L-tyrosine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293.15 K；5% (v/v) TacsimateTM, 0.1 M HEPES, pH 7.0, and 10% (w/v) polyethylene glycol monomethyl ether 5,000	Resolution 1.83 Å R-free 0.219
6QBY Crystal structure of VASH 2 in complex with SVBP Deposited 2018-12-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–66（66 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；0.2M Sodium formate 0.1M Bis-Tris propane pH 6.5 20% PEG3350	Resolution 2.09 Å R-free 0.230
6QBY Crystal structure of VASH 2 in complex with SVBP Deposited 2018-12-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–66（66 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；0.2M Sodium formate 0.1M Bis-Tris propane pH 6.5 20% PEG3350	Resolution 2.09 Å R-free 0.230
6WSL Cryo-EM structure of VASH1-SVBP bound to microtubules Deposited 2020-05-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain D 1–66（66 aa） Chain H 1–66（66 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
7ZCW Cryo-EM structure of GMPCPP-microtubules in complex with VASH2-SVBP Deposited 2022-03-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain D 1–66（66 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 6 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å

23 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SVBP_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–28； UniProt 25–52 Author chain D； PDBConstruct 1–28； UniProt 25–52

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6och
Deposition date deposition_date	2019-03-23
Structure title title	Crystal structure of VASH1-SVBP complex bound with parthenolide
Keywords keywords	tubulin carboxypeptidases, VASH1-SVBP complex, Parthenolide, microtubule detyrosination, hydrolase-hydrolase inhibitor complex; hydrolase/hydrolase inhibitor
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	30.10 Å
Radius of gyration Rg (electron density) rg_electron	29.27 Å
Forward intensity I(0) i0	65613600.00
Molecular weight molecular_weight	63570.0 kDa
Excluded volume excluded_volume	79678 Å³
Envelope volume envelope_volume	99868 Å³
Hydration-shell volume shell_volume	29503 Å³
Envelope diameter envelope_diameter	97.7 Å
Shell Rg shell_rg	35.24 Å
Envelope Rg envelope_rg	29.35 Å
Shape Rg shape_rg	29.28 Å
Total Rg total_rg	29.85 Å
Total atoms total_atoms	4511
Residues n_residues	539
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

▼

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

Maximum dimension Dmax dmax	97.1 Å
Rg (real space) rg_real	30.16 Å
Rg uncertainty (real space) rg_real_error	0.65 Å
I(0) (real space) i0_real	6.5610e+07
I(0) uncertainty (real space) i0_real_error	9.5820e+05
Rg (reciprocal space) rg_reciprocal	30.14 Å
I(0) (reciprocal space) i0_reciprocal	65610000.0000
Solution quality estimate total_estimate	0.8919
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	27.5 Å
Skewness Skewness skewness	0.317
Kurtosis Kurtosis kurtosis	-0.643
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	23140000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.933; Smooth: 0.933

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Tubulinyl-Tyr carboxypeptidase 1
Molecular weight formula_weight	28065.5 kDa
EC 编号 ec_number	3.4.17.17
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	5152

FVNRGGLPVDEATWERMWKHVAKIHPDGEKVAQRIRGATDLPKIPIPSVPTFQPSTPVPERLEAVQRYIRELQYNHTGTQFFEIKKSRPLTGLMDLAKEMTKEALPIKCLEAVILGIYLTNSMPTLERFPISFKTYFSGNYFRHIVLGVNFAGRYGALGMSRREDLMYKPPAFRTLSELVLDFEAAYGRCWHVLKKVKLGQSVSHDPHSVEQIEWKHSVLDVERLGRDDFRKELERHARDMR

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	Small vasohibin-binding protein
Molecular weight formula_weight	3394.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

KSAQQELKQRQRAEIYALNRVMTELEQQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21

Entity 3 Entity 3 non-polymer

Description description	parthenolide
Molecular weight formula_weight	248.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	561

▶

8. Citations (1)

▶

Unit-cell length a length_a	70.132 Å
Unit-cell length b length_b	90.162 Å
Unit-cell length c length_c	127.241 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	8

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

Resolution resolution	2.003 Å
Low-resolution limit resolution_low	47.121 Å
R factor r_factor	0.1817
R_work r_work	0.1798
R_free r_free	0.2293

fit	/app/data/saxs_computation/oc/6och/6och.fit
pddf	/app/data/pr_computation/oc/6och/6och.pr.out
profile	/app/data/saxs_computation/oc/6och/6och.dat

Crystal structure of VASH1-SVBP complex bound with parthenolide

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

Tubulinyl-Tyr carboxypeptidase 1

State in the Current Structure

Other States of the Same Protein in the Database

Small vasohibin-binding protein

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 (6)

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 non-polymer

Entity 6 Entity 6 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)