PDB-6och: Crystal structure of VASH1-SVBP complex bound with parthenolide

ID or keywords:

Entry

Database: PDB / ID: 6och

Title

Crystal structure of VASH1-SVBP complex bound with parthenolide

Components

Small vasohibin-binding protein
Tubulinyl-Tyr carboxypeptidase 1

Keywords

hydrolase/hydrolase inhibitor / tubulin carboxypeptidases / VASH1-SVBP complex / Parthenolide / microtubule detyrosination / hydrolase-hydrolase inhibitor complex

Function / homology

Function and homology information

regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / negative regulation of lymphangiogenesis / regulation of cellular senescence / Carboxyterminal post-translational modifications of tubulin / peptidase activator activity / negative regulation of endothelial cell migration / labyrinthine layer blood vessel development / axon development ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.003 Å

Authors

Li, F. / Luo, X. / Yu, H.

Funding support

United States, 1items

Citation

Journal: Nat.Struct.Mol.Biol. / Year: 2019
Title: Structural basis of tubulin detyrosination by vasohibins.
Authors: Li, F. / Hu, Y. / Qi, S. / Luo, X. / Yu, H.

History

Deposition	Mar 23, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 26, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jul 10, 2019	Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Jul 17, 2019	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Oct 11, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5	Oct 9, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6och.cif.gz	255.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6och.ent.gz	204 KB	Display	PDB format
PDBx/mmJSON format	6och.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6och_validation.pdf.gz	298 KB	Display	wwPDB validaton report
Full document	6och_full_validation.pdf.gz	298.9 KB	Display
Data in XML	6och_validation.xml.gz	1.8 KB	Display
Data in CIF	6och_validation.cif.gz	10.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oc/6och ftp://data.pdbj.org/pub/pdb/validation_reports/oc/6och	HTTPS FTP

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Related structure data

Related structure data	6ocfSC 6ocgC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6nvq-d 6j8n-2 6j9h-2 6k81-d 6j4u-d 4agu-2 3mwg-1 5p5i-d 1o7t-8 5jfv-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Tubulinyl-Tyr carboxypeptidase 1

B: Small vasohibin-binding protein

C: Tubulinyl-Tyr carboxypeptidase 1

D: Small vasohibin-binding protein

hetero molecules

64.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Tubulinyl-Tyr carboxypeptidase 1

B: Small vasohibin-binding protein

hetero molecules

defined by author&software
Evidence: gel filtration
32.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Tubulinyl-Tyr carboxypeptidase 1

D: Small vasohibin-binding protein

hetero molecules

defined by author&software
32 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	70.132, 90.162, 127.241
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

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Protein / Protein/peptide , 2 types, 4 molecules ACBD

#1: Protein	Tubulinyl-Tyr carboxypeptidase 1 / Tubulin carboxypeptidase 1 / Tyrosine carboxypeptidase 1 / TTCP 1 / Vasohibin-1 Mass: 28065.461 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VASH1, KIAA1036, VASH / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q7L8A9, tubulinyl-Tyr carboxypeptidase
#2: Protein/peptide	Small vasohibin-binding protein / Coiled coil domain-containing protein 23 Mass: 3394.833 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SVBP, CCDC23 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8N300

#1: Protein

Tubulinyl-Tyr carboxypeptidase 1 / Tubulin carboxypeptidase 1 / Tyrosine carboxypeptidase 1 / TTCP 1 / Vasohibin-1

Mass: 28065.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: VASH1, KIAA1036, VASH / Production host:

Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q7L8A9, tubulinyl-Tyr carboxypeptidase

#2: Protein/peptide

Small vasohibin-binding protein / Coiled coil domain-containing protein 23

Mass: 3394.833 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: SVBP, CCDC23 / Production host:

Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8N300

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Non-polymers , 4 types, 570 molecules

#3: Chemical	ChemComp-M4Y / parthenolide / (1aR,4E,7aS,10aS,10bR)-1a,5-dimethyl-8-methylidene-2,3,6,7,7a,8,10a,10b-octahydrooxireno[9,10]cyclodeca[1,2-b]furan-9(1 aH)-one Mass: 248.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₅H₂₀O₃
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 561 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.2 Å³/Da / Density % sol: 61.53 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonium sulfate, 0.1 M Bis-tris, pH 5.5, and 25 % (w/v) PEG 3350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.9792 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 8, 2018

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9792 Å / Relative weight: 1

Reflection

Resolution: 2→50 Å / Num. obs: 55055 / % possible obs: 99.9 % / Redundancy: 13 % / B_iso Wilson estimate: 24.39 Å² / R_merge(I) obs: 0.15 / R_pim(I) all: 0.043 / R_rim(I) all: 0.156 / Χ²: 0.984 / Net I/σ(I): 4.7

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2-2.03	12.8	2.046	2700	0.545	0.587	2.13	0.95	100
2.03-2.07	12.7	1.679	2702	0.69	0.485	1.749	0.999	100
2.07-2.11	12.5	1.451	2743	0.713	0.422	1.512	0.958	100
2.11-2.15	11.9	1.205	2672	0.763	0.362	1.259	0.954	99.8
2.15-2.2	11.5	1.029	2753	0.81	0.315	1.077	0.983	99.8
2.2-2.25	13.5	0.88	2726	0.874	0.246	0.914	1.008	100
2.25-2.31	13.5	0.751	2709	0.923	0.209	0.78	0.965	100
2.31-2.37	13.5	0.649	2720	0.929	0.182	0.674	0.982	100
2.37-2.44	13.5	0.547	2729	0.95	0.153	0.568	0.986	100
2.44-2.52	13.5	0.484	2718	0.956	0.136	0.503	0.994	100
2.52-2.61	13.3	0.381	2729	0.975	0.108	0.396	0.99	100
2.61-2.71	13	0.298	2747	0.981	0.085	0.31	0.999	99.8
2.71-2.84	11.6	0.248	2744	0.984	0.075	0.259	0.99	99.8
2.84-2.99	13.9	0.187	2737	0.992	0.052	0.194	0.99	100
2.99-3.17	13.9	0.144	2782	0.995	0.04	0.149	1.012	100
3.17-3.42	13.6	0.114	2751	0.996	0.032	0.119	1.014	100
3.42-3.76	13.2	0.093	2785	0.996	0.027	0.097	1.045	100
3.76-4.31	11.9	0.078	2790	0.997	0.023	0.082	1.043	99.6
4.31-5.43	13.6	0.07	2842	0.997	0.02	0.073	0.919	100
5.43-50	12.3	0.06	2976	0.998	0.018	0.063	0.911	99.7

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Processing

Software

Name	Version	Classification
PHENIX	1.13_2998	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6OCF

6ocf

Resolution: 2.003→47.121 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.77

	R_factor	Num. reflection	% reflection
R_free	0.2293	1998	3.8 %
R_work	0.1798	-	-
obs	0.1817	52633	95.7 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 131.45 Å² / B_iso mean: 34.0636 Å² / B_iso min: 10.45 Å²

Refinement step

Cycle: final / Resolution: 2.003→47.121 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4399	0	114	561	5074
B_iso mean	-	-	64.74	41.04	-
Num. residues	-	-	-	-	539

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.0028-2.0529	0.3263	81	0.2734	2036	2117	55
2.0529-2.1084	0.2948	132	0.2459	3364	3496	90
2.1084-2.1704	0.3123	142	0.2265	3591	3733	97
2.1704-2.2405	0.2479	146	0.2077	3723	3869	99
2.2405-2.3205	0.2623	148	0.1983	3730	3878	100
2.3205-2.4134	0.2446	148	0.1834	3758	3906	100
2.4134-2.5233	0.2403	148	0.185	3734	3882	100
2.5233-2.6563	0.2389	148	0.1817	3757	3905	100
2.6563-2.8227	0.2185	148	0.1817	3764	3912	100
2.8227-3.0406	0.2362	149	0.1748	3778	3927	100
3.0406-3.3465	0.2055	150	0.1653	3797	3947	100
3.3465-3.8306	0.2038	150	0.1562	3791	3941	100
3.8306-4.8254	0.1841	151	0.1464	3847	3998	100
4.8254-47.1338	0.2434	157	0.1929	3965	4122	98

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	5.3331	-2.5136	0.9848	7.0686	-5.7695	7.3929	0.1546	-0.2309	-0.1116	0.1696	0.2772	0.4227	-0.0537	-0.3989	-0.3562	0.1789	-0.0128	0.06	0.1383	-0.1069	0.2342	-12.973	11.5	50.506
2	2.6299	0.7536	-1.5	1.2513	-0.1397	3.4309	0.2203	-0.0961	0.3805	0.0423	-0.0742	0.1456	-0.4766	-0.0684	-0.0852	0.218	-0.0008	0.0337	0.1097	-0.0426	0.2208	-9.776	19.21	51.364
3	6.4855	-2.3132	-2.0832	2.255	3.7404	7.0245	0.5297	0.0891	1.3103	-0.2844	-0.438	0.2286	-1.4267	-0.4917	0.1144	0.9699	0.0367	0.1909	0.2877	-0.1141	0.5921	-14.903	30.19	53.505
4	2.1809	0.1212	-0.414	6.6606	-1.6394	7.4755	0.0791	0.0089	-0.1319	0.1438	0.2428	-0.5439	0.1379	0.2441	-0.2505	0.1691	0.0081	-0.0675	0.1664	-0.1322	0.2364	4.226	-6.868	58.765
5	3.9605	-1.2548	0.7207	5.8725	1.0407	6.4396	-0.0498	0.3989	0.4599	-0.7461	0.2404	0.9011	-0.5999	-0.2323	-0.1572	0.3065	0.0067	-0.0901	0.2943	0.1337	0.3302	-9.082	1.668	-1.577
6	3.9291	0.9702	0.3254	6.4296	-1.7379	2.6655	-0.0986	0.7819	-0.2247	-0.7813	0.1383	0.0437	0.5144	0.4788	-0.0153	0.2719	0.0385	-0.0624	0.2892	-0.018	0.1688	-2.162	-11.327	-0.08
7	3.3253	2.1179	4.0499	2.9152	4.6658	7.6793	0.0304	-0.0921	0.1109	0.2767	-0.083	-0.0258	0.6297	0.2039	0.0125	0.1905	0.0641	0.0479	0.1173	0.0478	0.176	6.148	3.996	24.807
8	0.0195	-0.1192	-0.2886	3.8711	2.3915	2.504	0.016	0.1139	0.1702	-0.184	-0.0695	0.229	-0.1056	-0.2679	0.0531	0.1189	0.0175	0.0079	0.187	0.0576	0.2097	-3.957	9.109	13.255
9	2.5205	0.1682	-1.7201	1.9143	-1.1115	8.3757	0.0087	0.3251	0.2673	-0.1263	-0.0745	0.0242	-0.2514	0.1211	0.0104	0.1079	0.0157	-0.0083	0.1552	0.047	0.1977	8.26	18.229	12.33
10	4.0213	0.9277	0.0355	3.4512	4.2351	6.4469	0.1161	0.1617	-0.2019	-0.076	0.0667	-0.6878	-0.2821	0.43	-0.2667	0.181	-0.0035	0.0135	0.2135	0.0799	0.3175	13.216	12.434	14.623
11	3.3582	-0.4074	-2.7554	1.9373	0.1828	4.2116	-0.0108	0.0317	0.1042	-0.0296	-0.0135	-0.222	-0.0582	0.1828	0.0206	0.128	0.0161	-0.0155	0.1539	0.0416	0.2091	12.701	18.947	13.821
12	8.4139	2.5871	-1.07	5.6625	-1.9807	5.076	-0.0089	0.0323	0.9968	-0.005	-0.0522	-0.361	-0.734	0.4756	0.0216	0.3484	-0.0166	0	0.1745	0.0186	0.3788	10.569	29.989	13.417
13	6.7559	-0.2244	-1.8459	8.1207	0.2399	8.8497	0.0903	0.2327	0.1619	-0.019	0.005	0.139	0.1192	0.15	-0.0748	0.1573	0.0245	-0.044	0.11	0.0313	0.0627	-3.318	-5.671	5.697
14	3.5006	0.6718	0.478	4.0866	-2.666	5.661	0.1389	-0.279	0.388	1.0214	0.3297	-1.1058	-0.6143	0.3845	-0.2644	0.4148	0.0263	-0.1693	0.3114	-0.1566	0.4109	8.986	0.108	66.651
15	7.4458	-1.2957	1.1902	7.8512	0.8655	0.4972	-0.159	-0.6018	-0.5942	0.7987	0.3511	0.0154	0.7459	0.1034	-0.1888	0.3529	0.0163	-0.0923	0.2171	-0.0038	0.2756	2.059	-12.653	64.885
16	2.527	-2.2665	3.2676	3.1719	-4.6919	6.9007	0.114	0.113	-0.065	-0.1709	0.0006	0.1284	0.4386	-0.3003	-0.1471	0.1782	-0.0717	0.0355	0.1144	-0.0576	0.1867	-5.728	3.717	39.921
17	0.3676	0.0247	0.254	3.5105	-2.3237	2.6111	-0.0036	-0.015	0.0609	0.2579	0.0146	-0.208	-0.2602	0.3554	-0.0358	0.1597	-0.0323	0.0136	0.2041	-0.0822	0.1943	4.202	8.425	52.24
18	1.6991	-0.249	-1.459	1.4921	0.9904	6.3151	0.1351	-0.2758	0.3313	0.1573	-0.0338	0.1218	-0.3809	0.0589	-0.1918	0.1807	-0.057	0.0791	0.1646	-0.0791	0.2118	-8.065	17.231	53.213

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN C AND RESID 212:226 )	C	212 - 226
2	X-RAY DIFFRACTION	2	( CHAIN C AND RESID 227:277 )	C	227 - 277
3	X-RAY DIFFRACTION	3	( CHAIN C AND RESID 278:302 )	C	278 - 302
4	X-RAY DIFFRACTION	4	( CHAIN D AND RESID 25:51 )	D	25 - 51
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 61:84 )	A	61 - 84
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 85:105 )	A	85 - 105
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 106:132 )	A	106 - 132
8	X-RAY DIFFRACTION	8	( CHAIN A AND RESID 133:180 )	A	133 - 180
9	X-RAY DIFFRACTION	9	( CHAIN A AND RESID 181:211 )	A	181 - 211
10	X-RAY DIFFRACTION	10	( CHAIN A AND RESID 212:226 )	A	212 - 226
11	X-RAY DIFFRACTION	11	( CHAIN A AND RESID 227:269 )	A	227 - 269
12	X-RAY DIFFRACTION	12	( CHAIN A AND RESID 270:302 )	A	270 - 302
13	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 25:52 )	B	25 - 52
14	X-RAY DIFFRACTION	14	( CHAIN C AND RESID 61:84 )	C	61 - 84
15	X-RAY DIFFRACTION	15	( CHAIN C AND RESID 85:105 )	C	85 - 105
16	X-RAY DIFFRACTION	16	( CHAIN C AND RESID 106:132 )	C	106 - 132
17	X-RAY DIFFRACTION	17	( CHAIN C AND RESID 133:180 )	C	133 - 180
18	X-RAY DIFFRACTION	18	( CHAIN C AND RESID 181:211 )	C	181 - 211

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-Protein / Protein/peptide , 2 types, 4 molecules ACBD

-Non-polymers , 4 types, 570 molecules

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+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein / Protein/peptide , 2 types, 4 molecules ACBD

-
Non-polymers , 4 types, 570 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi