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- PDB-6j4s: Structural basis of tubulin detyrosination by vasohibins-SVBP enz... -

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Basic information

Entry
Database: PDB / ID: 6j4s
TitleStructural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications
Components
  • Small vasohibin-binding protein
  • Tubulinyl-Tyr carboxypeptidase 2
KeywordsHYDROLASE / carboxypeptidase / tubulin / microtubule.
Function / homology
Function and homology information


cell-cell fusion / regulation of metallopeptidase activity / syncytium formation by plasma membrane fusion / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / Carboxyterminal post-translational modifications of tubulin / peptidase activator activity / labyrinthine layer blood vessel development / negative regulation of endothelial cell migration / axon development ...cell-cell fusion / regulation of metallopeptidase activity / syncytium formation by plasma membrane fusion / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / Carboxyterminal post-translational modifications of tubulin / peptidase activator activity / labyrinthine layer blood vessel development / negative regulation of endothelial cell migration / axon development / protein secretion / regulation of angiogenesis / metallocarboxypeptidase activity / negative regulation of protein ubiquitination / positive regulation of endothelial cell proliferation / positive regulation of angiogenesis / apical part of cell / actin binding / microtubule binding / cytoskeleton / proteolysis / extracellular region / cytoplasm / cytosol
Similarity search - Function
Tubulinyl-Tyr carboxypeptidase / Small vasohibin-binding protein / Vasohibin / Coiled-coil domain-containing protein 23
Similarity search - Domain/homology
PHOSPHATE ION / Tubulinyl-Tyr carboxypeptidase 2 / Small vasohibin-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWang, N. / Bao, H. / Huang, H.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2018YFC1004500 China
National Natural Science Foundation of Chinathe Thousand Young Talents Program China
National Natural Science Foundation of ChinaK18221002 China
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2019
Title: Structural basis of tubulin detyrosination by the vasohibin-SVBP enzyme complex.
Authors: Wang, N. / Bosc, C. / Ryul Choi, S. / Boulan, B. / Peris, L. / Olieric, N. / Bao, H. / Krichen, F. / Chen, L. / Andrieux, A. / Olieric, V. / Moutin, M.J. / Steinmetz, M.O. / Huang, H.
History
DepositionJan 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tubulinyl-Tyr carboxypeptidase 2
B: Small vasohibin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7146
Polymers48,3432
Non-polymers3714
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-15 kcal/mol
Surface area14350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.198, 111.523, 127.151
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Tubulinyl-Tyr carboxypeptidase 2 / Vasohibin-2 / Vasohibin-like protein


Mass: 40520.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VASH2, VASHL / Plasmid: RSFduet / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q86V25, tubulinyl-Tyr carboxypeptidase
#2: Protein Small vasohibin-binding protein / Coiled coil domain-containing protein 23


Mass: 7821.939 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SVBP, CCDC23 / Plasmid: RSFduet / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8N300
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.79 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 6.8
Details: full-length V2-SVBP complex at a concentration of 15 mg/mL was crystallized in 1.8 M sodium/potassium phosphate, pH 6.8
PH range: 6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 14701 / % possible obs: 99.7 % / Redundancy: 10.3 % / Biso Wilson estimate: 38.75 Å2 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.048 / Net I/σ(I): 15.8
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.203 / Num. unique obs: 1410 / CC1/2: 0.563 / Rpim(I) all: 0.505 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J4O

6j4o


Resolution: 2.8→44.304 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.17
RfactorNum. reflection% reflection
Rfree0.2271 706 5.54 %
Rwork0.172 --
obs0.1749 12747 95.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→44.304 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2309 0 23 68 2400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092385
X-RAY DIFFRACTIONf_angle_d1.0153208
X-RAY DIFFRACTIONf_dihedral_angle_d12.5181448
X-RAY DIFFRACTIONf_chiral_restr0.052339
X-RAY DIFFRACTIONf_plane_restr0.01404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-3.01620.2991190.21741989X-RAY DIFFRACTION80
3.0162-3.31970.26081650.1942447X-RAY DIFFRACTION100
3.3197-3.79980.21351500.16342488X-RAY DIFFRACTION100
3.7998-4.78650.19251250.14242555X-RAY DIFFRACTION100
4.7865-44.30990.22031470.1812562X-RAY DIFFRACTION98
Refinement TLS params.

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

IDL11 (°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)
13.40821.0861-0.56353.646-1.13441.58440.14640.27940.7824-0.07640.21340.2666-0.361-0.1819-0.20280.20340.02250.06960.28540.05770.2443-2.6139-27.65311.8736
22.77620.2702-0.00552.27570.143.45420.0046-0.2457-0.28720.73640.29290.28850.0095-0.0952-0.01430.33850.0710.06190.2550.08630.1213-7.7305-42.807618.0454
36.59840.86450.93138.77110.16177.56260.21220.01720.46020.26970.1722-0.3422-0.60470.3222-0.17070.2898-0.09810.19630.30850.07290.36683.9912-19.76581.1054
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 49 through 169 )
2X-RAY DIFFRACTION2chain 'A' and (resid 170 through 298 )
3X-RAY DIFFRACTION3chain 'B' and (resid 24 through 55 )

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