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- PDB-6j4u: Structural basis of tubulin detyrosination by vasohibins-SVBP enz... -

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Basic information

Entry
Database: PDB / ID: 6j4u
TitleStructural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications
Components
  • Small vasohibin-binding protein
  • Tubulinyl-Tyr carboxypeptidase 1
KeywordsHYDROLASE / carboxypeptidase / tubulin / microtubule.
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 / negative regulation of endothelial cell migration / labyrinthine layer blood vessel development / peptidase activator activity / axon development ...regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / negative regulation of lymphangiogenesis / regulation of cellular senescence / Carboxyterminal post-translational modifications of tubulin / negative regulation of endothelial cell migration / labyrinthine layer blood vessel development / peptidase activator activity / axon development / negative regulation of endothelial cell proliferation / negative regulation of blood vessel endothelial cell migration / protein secretion / regulation of angiogenesis / metallocarboxypeptidase activity / negative regulation of protein ubiquitination / negative regulation of angiogenesis / response to wounding / apical part of cell / actin binding / angiogenesis / microtubule binding / cytoskeleton / regulation of cell cycle / endoplasmic reticulum / proteolysis / extracellular space / extracellular region / cytoplasm
Similarity search - Function
Tubulinyl-Tyr carboxypeptidase / Small vasohibin-binding protein / Vasohibin / Coiled-coil domain-containing protein 23
Similarity search - Domain/homology
Tubulinyl-Tyr carboxypeptidase 1 / Small vasohibin-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.998 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 1
B: Small vasohibin-binding protein


Theoretical massNumber of molelcules
Total (without water)36,8572
Polymers36,8572
Non-polymers00
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-15 kcal/mol
Surface area14480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.512, 71.453, 128.108
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-593-

HOH

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Components

#1: Protein Tubulinyl-Tyr carboxypeptidase 1 / Tubulin carboxypeptidase 1 / Tyrosine carboxypeptidase 1 / TTCP 1 / Vasohibin-1


Mass: 29034.707 Da / Num. of mol.: 1 / Mutation: E71S/A72H/K79M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VASH1, KIAA1036, VASH / Plasmid: RSFdeut / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7L8A9, 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: RSFdeut / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8N300
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.76 Å3/Da / Density % sol: 55.48 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 5
Details: 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 ...Details: 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.
PH range: 5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.998→50 Å / Num. obs: 28511 / % possible obs: 99.9 % / Redundancy: 12.4 % / Biso Wilson estimate: 39.4 Å2 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.023 / Net I/σ(I): 24.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 9.5 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2759 / CC1/2: 0.738 / Rpim(I) all: 0.358 / % possible all: 99.5

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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: 1.998→47.695 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.23
RfactorNum. reflection% reflection
Rfree0.2036 1469 5.17 %
Rwork0.1681 --
obs0.1699 28433 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.998→47.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2248 0 0 238 2486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072305
X-RAY DIFFRACTIONf_angle_d0.8693111
X-RAY DIFFRACTIONf_dihedral_angle_d12.6271921
X-RAY DIFFRACTIONf_chiral_restr0.053333
X-RAY DIFFRACTIONf_plane_restr0.005402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9977-2.06910.33141460.27822587X-RAY DIFFRACTION98
2.0691-2.1520.26621380.22592664X-RAY DIFFRACTION100
2.152-2.24990.21961310.20152669X-RAY DIFFRACTION100
2.2499-2.36850.22341310.1912682X-RAY DIFFRACTION100
2.3685-2.51690.22771760.18542644X-RAY DIFFRACTION100
2.5169-2.71120.19741510.18022678X-RAY DIFFRACTION100
2.7112-2.9840.22941540.17532703X-RAY DIFFRACTION100
2.984-3.41570.21061530.16672707X-RAY DIFFRACTION100
3.4157-4.3030.17531340.14212750X-RAY DIFFRACTION100
4.303-47.70870.18581550.15672880X-RAY DIFFRACTION99
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)
17.7694-0.41011.29736.3468-0.40126.52380.238-1.0622-0.34510.9844-0.363-0.31160.23920.68540.09740.4831-0.08290.01590.76680.2010.403240.06765.480434.1161
22.86341.0368-2.26861.22140.51885.65620.0186-0.1953-0.13090.05830.0470.03890.1477-0.2668-0.07830.2413-0.0011-0.02880.24070.00240.245751.239171.149215.3615
31.63970.57051.39674.85963.07237.3438-0.0261-0.23890.18120.22370.056-0.0296-0.2187-0.1817-0.03410.21310.0190.00720.2482-0.02560.271761.301282.958319.0752
46.93041.30722.23272.3951-0.30696.0955-0.29150.17270.5443-0.07080.1755-0.5737-0.60190.99580.02780.3995-0.0059-0.02010.5998-0.05760.538473.439581.264317.1714
57.2955-0.3371-0.18172.87724.67587.8664-0.0855-0.3486-0.1739-0.22330.0024-0.0535-0.02990.2630.08810.3377-0.03960.01880.4460.12370.29838.088267.446426.9361
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 61 through 105 )
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 180 )
3X-RAY DIFFRACTION3chain 'A' and (resid 181 through 269 )
4X-RAY DIFFRACTION4chain 'A' and (resid 270 through 307 )
5X-RAY DIFFRACTION5chain 'B' and (resid 24 through 52 )

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