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- PDB-6nvq: Crystal structure of the VASH1-SVBP complex -

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Basic information

Entry
Database: PDB / ID: 6nvq
TitleCrystal structure of the VASH1-SVBP complex
Components
  • Small vasohibin-binding protein
  • Tubulinyl-Tyr carboxypeptidase 1
KeywordsHYDROLASE / TYROSINE CARBOXYPEPTIDASE
Function / homology
Function and homology information


regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / Carboxyterminal post-translational modifications of tubulin / regulation of cellular senescence / negative regulation of lymphangiogenesis / peptidase activator activity / labyrinthine layer blood vessel development / negative regulation of endothelial cell migration / axon development ...regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / Carboxyterminal post-translational modifications of tubulin / regulation of cellular senescence / negative regulation of lymphangiogenesis / peptidase activator activity / labyrinthine layer blood vessel development / negative regulation of endothelial cell migration / 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 / microtubule binding / angiogenesis / cytoskeleton / regulation of cell cycle / 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 / SAD / Resolution: 2.1 Å
AuthorsAdamopoulos, A. / Perrakis, A. / Heidebrecht, T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2019
Title: Crystal structure of the tubulin tyrosine carboxypeptidase complex VASH1-SVBP.
Authors: Adamopoulos, A. / Landskron, L. / Heidebrecht, T. / Tsakou, F. / Bleijerveld, O.B. / Altelaar, M. / Nieuwenhuis, J. / Celie, P.H.N. / Brummelkamp, T.R. / Perrakis, A.
History
DepositionFeb 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Tubulinyl-Tyr carboxypeptidase 1
B: Small vasohibin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4454
Polymers44,2602
Non-polymers1842
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, monomer with disordered N and C termini in both chains
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-14 kcal/mol
Surface area14180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.453, 128.929, 45.222
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 35835.816 Da / Num. of mol.: 1 / Mutation: C169A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VASH1, KIAA1036, VASH / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q7L8A9, tubulinyl-Tyr carboxypeptidase
#2: Protein Small vasohibin-binding protein / Coiled coil domain-containing protein 23


Mass: 8424.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SVBP, CCDC23 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8N300
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 3.23 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8 / Details: 19% PEG 3000, 0.1M Tris-HCl, 0.2M calcium chloride / PH range: 8-8.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.1→47.61 Å / Num. obs: 24696 / % possible obs: 99.7 % / Redundancy: 4.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.062 / Net I/σ(I): 12.8
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.538 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3536 / CC1/2: 0.518 / % possible all: 51.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
SCALAdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→47.61 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.96 / SU B: 11.353 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.144 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21428 1259 5.1 %RANDOM
Rwork0.19751 ---
obs0.19839 23437 99.48 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 57.224 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å20 Å2
2---1.87 Å20 Å2
3---2.45 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2228 0 12 76 2316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0132297
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172186
X-RAY DIFFRACTIONr_angle_refined_deg1.221.6553096
X-RAY DIFFRACTIONr_angle_other_deg1.1151.5795062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2645272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.31120.511137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72215420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2691524
X-RAY DIFFRACTIONr_chiral_restr0.050.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022527
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02513
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1533.9091088
X-RAY DIFFRACTIONr_mcbond_other2.153.9051087
X-RAY DIFFRACTIONr_mcangle_it3.0395.8531357
X-RAY DIFFRACTIONr_mcangle_other3.0385.8581358
X-RAY DIFFRACTIONr_scbond_it3.2134.4171209
X-RAY DIFFRACTIONr_scbond_other3.2134.4211210
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8416.4321739
X-RAY DIFFRACTIONr_long_range_B_refined6.61544.3892445
X-RAY DIFFRACTIONr_long_range_B_other6.61644.4312446
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 80 -
Rwork0.337 1739 -
obs--99.4 %
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)
114.531210.9523.62698.40922.90551.14020.0012-0.2233-0.13950.0578-0.24350.16160.1689-0.23010.24230.3794-0.12230.07320.361-0.06340.4743-16.698521.0062-7.5133
28.19831.26361.71424.2449-2.49777.2329-0.01260.10350.1617-0.4455-0.11440.0543-0.3112-0.15090.1270.13170.04190.01730.0215-0.02280.1486-2.528827.3467-7.2409
37.76532.39551.28935.0818-1.39920.9596-0.1195-0.1852-0.07040.0509-0.0386-0.41-0.0784-0.03030.15810.31430.0065-0.03190.27390.00010.244510.727435.0764-2.7356
46.02040.4108-0.40175.21971.44118.10450.0255-0.15250.66340.2625-0.07070.0896-0.7505-0.08770.04520.21780.1056-0.0140.0987-0.0660.3122-6.487136.0752-2.1256
50.9937-0.59060.67253.2916-1.971.61840.12710.03040.0654-0.1405-0.20820.12410.0804-0.10460.08110.02950.03620.01820.1679-0.10020.2249-1.19116.54023.1864
63.99591.6140.60424.07490.94911.35910.1314-0.46660.2030.388-0.1203-0.1697-0.1030.059-0.0110.0806-0.040.0160.0802-0.06610.14759.794118.915719.5408
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B26 - 32
2X-RAY DIFFRACTION2B33 - 47
3X-RAY DIFFRACTION3B48 - 53
4X-RAY DIFFRACTION4C60 - 94
5X-RAY DIFFRACTION5C95 - 167
6X-RAY DIFFRACTION6C168 - 304

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