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- PDB-6qby: Crystal structure of VASH 2 in complex with SVBP -

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Basic information

Entry
Database: PDB / ID: 6qby
TitleCrystal structure of VASH 2 in complex with SVBP
Components
  • Small vasohibin-binding protein
  • Tubulinyl-Tyr carboxypeptidase 2
KeywordsCYTOSOLIC PROTEIN / Tubulin carboxypeptidase / Cysteine protease / Complex
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
Tubulinyl-Tyr carboxypeptidase 2 / Small vasohibin-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.09 Å
AuthorsChoi, S.R. / Olieric, V. / Steinmetz, M.O. / Olieric, N.
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
DepositionDec 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.ls_percent_reflns_obs
Revision 1.2Jul 3, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / 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 1.3Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Jul 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_author.identifier_ORCID
Revision 1.5May 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
A: Tubulinyl-Tyr carboxypeptidase 2
B: Small vasohibin-binding protein
C: Tubulinyl-Tyr carboxypeptidase 2
D: Small vasohibin-binding protein


Theoretical massNumber of molelcules
Total (without water)77,8214
Polymers77,8214
Non-polymers00
Water4,774265
1
A: Tubulinyl-Tyr carboxypeptidase 2
B: Small vasohibin-binding protein


  • defined by author&software
  • Evidence: isothermal titration calorimetry, 1:1 ratio binding, gel filtration, Elutes from the same gel filtration peak, light scattering, Multi angle light scattering indicates 1:1 binding, assay ...Evidence: isothermal titration calorimetry, 1:1 ratio binding, gel filtration, Elutes from the same gel filtration peak, light scattering, Multi angle light scattering indicates 1:1 binding, assay for oligomerization, When co-expressed in E.coli, affinity chromatography for the HIS6 tag on SVBP co-purified untagged Vasohibin 2
  • 38.9 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)38,9102
Polymers38,9102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-12 kcal/mol
Surface area13750 Å2
MethodPISA
2
C: Tubulinyl-Tyr carboxypeptidase 2
D: Small vasohibin-binding protein


  • defined by author&software
  • Evidence: isothermal titration calorimetry, 1:1 ratio binding, gel filtration, Elutes from the same gel filtration peak, light scattering, Multi angle light scattering indicates 1:1 binding, assay ...Evidence: isothermal titration calorimetry, 1:1 ratio binding, gel filtration, Elutes from the same gel filtration peak, light scattering, Multi angle light scattering indicates 1:1 binding, assay for oligomerization, When co-expressed in E.coli, affinity chromatography for the HIS6 tag on SVBP co-purified untagged Vasohibin 2
  • 38.9 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)38,9102
Polymers38,9102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-14 kcal/mol
Surface area13930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.887, 119.887, 102.636
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 29999.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VASH2, VASHL / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q86V25, tubulinyl-Tyr carboxypeptidase
#2: Protein Small vasohibin-binding protein / Coiled coil domain-containing protein 23


Mass: 8911.196 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) / References: UniProt: Q8N300
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.74 Å3/Da / Density % sol: 60 % / Description: Hexagonal cylinder
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Sodium formate 0.1M Bis-Tris propane pH 6.5 20% PEG3350
PH range: 6.2-6.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 6, 2018
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→103.83 Å / Num. obs: 30821 / % possible obs: 99.9 % / Redundancy: 10.9 % / Net I/σ(I): 19.2
Reflection shellResolution: 2.113→2.345 Å / Redundancy: 9 % / Num. unique obs: 1542 / % possible all: 78.5

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.09→103.83 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.922 / SU R Cruickshank DPI: 0.293 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.303 / SU Rfree Blow DPI: 0.222 / SU Rfree Cruickshank DPI: 0.221
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1434 4.65 %RANDOM
Rwork0.19 ---
obs0.192 30812 60.7 %-
Displacement parametersBiso mean: 53.52 Å2
Baniso -1Baniso -2Baniso -3
1-1.9981 Å20 Å20 Å2
2--1.9981 Å20 Å2
3----3.9962 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: 1 / Resolution: 2.09→103.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4442 0 0 265 4707
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014555HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.046151HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1596SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes98HARMONIC2
X-RAY DIFFRACTIONt_gen_planes658HARMONIC5
X-RAY DIFFRACTIONt_it4555HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.93
X-RAY DIFFRACTIONt_other_torsion17.85
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion580SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5325SEMIHARMONIC4
LS refinement shellResolution: 2.09→2.16 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.226 -5.36 %
Rwork0.209 159 -
obs--3.37 %
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)
10.83110.46570.30061.06340.092.4485-0.02990.0529-0.0469-0.00610.08020.0103-0.19010.3598-0.0503-0.0716-0.0640.01820.0289-0.0559-0.12822.4105-66.4223-27.6481
22.7240.66952.72151.2318-1.54955.3693-0.37531.014-0.0038-0.10390.12440.2366-0.85020.69190.2508-0.0528-0.48420.02390.0796-0.0219-0.496110.8431-49.1223-35.4026
31.69960.2077-0.65372.0039-0.04582.2055-0.00870.17390.3918-0.13770.22820.196-0.3952-0.2773-0.2196-0.14560.03880.0138-0.2530.0637-0.249817.704-31.3036-3.5206
43.6497-1.536-1.5914-2.20022.77696.97770.0035-0.05390.6631-0.12310.1467-0.2977-0.3663-0.39-0.15010.02580.31640.1292-0.25520.0895-0.04798.7265-18.68148.4344
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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