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- PDB-6jzc: Structural basis of tubulin detyrosination -

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Basic information

Entry
Database: PDB / ID: 6jzc
TitleStructural basis of tubulin detyrosination
Components
  • Small vasohibin-binding protein
  • Tubulinyl-Tyr carboxypeptidase 2
KeywordsCYTOSOLIC PROTEIN / VASH2 / SVBP / tubulin detyrosination
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 / placenta blood vessel development / labyrinthine layer development / negative regulation of endothelial cell migration ...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 / placenta blood vessel development / labyrinthine layer development / negative regulation of endothelial cell migration / labyrinthine layer blood vessel development / 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 / cytosol / 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 2 / Small vasohibin-binding protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.201 Å
AuthorsChen, Z. / Ling, Y. / Zeyuan, G. / Zhu, L.
CitationJournal: Nat Commun / Year: 2019
Title: Structural basis of tubulin detyrosination by VASH2/SVBP heterodimer.
Authors: Zhou, C. / Yan, L. / Zhang, W.H. / Liu, Z.
History
DepositionMay 1, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.2Aug 7, 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_author.name
Revision 1.3Mar 27, 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: Tubulinyl-Tyr carboxypeptidase 2
C: Small vasohibin-binding protein
D: Small vasohibin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,57012
Polymers101,8334
Non-polymers7378
Water4,684260
1
A: Tubulinyl-Tyr carboxypeptidase 2
D: Small vasohibin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2856
Polymers50,9172
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-17 kcal/mol
Surface area14850 Å2
MethodPISA
2
B: Tubulinyl-Tyr carboxypeptidase 2
C: Small vasohibin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2856
Polymers50,9172
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-17 kcal/mol
Surface area14860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.803, 120.932, 193.194
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: 40568.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vash2, Vashl / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8C5G2, tubulinyl-Tyr carboxypeptidase
#2: Protein Small vasohibin-binding protein / Coiled coil domain-containing protein 23


Mass: 10347.556 Da / Num. of mol.: 2
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.: 8 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: HEPES, Ammonium sulphate, potassium chloride

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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 PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 48774 / % possible obs: 99.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 33.35 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.041 / Net I/σ(I): 12.9
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.821 / Num. unique obs: 4139 / CC1/2: 0.895 / Rpim(I) all: 0.346 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(1.14rc3_3206: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.201→48.298 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.68
RfactorNum. reflection% reflection
Rfree0.2148 2386 4.9 %
Rwork0.1809 --
obs0.1826 48689 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.201→48.298 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4712 0 48 260 5020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074871
X-RAY DIFFRACTIONf_angle_d0.8516549
X-RAY DIFFRACTIONf_dihedral_angle_d15.0642951
X-RAY DIFFRACTIONf_chiral_restr0.049688
X-RAY DIFFRACTIONf_plane_restr0.006827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.201-2.24590.30571420.25782634X-RAY DIFFRACTION98
2.2459-2.29480.2861270.24352704X-RAY DIFFRACTION100
2.2948-2.34810.26611110.23852730X-RAY DIFFRACTION100
2.3481-2.40690.2991330.22152687X-RAY DIFFRACTION100
2.4069-2.47190.26181470.21422685X-RAY DIFFRACTION100
2.4719-2.54470.24551490.21032707X-RAY DIFFRACTION100
2.5447-2.62680.26321550.20332684X-RAY DIFFRACTION100
2.6268-2.72070.25631440.19722714X-RAY DIFFRACTION100
2.7207-2.82960.22931440.19252697X-RAY DIFFRACTION99
2.8296-2.95830.20951410.18282716X-RAY DIFFRACTION100
2.9583-3.11430.27171570.1922700X-RAY DIFFRACTION100
3.1143-3.30940.22991390.18092735X-RAY DIFFRACTION100
3.3094-3.56480.20131320.17272749X-RAY DIFFRACTION100
3.5648-3.92340.19471340.16282727X-RAY DIFFRACTION100
3.9234-4.49080.15451470.14132772X-RAY DIFFRACTION100
4.4908-5.65650.17281420.16012772X-RAY DIFFRACTION99
5.6565-48.31010.21671420.18862890X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 22.1545 Å / Origin y: 38.4036 Å / Origin z: 95.3959 Å
111213212223313233
T0.2509 Å2-0.0277 Å20.0017 Å2-0.224 Å20.011 Å2--0.2805 Å2
L0.0548 °2-0.0382 °2-0.0497 °2-0.2041 °2-0.1792 °2--1.8908 °2
S0.0243 Å °0.0026 Å °-0.0025 Å °-0.0119 Å °-0.0045 Å °0.0063 Å °0.1541 Å °0.0277 Å °-0.0166 Å °
Refinement TLS groupSelection details: all

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