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- PDB-6j4q: Structural basis of tubulin detyrosination by vasohibins-SVBP enz... -

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Basic information

Entry
Database: PDB / ID: 6j4q
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 / inhibitor / TPCK
Function / homology
Function and homology information


cell-cell fusion / regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / syncytium formation by plasma membrane fusion / Carboxyterminal post-translational modifications of tubulin / peptidase activator activity / metallocarboxypeptidase activity / labyrinthine layer blood vessel development / negative regulation of endothelial cell migration ...cell-cell fusion / regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / syncytium formation by plasma membrane fusion / Carboxyterminal post-translational modifications of tubulin / peptidase activator activity / metallocarboxypeptidase activity / labyrinthine layer blood vessel development / negative regulation of endothelial cell migration / axon development / protein secretion / regulation of angiogenesis / positive regulation of endothelial cell proliferation / negative regulation of protein ubiquitination / 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
Chem-TQ8 / Tubulinyl-Tyr carboxypeptidase 2 / Small vasohibin-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
F: Tubulinyl-Tyr carboxypeptidase 2
G: Small vasohibin-binding protein
J: Tubulinyl-Tyr carboxypeptidase 2
K: Small vasohibin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,14919
Polymers148,5778
Non-polymers2,57211
Water4,522251
1
A: Tubulinyl-Tyr carboxypeptidase 2
B: Small vasohibin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0326
Polymers37,1442
Non-polymers8884
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-16 kcal/mol
Surface area14350 Å2
MethodPISA
2
C: Tubulinyl-Tyr carboxypeptidase 2
D: Small vasohibin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5884
Polymers37,1442
Non-polymers4442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-13 kcal/mol
Surface area14150 Å2
MethodPISA
3
F: Tubulinyl-Tyr carboxypeptidase 2
G: Small vasohibin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9405
Polymers37,1442
Non-polymers7963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-17 kcal/mol
Surface area14540 Å2
MethodPISA
4
J: Tubulinyl-Tyr carboxypeptidase 2
K: Small vasohibin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5884
Polymers37,1442
Non-polymers4442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-15 kcal/mol
Surface area13720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.177, 117.177, 209.044
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 29322.422 Da / Num. of mol.: 4
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.: 4
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-TQ8 / N-[(2S)-4-chloro-3-oxo-1-phenyl-butan-2-yl]-4-methyl-benzenesulfonamide / CAS329306


Mass: 351.848 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H18ClNO3S / Comment: protease inhibitor*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.79 Å3/Da / Density % sol: 55.91 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7
Details: V2c-SVBP was mixed with the inhibitor TPCK at a mole ratio of 1:5 and incubated on ice for 30 min. Then, the resulting co-complex of V2c-SVBP-TPCK was crystallized in 1.0 M sodium malonate, pH 7.0.
PH range: 7

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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: Apr 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 51721 / % possible obs: 100 % / Redundancy: 9.9 % / Biso Wilson estimate: 41.06 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.03 / Net I/σ(I): 25.6
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 10 % / Rmerge(I) obs: 1.767 / Num. unique obs: 5049 / CC1/2: 0.621 / Rpim(I) all: 0.585 / % possible all: 100

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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: 2.7→49.307 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.8
RfactorNum. reflection% reflection
Rfree0.247 2213 5.09 %
Rwork0.1835 --
obs0.1868 43495 93.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→49.307 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8966 0 162 251 9379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019360
X-RAY DIFFRACTIONf_angle_d1.19212645
X-RAY DIFFRACTIONf_dihedral_angle_d10.3675607
X-RAY DIFFRACTIONf_chiral_restr0.061348
X-RAY DIFFRACTIONf_plane_restr0.0071598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.75870.39830.27231300X-RAY DIFFRACTION49
2.7587-2.82290.3935740.25921759X-RAY DIFFRACTION64
2.8229-2.89350.29741570.24922397X-RAY DIFFRACTION90
2.8935-2.97170.29221630.23862670X-RAY DIFFRACTION99
2.9717-3.05920.38221100.23352749X-RAY DIFFRACTION100
3.0592-3.15790.32641330.2272757X-RAY DIFFRACTION100
3.1579-3.27070.29651580.21442711X-RAY DIFFRACTION100
3.2707-3.40170.27561460.20982695X-RAY DIFFRACTION100
3.4017-3.55640.25951730.18562735X-RAY DIFFRACTION100
3.5564-3.74390.25351570.17652727X-RAY DIFFRACTION100
3.7439-3.97830.20791470.15532726X-RAY DIFFRACTION100
3.9783-4.28530.21721530.15142735X-RAY DIFFRACTION100
4.2853-4.71630.19221460.1382787X-RAY DIFFRACTION100
4.7163-5.3980.2011360.15132777X-RAY DIFFRACTION100
5.398-6.79810.24011410.19332837X-RAY DIFFRACTION100
6.7981-49.31570.20611360.17222920X-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)
10.1941-0.0741-0.01840.81490.08180.4423-0.1498-0.16770.2390.1152-0.00550.1149-0.7183-0.2377-0.00561.01640.25240.0145-0.1568-0.0680.363-12.566779.681937.5371
21.999-0.1699-0.54932.2652-0.43071.22510.0567-0.3969-0.38730.2946-0.1019-0.3001-0.02590.23090.08020.5467-0.0503-0.06680.10260.07440.27773.972165.604742.3984
32.6344-0.3043-0.21053.6775-1.40881.0771-0.0160.14530.2445-0.21490.11260.11680.0311-0.0442-0.05710.90660.132-0.06620.16610.050.282-9.258885.979129.1598
41.36650.43330.20781.70861.16620.82660.1920.37340.3405-0.0032-0.1865-0.4447-0.49650.00510.02420.60950.00360.05050.19670.05710.468749.271279.944733.8853
54.66010.62130.3491.17160.2472.71270.28350.2194-0.00190.21-0.16780.0115-0.0642-0.0143-0.07720.35120.0507-0.0090.1596-0.02410.163137.032268.615830.1955
64.2624-2.8889-1.11056.38382.16765.47980.41790.2372-0.13830.0302-0.26010.0582-0.0842-0.0475-0.16780.2811-0.0251-0.07020.1918-0.05840.203531.897866.098430.4687
72.69210.504-1.69351.87260.49923.05640.29361.0609-0.5823-0.1267-0.28210.1010.10290.0543-0.0280.46810.1898-0.1370.5796-0.16760.321828.068463.375621.0908
84.71350.53210.95637.1130.7932.46270.2744-0.445-0.14130.6095-0.1029-0.4315-0.0479-0.0096-0.13930.6201-0.0880.0460.13350.01250.407847.250386.491741.7744
92.002-0.2032-0.9530.02840.24383.31440.06840.4672-0.3091-0.055-0.1044-0.05210.57680.16460.06080.62620.4566-0.07011.3069-0.18670.339424.030662.47998.6956
104.01361.14661.36642.52890.91870.80590.31230.9616-0.8203-0.5517-0.2421-0.2369-0.1878-0.4513-0.03140.86090.67480.04322.2283-0.07790.798429.176458.2656-4.1489
112.9402-3.9236-0.3885.49450.53990.14940.38280.96540.4042-0.4953-0.2969-0.32320.04831.0021-0.07450.45920.1449-0.01010.71770.0150.28636.382578.1414-4.0572
123.7623-0.5366-2.98762.4041.46572.93750.29360.161-0.18180.0114-0.0443-0.13070.25670.9337-0.20310.45260.1528-0.12420.5444-0.15380.27288.049871.37998.1892
132.7994-0.2398-0.37295.25670.31983.76310.09130.1407-0.0739-0.09020.154-0.07740.14930.1542-0.24110.27580.098-0.1220.42-0.12890.218-4.391561.69414.418
147.41234.18910.74194.9189-1.06461.2360.5257-0.1044-0.40660.6581-0.2063-0.20520.3019-0.0279-0.31150.27950.13-0.06780.3111-0.10960.2393-6.310960.151416.1498
156.46232.75220.96858.51171.58766.8737-0.0161-0.33510.39560.1775-0.06480.9065-0.3937-1.05040.07370.27830.0928-0.04850.5921-0.12530.3814-17.757461.914911.3973
161.01240.4283-0.3380.3687-0.65351.52690.07010.2553-0.0651-0.10220.0739-0.11020.550.3529-0.05380.63580.30250.04761.3991-0.08070.329518.607863.0922-4.1445
173.88390.9495-0.53841.9279-0.69982.7590.118-0.12010.55960.3238-0.01440.0539-0.87550.3403-0.10680.7096-0.08960.16710.3905-0.05040.402543.419385.059966.6149
183.24310.7863-1.59987.07011.08755.1034-0.1386-0.59960.62880.0334-0.02440.7617-0.5425-0.30930.17520.58540.06240.1550.3773-0.17110.362830.706177.043173.6352
196.033-0.97710.42712.299-0.32751.6375-0.0736-0.0018-0.098-0.30160.0902-0.2829-0.03220.3363-0.01410.3257-0.02750.15010.4249-0.04530.270341.423164.377670.0922
202.2308-0.70970.76793.1022-0.73530.4162-0.1843-0.580.32480.53580.3088-0.2093-0.22390.013-0.10960.4086-0.00180.12880.4951-0.08160.265541.116766.921381.6079
215.066-5.8474-5.86737.72615.9487.4925-0.7439-0.7033-0.5071.07360.27840.74120.6468-0.45370.4830.44640.00350.14570.6767-0.01480.400235.032156.432182.1539
228.6753-5.9532-2.71366.73663.2924.86220.17010.2950.0339-0.011-0.501-0.3544-0.42440.05250.32760.728-0.16480.22420.36490.03920.435950.351985.394858.1003
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 49 through 159 )
2X-RAY DIFFRACTION2chain 'A' and (resid 160 through 295 )
3X-RAY DIFFRACTION3chain 'B' and (resid 27 through 59 )
4X-RAY DIFFRACTION4chain 'C' and (resid 49 through 159 )
5X-RAY DIFFRACTION5chain 'C' and (resid 160 through 215 )
6X-RAY DIFFRACTION6chain 'C' and (resid 216 through 258 )
7X-RAY DIFFRACTION7chain 'C' and (resid 259 through 293 )
8X-RAY DIFFRACTION8chain 'D' and (resid 26 through 59 )
9X-RAY DIFFRACTION9chain 'F' and (resid 49 through 73 )
10X-RAY DIFFRACTION10chain 'F' and (resid 74 through 86 )
11X-RAY DIFFRACTION11chain 'F' and (resid 87 through 120 )
12X-RAY DIFFRACTION12chain 'F' and (resid 121 through 175 )
13X-RAY DIFFRACTION13chain 'F' and (resid 176 through 258 )
14X-RAY DIFFRACTION14chain 'F' and (resid 259 through 275 )
15X-RAY DIFFRACTION15chain 'F' and (resid 276 through 294 )
16X-RAY DIFFRACTION16chain 'G' and (resid 27 through 58 )
17X-RAY DIFFRACTION17chain 'J' and (resid 49 through 159 )
18X-RAY DIFFRACTION18chain 'J' and (resid 160 through 175 )
19X-RAY DIFFRACTION19chain 'J' and (resid 176 through 239 )
20X-RAY DIFFRACTION20chain 'J' and (resid 240 through 275 )
21X-RAY DIFFRACTION21chain 'J' and (resid 276 through 295 )
22X-RAY DIFFRACTION22chain 'K' and (resid 29 through 57 )

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