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- PDB-6j4v: Structural basis of tubulin detyrosination by vasohibins-SVBP enz... -

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Basic information

Entry
Database: PDB / ID: 6j4v
TitleStructural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications
Components
  • Small vasohibin-binding protein
  • Tubulin alpha-1B chain
  • Tubulinyl-Tyr carboxypeptidase 2
KeywordsHYDROLASE / carboxypeptidase / tubulin / microtubule.
Function / homology
Function and homology information


cell-cell fusion / syncytium formation by plasma membrane fusion / regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / Post-chaperonin tubulin folding pathway / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / peptidase activator activity ...cell-cell fusion / syncytium formation by plasma membrane fusion / regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / Post-chaperonin tubulin folding pathway / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / peptidase activator activity / cytoskeleton-dependent intracellular transport / Intraflagellar transport / Sealing of the nuclear envelope (NE) by ESCRT-III / Gap junction assembly / Formation of tubulin folding intermediates by CCT/TriC / COPI-independent Golgi-to-ER retrograde traffic / Kinesins / Assembly and cell surface presentation of NMDA receptors / negative regulation of endothelial cell migration / COPI-dependent Golgi-to-ER retrograde traffic / labyrinthine layer blood vessel development / axon development / Recycling pathway of L1 / RHOH GTPase cycle / protein secretion / RHO GTPases activate IQGAPs / Hedgehog 'off' state / regulation of angiogenesis / cytoplasmic microtubule / metallocarboxypeptidase activity / microtubule-based process / COPI-mediated anterograde transport / Activation of AMPK downstream of NMDARs / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / negative regulation of protein ubiquitination / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / cellular response to interleukin-4 / positive regulation of endothelial cell proliferation / RHO GTPases Activate Formins / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / PKR-mediated signaling / structural constituent of cytoskeleton / microtubule cytoskeleton organization / Aggrephagy / HCMV Early Events / Separation of Sister Chromatids / positive regulation of angiogenesis / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / double-stranded RNA binding / apical part of cell / mitotic cell cycle / actin binding / microtubule binding / microtubule / cytoskeleton / cell division / GTPase activity / ubiquitin protein ligase binding / GTP binding / structural molecule activity / proteolysis / extracellular region / cytosol / cytoplasm
Similarity search - Function
Tubulinyl-Tyr carboxypeptidase / Small vasohibin-binding protein / Vasohibin / Coiled-coil domain-containing protein 23 / Alpha tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. ...Tubulinyl-Tyr carboxypeptidase / Small vasohibin-binding protein / Vasohibin / Coiled-coil domain-containing protein 23 / Alpha tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Tubulin alpha-1B chain / Tubulinyl-Tyr carboxypeptidase 2 / Small vasohibin-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.2Jan 15, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.3Nov 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

Downloads & links

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Assembly

Deposited unit
A: Tubulinyl-Tyr carboxypeptidase 2
B: Small vasohibin-binding protein
C: Tubulin alpha-1B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0109
Polymers39,4523
Non-polymers5586
Water4,306239
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.281, 122.413, 194.269
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-625-

HOH

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 29322.422 Da / Num. of mol.: 1
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: 7805.874 Da / Num. of mol.: 1 / Mutation: C58S
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

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 2323.269 Da / Num. of mol.: 1 / Mutation: E450C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TUBA1B / Plasmid: pGEX6p / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P68363

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Non-polymers , 3 types, 245 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 239 / 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: 3.1 Å3/Da / Density % sol: 60.32 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 8.2
Details: For crystallization of V2c-SVBP C58S in complex with the maTail peptide the components were mixed in a 1:3 molar ratio and incubated at room temperature for 24 h before setting up ...Details: For crystallization of V2c-SVBP C58S in complex with the maTail peptide the components were mixed in a 1:3 molar ratio and incubated at room temperature for 24 h before setting up crystallization trials. The resulting V2c-SVBP S58C-maTail complex was crystallized in 1.4 M sodium/potassium phosphate, pH 8.2.
PH range: 8.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 28792 / % possible obs: 99 % / Redundancy: 9.6 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.04 / Net I/σ(I): 12.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2635 / CC1/2: 0.866 / Rpim(I) all: 0.196 / % possible all: 91.2

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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: 2.1→38.045 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.09
RfactorNum. reflection% reflection
Rfree0.1996 1436 5.04 %
Rwork0.1688 --
obs0.1704 28518 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→38.045 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2348 0 34 239 2621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072434
X-RAY DIFFRACTIONf_angle_d0.7873271
X-RAY DIFFRACTIONf_dihedral_angle_d11.1191466
X-RAY DIFFRACTIONf_chiral_restr0.05341
X-RAY DIFFRACTIONf_plane_restr0.005412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.17510.29971520.25322467X-RAY DIFFRACTION92
2.1751-2.26220.28881150.21882686X-RAY DIFFRACTION99
2.2622-2.36510.24051500.19142689X-RAY DIFFRACTION100
2.3651-2.48980.22081430.19082713X-RAY DIFFRACTION100
2.4898-2.64580.21051410.18992733X-RAY DIFFRACTION100
2.6458-2.850.23721420.17862718X-RAY DIFFRACTION100
2.85-3.13670.2151540.18472717X-RAY DIFFRACTION100
3.1367-3.59020.18881520.16232733X-RAY DIFFRACTION100
3.5902-4.52220.15931400.13062761X-RAY DIFFRACTION100
4.5222-38.05120.17931470.16252865X-RAY DIFFRACTION100
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)
15.8922-2.67740.34934.3557-1.32554.8483-0.1175-0.7234-0.09360.3220.13320.34450.1683-0.801-0.07090.3397-0.02990.08360.6522-0.01460.299441.651928.394389.6191
24.60375.1375-1.15698.49080.85473.91230.1591-0.9961-0.08440.6058-0.3496-0.6411-0.0220.35160.17710.259-0.0001-0.03960.6849-0.00860.318356.224829.087190.8074
32.9742-0.56912.44150.23530.32478.75780.09080.2551-0.0654-0.0828-0.0729-0.0111-0.41550.34840.02950.2364-0.05610.01250.32490.03420.242949.885831.539960.8811
46.0061-0.97924.05811.4805-0.32337.26710.0567-0.43790.07320.1254-0.02580.2708-0.1029-0.4006-0.03530.2341-0.03280.02950.2582-0.01180.268639.076429.862473.2473
52.99460.44760.44686.6223-2.95467.38060.1797-0.1963-0.22370.52330.14460.19320.2704-0.2906-0.24620.2466-0.0386-0.03560.2061-0.03320.247837.676817.078365.6026
63.33761.36231.19276.8508-1.16544.08130.00340.1297-0.3485-0.22010.0455-0.21760.48320.1283-0.03810.21860.01790.0180.1759-0.030.253344.618712.9461.5963
74.1755-1.35471.43818.0709-2.30724.0512-0.00830.032-0.0494-0.02490.37920.71620.0902-0.5608-0.47940.2157-0.0658-0.02030.3155-0.00260.296732.394618.795163.6176
83.6074-2.7453-0.78032.16780.91492.6175-0.2079-0.0156-0.10790.3580.14580.72130.3591-0.34690.08050.3233-0.0899-0.03580.33790.00120.412227.930314.294864.579
95.4669-2.5843-0.07716.8137-2.87447.27990.03520.5553-0.1059-1.27450.07620.61770.2974-0.7964-0.23850.4492-0.0873-0.14520.3683-0.04820.379630.468210.355253.0038
107.6974-4.11851.05357.72270.83015.2770.0009-0.2714-0.09550.1960.0379-0.3361-0.09580.4999-0.03640.2161-0.08150.0270.44970.01760.17651.81226.957383.5135
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 49 through 73 )
2X-RAY DIFFRACTION2chain 'A' and (resid 74 through 94 )
3X-RAY DIFFRACTION3chain 'A' and (resid 95 through 121 )
4X-RAY DIFFRACTION4chain 'A' and (resid 122 through 169 )
5X-RAY DIFFRACTION5chain 'A' and (resid 170 through 200 )
6X-RAY DIFFRACTION6chain 'A' and (resid 201 through 239 )
7X-RAY DIFFRACTION7chain 'A' and (resid 240 through 258 )
8X-RAY DIFFRACTION8chain 'A' and (resid 259 through 275 )
9X-RAY DIFFRACTION9chain 'A' and (resid 276 through 294 )
10X-RAY DIFFRACTION10chain 'B' and (resid 24 through 59 )

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