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- PDB-6j8f: Crystal structure of SVBP-VASH1 with peptide mimic the C-terminal... -

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Basic information

Entry
Database: PDB / ID: 6j8f
TitleCrystal structure of SVBP-VASH1 with peptide mimic the C-terminal of alpha-tubulin
Components
  • 8-mer peptide
  • Small vasohibin-binding protein
  • Tubulinyl-Tyr carboxypeptidase 1
KeywordsPEPTIDE BINDING PROTEIN/HYDROLASE / protease / complex / PEPTIDE BINDING PROTEIN / Structural Genomics / PSI-2 / Protein Structure Initiative / Structural Genomics Consortium / SGC / PEPTIDE BINDING PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / Post-chaperonin tubulin folding pathway / organelle transport along microtubule / axonemal microtubule / negative regulation of lymphangiogenesis / regulation of cellular senescence / Cilium Assembly / cytoskeleton-dependent intracellular transport ...regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / Post-chaperonin tubulin folding pathway / organelle transport along microtubule / axonemal microtubule / negative regulation of lymphangiogenesis / regulation of cellular senescence / Cilium Assembly / cytoskeleton-dependent intracellular transport / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Carboxyterminal post-translational modifications of tubulin / peptidase activator activity / forebrain morphogenesis / glial cell differentiation / Intraflagellar transport / neuron projection arborization / Sealing of the nuclear envelope (NE) by ESCRT-III / cerebellar cortex morphogenesis / flagellated sperm motility / Formation of tubulin folding intermediates by CCT/TriC / dentate gyrus development / Gap junction assembly / Prefoldin mediated transfer of substrate to CCT/TriC / COPI-independent Golgi-to-ER retrograde traffic / Kinesins / centrosome cycle / Assembly and cell surface presentation of NMDA receptors / labyrinthine layer blood vessel development / pyramidal neuron differentiation / negative regulation of endothelial cell migration / motor behavior / COPI-dependent Golgi-to-ER retrograde traffic / smoothened signaling pathway / response to L-glutamate / regulation of synapse organization / axon development / startle response / negative regulation of endothelial cell proliferation / locomotory exploration behavior / Recycling pathway of L1 / microtubule polymerization / negative regulation of blood vessel endothelial cell migration / protein secretion / sperm flagellum / response to tumor necrosis factor / regulation of angiogenesis / RHO GTPases activate IQGAPs / microtubule-based process / Hedgehog 'off' state / response to mechanical stimulus / Activation of AMPK downstream of NMDARs / COPI-mediated anterograde transport / condensed chromosome / homeostasis of number of cells within a tissue / metallocarboxypeptidase activity / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / negative regulation of protein ubiquitination / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Resolution of Sister Chromatid Cohesion / cellular response to calcium ion / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / negative regulation of angiogenesis / adult locomotory behavior / AURKA Activation by TPX2 / Translocation of SLC2A4 (GLUT4) to the plasma membrane / intracellular protein transport / RHO GTPases Activate Formins / synapse organization / neuromuscular junction / visual learning / PKR-mediated signaling / recycling endosome / cerebral cortex development / structural constituent of cytoskeleton / memory / response to wounding / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / HCMV Early Events / neuron migration / Aggrephagy / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / apical part of cell / Regulation of PLK1 Activity at G2/M Transition / mitotic cell cycle / actin binding / microtubule cytoskeleton / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / neuron apoptotic process / gene expression / angiogenesis
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
Tubulin alpha-1A chain / Tubulinyl-Tyr carboxypeptidase 1 / Small vasohibin-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.283 Å
AuthorsLiao, S. / Gao, J. / Xu, C. / Structural Genomics Consortium (SGC)
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31500601 China
National Natural Science Foundation of China31570737 China
National Natural Science Foundation of China31770806 China
CitationJournal: Cell Res. / Year: 2019
Title: Molecular basis of vasohibins-mediated detyrosination and its impact on spindle function and mitosis.
Authors: Liao, S. / Rajendraprasad, G. / Wang, N. / Eibes, S. / Gao, J. / Yu, H. / Wu, G. / Tu, X. / Huang, H. / Barisic, M. / Xu, C.
History
DepositionJan 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 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 1.2Mar 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
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Small vasohibin-binding protein
B: Tubulinyl-Tyr carboxypeptidase 1
C: 8-mer peptide


Theoretical massNumber of molelcules
Total (without water)33,9933
Polymers33,9933
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-17 kcal/mol
Surface area13830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.950, 108.377, 46.896
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/peptide Small vasohibin-binding protein / Coiled coil domain-containing protein 23


Mass: 5410.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SVBP, CCDC23
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8N300
#2: Protein Tubulinyl-Tyr carboxypeptidase 1 / Tubulin carboxypeptidase 1 / Tyrosine carboxypeptidase 1 / TTCP 1 / Vasohibin-1


Mass: 27668.096 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VASH1, KIAA1036, VASH / Production host: Escherichia coli (E. coli) / References: UniProt: Q7L8A9, tubulinyl-Tyr carboxypeptidase
#3: Protein/peptide 8-mer peptide


Mass: 914.891 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q71U36*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M Na citrate tribasic dihydrate pH 5.0, 18% PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.28→54.19 Å / Num. obs: 16147 / % possible obs: 99.9 % / Redundancy: 12.5 % / Net I/σ(I): 10.9
Reflection shellResolution: 2.28→2.41 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2322 / CC1/2: 0.726 / Rpim(I) all: 0.491 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIX(1.14_3260: ???)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: low resolution SeMet structure

Resolution: 2.283→54.188 Å / SU ML: 0.25 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 27.74
RfactorNum. reflection% reflection
Rfree0.2369 828 5.14 %
Rwork0.1995 --
obs0.2015 16109 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.283→54.188 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2141 0 0 44 2185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032176
X-RAY DIFFRACTIONf_angle_d0.6852936
X-RAY DIFFRACTIONf_dihedral_angle_d5.7411325
X-RAY DIFFRACTIONf_chiral_restr0.043314
X-RAY DIFFRACTIONf_plane_restr0.004378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2825-2.42550.32661410.28172488X-RAY DIFFRACTION100
2.4255-2.61280.33911380.2632518X-RAY DIFFRACTION100
2.6128-2.87570.28061320.22592496X-RAY DIFFRACTION100
2.8757-3.29180.22591300.20192538X-RAY DIFFRACTION100
3.2918-4.14710.21241250.18122567X-RAY DIFFRACTION100
4.1471-54.20380.21111620.17772674X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 26.5379 Å / Origin y: 19.938 Å / Origin z: 10.6746 Å
111213212223313233
T0.2786 Å20.022 Å2-0.0092 Å2-0.2648 Å2-0.0144 Å2--0.2899 Å2
L0.956 °2-0.3296 °2-0.0942 °2-1.0518 °2-0.2592 °2--0.5915 °2
S0.0031 Å °-0.0061 Å °0.0053 Å °0.0271 Å °-0.0067 Å °-0.0436 Å °-0.0849 Å °-0.0281 Å °-0.0002 Å °
Refinement TLS groupSelection details: all

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