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- PDB-6jzd: Crystal structure of peptide-bound VASH2-SVBP complex -

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Basic information

Entry
Database: PDB / ID: 6jzd
TitleCrystal structure of peptide-bound VASH2-SVBP complex
Components
  • GLU-GLY-GLU-GLU-TYR
  • Small vasohibin-binding protein
  • Tubulinyl-Tyr carboxypeptidase 2
KeywordsCYTOSOLIC PROTEIN / VASH2 / SVBP / tubulin detyrosination
Function / homology
Function and homology information


labyrinthine layer development / cell-cell fusion / regulation of metallopeptidase activity / syncytium formation by cell-cell fusion / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cargo trafficking to the periciliary membrane / Sealing of the nuclear envelope (NE) by ESCRT-III / Carboxyterminal post-translational modifications of tubulin ...labyrinthine layer development / cell-cell fusion / regulation of metallopeptidase activity / syncytium formation by cell-cell fusion / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cargo trafficking to the periciliary membrane / Sealing of the nuclear envelope (NE) by ESCRT-III / Carboxyterminal post-translational modifications of tubulin / Intraflagellar transport / COPI-independent Golgi-to-ER retrograde traffic / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / pyramidal neuron differentiation / placenta blood vessel development / COPI-mediated anterograde transport / Kinesins / labyrinthine layer blood vessel development / PKR-mediated signaling / Aggrephagy / RHO GTPases activate IQGAPs / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / COPI-dependent Golgi-to-ER retrograde traffic / glial cell differentiation / Resolution of Sister Chromatid Cohesion / The role of GTSE1 in G2/M progression after G2 checkpoint / Recycling pathway of L1 / dentate gyrus development / Carboxyterminal post-translational modifications of tubulin / axonemal microtubule / organelle transport along microtubule / Hedgehog 'off' state / RHO GTPases Activate Formins / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Separation of Sister Chromatids / Anchoring of the basal body to the plasma membrane / forebrain morphogenesis / Recruitment of NuMA to mitotic centrosomes / AURKA Activation by TPX2 / cerebellar cortex morphogenesis / Regulation of PLK1 Activity at G2/M Transition / MHC class II antigen presentation / neuron projection arborization / smoothened signaling pathway / homeostasis of number of cells within a tissue / motor behavior / adult behavior / negative regulation of endothelial cell migration / response to L-glutamate / centrosome cycle / peptidase activator activity / startle response / 'de novo' protein folding / axon development / flagellated sperm motility / regulation of synapse organization / locomotory exploration behavior / protein secretion / microtubule polymerization / response to tumor necrosis factor / regulation of angiogenesis / response to mechanical stimulus / neuron apoptotic process / neurogenesis / sperm flagellum / adult locomotory behavior / cytoplasmic microtubule / condensed chromosome / positive regulation of endothelial cell proliferation / metallocarboxypeptidase activity / negative regulation of protein ubiquitination / cellular response to calcium ion / gene expression / visual learning / locomotory behavior / hippocampus development / neuromuscular junction / myelin sheath / neuron migration / memory / cerebral cortex development / intracellular protein transport / synapse organization / microtubule cytoskeleton organization / recycling endosome / structural constituent of cytoskeleton / positive regulation of angiogenesis / cytoplasmic ribonucleoprotein granule / apical part of cell / microtubule cytoskeleton / cilium / neuron differentiation / mitotic cell cycle / protein-folding chaperone binding / actin binding / microtubule binding / microtubule
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 2 / Small vasohibin-binding protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.479 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

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Assembly

Deposited unit
A: Tubulinyl-Tyr carboxypeptidase 2
B: Small vasohibin-binding protein
C: GLU-GLY-GLU-GLU-TYR


Theoretical massNumber of molelcules
Total (without water)52,5413
Polymers52,5413
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-21 kcal/mol
Surface area14500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.004, 111.339, 126.317
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: 40536.906 Da / Num. of mol.: 1 / Mutation: C158A
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.: 1
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: Protein/peptide GLU-GLY-GLU-GLU-TYR


Mass: 1656.568 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P68369*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.48 Å3/Da / Density % sol: 50.33 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: HEPES, potassium chloride, Ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 18801 / % possible obs: 99.6 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.025 / Net I/σ(I): 17.1
Reflection shellResolution: 2.48→2.58 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.759 / Num. unique obs: 2048 / CC1/2: 0.764 / Rpim(I) all: 0.332 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(1.14rc3_3206: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.479→44.11 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2296 911 4.85 %
Rwork0.1793 --
obs0.1816 18768 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.479→44.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2402 0 0 16 2418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082462
X-RAY DIFFRACTIONf_angle_d0.9433315
X-RAY DIFFRACTIONf_dihedral_angle_d16.1041492
X-RAY DIFFRACTIONf_chiral_restr0.053348
X-RAY DIFFRACTIONf_plane_restr0.005422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4787-2.60940.31891380.25112448X-RAY DIFFRACTION98
2.6094-2.77280.25391390.22912528X-RAY DIFFRACTION100
2.7728-2.98690.27831250.20942530X-RAY DIFFRACTION100
2.9869-3.28740.27591300.21442541X-RAY DIFFRACTION100
3.2874-3.76290.26351310.19022559X-RAY DIFFRACTION99
3.7629-4.73990.19531160.15332584X-RAY DIFFRACTION99
4.7399-44.11710.19661320.16462667X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 3.8197 Å / Origin y: 22.1721 Å / Origin z: -9.8623 Å
111213212223313233
T0.4035 Å2-0.0288 Å20.022 Å2-0.4845 Å2-0.0196 Å2--0.4206 Å2
L2.0739 °2-0.3446 °2-0.5696 °2-3.02 °20.3909 °2--2.0512 °2
S0.0733 Å °0.0034 Å °0.2797 Å °-0.1396 Å °0.0885 Å °-0.0598 Å °-0.183 Å °0.0303 Å °-0.1645 Å °
Refinement TLS groupSelection details: all

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