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- PDB-6j9h: Crystal structure of SVBP-VASH1 complex -

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Basic information

Entry
Database: PDB / ID: 6j9h
TitleCrystal structure of SVBP-VASH1 complex
Components
  • Small vasohibin-binding protein
  • Tubulinyl-Tyr carboxypeptidase 1
KeywordsPEPTIDE BINDING PROTEIN/HYDROLASE / protease / complex / PEPTIDE BINDING PROTEIN / Structural Genomics / 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 / negative regulation of lymphangiogenesis / regulation of cellular senescence / Carboxyterminal post-translational modifications of tubulin / negative regulation of endothelial cell migration / labyrinthine layer blood vessel development / peptidase activator activity / axon development ...regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / negative regulation of lymphangiogenesis / regulation of cellular senescence / Carboxyterminal post-translational modifications of tubulin / negative regulation of endothelial cell migration / labyrinthine layer blood vessel development / peptidase activator activity / axon development / negative regulation of endothelial cell proliferation / negative regulation of blood vessel endothelial cell migration / protein secretion / regulation of angiogenesis / metallocarboxypeptidase activity / negative regulation of protein ubiquitination / negative regulation of angiogenesis / response to wounding / apical part of cell / actin binding / angiogenesis / microtubule binding / cytoskeleton / regulation of cell cycle / endoplasmic reticulum / proteolysis / extracellular space / extracellular region / 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 1 / Small vasohibin-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 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 22, 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 1.2Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Small vasohibin-binding protein
B: Tubulinyl-Tyr carboxypeptidase 1
C: Small vasohibin-binding protein
D: Tubulinyl-Tyr carboxypeptidase 1


Theoretical massNumber of molelcules
Total (without water)70,9804
Polymers70,9804
Non-polymers00
Water2,288127
1
A: Small vasohibin-binding protein
B: Tubulinyl-Tyr carboxypeptidase 1


Theoretical massNumber of molelcules
Total (without water)35,4902
Polymers35,4902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-12 kcal/mol
Surface area14470 Å2
MethodPISA
2
C: Small vasohibin-binding protein
D: Tubulinyl-Tyr carboxypeptidase 1


Theoretical massNumber of molelcules
Total (without water)35,4902
Polymers35,4902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-12 kcal/mol
Surface area13850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.516, 93.372, 126.041
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Small vasohibin-binding protein / Coiled coil domain-containing protein 23


Mass: 7821.939 Da / Num. of mol.: 2
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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VASH1, KIAA1036, VASH
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q7L8A9, tubulinyl-Tyr carboxypeptidase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.96 Å3/Da / Density % sol: 58.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M Na citrate tribasic dihydrate pH 5.5, 16% PEG 8000, 0.01M Cadmium chloride hydrate

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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: Jun 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.31→75.03 Å / Num. obs: 37912 / % possible obs: 99.9 % / Redundancy: 12.6 % / Rpim(I) all: 0.075 / Net I/σ(I): 8.8
Reflection shellResolution: 2.31→2.43 Å / Redundancy: 13.3 % / Mean I/σ(I) obs: 3.4 / Num. unique obs: 5413 / CC1/2: 0.895 / Rpim(I) all: 0.428 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: 000)refinement
XDSdata reduction
XDSdata scaling
PHENIX(1.14_3260: 000)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J91

6j91


Resolution: 2.31→62.201 Å / SU ML: 0.24 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 31.67
RfactorNum. reflection% reflection
Rfree0.2709 1781 4.71 %
Rwork0.2477 --
obs0.2488 37795 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.31→62.201 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4309 0 0 127 4436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074409
X-RAY DIFFRACTIONf_angle_d1.3765942
X-RAY DIFFRACTIONf_dihedral_angle_d11.3512706
X-RAY DIFFRACTIONf_chiral_restr0.065635
X-RAY DIFFRACTIONf_plane_restr0.006764
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3063-2.36870.3411320.29792711X-RAY DIFFRACTION100
2.3687-2.43840.29561220.28022751X-RAY DIFFRACTION100
2.4384-2.51710.31321400.28212715X-RAY DIFFRACTION100
2.5171-2.60710.26581320.28762742X-RAY DIFFRACTION100
2.6071-2.71150.28631400.27172739X-RAY DIFFRACTION100
2.7115-2.83490.32511460.27422742X-RAY DIFFRACTION100
2.8349-2.98430.28751370.28242753X-RAY DIFFRACTION100
2.9843-3.17130.29771350.27382761X-RAY DIFFRACTION100
3.1713-3.41610.3021480.26662756X-RAY DIFFRACTION100
3.4161-3.75990.30751370.24562773X-RAY DIFFRACTION100
3.7599-4.30380.24941330.20732794X-RAY DIFFRACTION100
4.3038-5.42190.2241470.21652842X-RAY DIFFRACTION100
5.4219-62.22350.23351320.24142935X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -0.1665 Å / Origin y: -10.0602 Å / Origin z: -32.9116 Å
111213212223313233
T0.2129 Å20.0091 Å20.0254 Å2-0.2331 Å2-0.0266 Å2--0.2936 Å2
L0.4867 °20.0497 °20.3799 °2-0.3938 °20.4404 °2--1.4544 °2
S0.1175 Å °0.0311 Å °0.0056 Å °0.0612 Å °-0.0121 Å °-0.0152 Å °0.0852 Å °0.0635 Å °-0.0909 Å °
Refinement TLS groupSelection details: all

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