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- PDB-6jze: Crystal structure of VASH2-SVBP complex with the magic triangle I3C -

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Basic information

Entry
Database: PDB / ID: 6jze
TitleCrystal structure of VASH2-SVBP complex with the magic triangle I3C
Components
  • Small vasohibin-binding protein
  • Tubulinyl-Tyr carboxypeptidase 2
KeywordsCYTOSOLIC PROTEIN / VASH2 / SVBP / tubulin detyrosination
Function / homology
Function and homology information


cell-cell fusion / regulation of metallopeptidase activity / syncytium formation by plasma membrane fusion / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / Carboxyterminal post-translational modifications of tubulin / peptidase activator activity / placenta blood vessel development / labyrinthine layer development / labyrinthine layer blood vessel development ...cell-cell fusion / regulation of metallopeptidase activity / syncytium formation by plasma membrane fusion / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / Carboxyterminal post-translational modifications of tubulin / peptidase activator activity / placenta blood vessel development / labyrinthine layer development / labyrinthine layer blood vessel development / negative regulation of endothelial cell migration / axon development / protein secretion / regulation of angiogenesis / metallocarboxypeptidase activity / negative regulation of protein ubiquitination / positive regulation of endothelial cell proliferation / positive regulation of angiogenesis / apical part of cell / actin binding / microtubule binding / cytoskeleton / proteolysis / extracellular region / cytoplasm / cytosol
Similarity search - Function
Tubulinyl-Tyr carboxypeptidase / Small vasohibin-binding protein / Vasohibin / Coiled-coil domain-containing protein 23
Similarity search - Domain/homology
Chem-I3C / Tubulinyl-Tyr carboxypeptidase 2 / Small vasohibin-binding protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.51 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 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 2.0Apr 5, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: database_2 / entity ...database_2 / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / reflns_shell / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _reflns_shell.number_unique_obs

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3966
Polymers46,1602
Non-polymers2,2354
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-15 kcal/mol
Surface area15390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.690, 111.115, 126.454
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-547-

HOH

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Components

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


Mass: 35812.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / 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
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Homo sapiens (human) / Gene: SVBP, CCDC23 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8N300
#3: Chemical
ChemComp-I3C / 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid / 5-Amino-2,4,6-triiodoisophthalic acid


Mass: 558.835 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C8H4I3NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.64 Å3/Da / Density % sol: 53.44 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: BIS-TRIS propane, Sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Oct 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.51→50 Å / Num. obs: 33755 / % possible obs: 100 % / Redundancy: 25.6 % / Biso Wilson estimate: 42.61 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.018 / Net I/σ(I): 53.8
Reflection shellResolution: 2.51→2.6 Å / Rmerge(I) obs: 0.421 / Num. unique obs: 33755 / CC1/2: 0.982 / Rpim(I) all: 0.096

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Processing

Software
NameVersionClassification
PHENIX1.14RC3_3206refinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.51→41.73 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.515
RfactorNum. reflection% reflection
Rfree0.266 3351 9.99 %
Rwork0.221 --
obs0.225 33548 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.59 Å2
Refinement stepCycle: LAST / Resolution: 2.51→41.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2379 0 64 77 2520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112505
X-RAY DIFFRACTIONf_angle_d1.1323384
X-RAY DIFFRACTIONf_dihedral_angle_d20.793961
X-RAY DIFFRACTIONf_chiral_restr0.058348
X-RAY DIFFRACTIONf_plane_restr0.007429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.550.34781370.28291253X-RAY DIFFRACTION99
2.55-2.590.35711410.28271268X-RAY DIFFRACTION100
2.59-2.630.35481410.26941254X-RAY DIFFRACTION100
2.63-2.670.311370.25981255X-RAY DIFFRACTION100
2.67-2.720.34321410.26081273X-RAY DIFFRACTION100
2.72-2.760.35431400.27571268X-RAY DIFFRACTION100
2.76-2.820.38391370.27121254X-RAY DIFFRACTION100
2.82-2.880.30351390.26561286X-RAY DIFFRACTION100
2.88-2.940.31731380.27381241X-RAY DIFFRACTION100
2.94-3.010.3741450.26961301X-RAY DIFFRACTION100
3.01-3.080.25931390.26481234X-RAY DIFFRACTION100
3.08-3.160.3281450.22581303X-RAY DIFFRACTION100
3.16-3.260.27491360.2351222X-RAY DIFFRACTION100
3.26-3.360.31741370.23911256X-RAY DIFFRACTION99
3.36-3.480.31941430.21891267X-RAY DIFFRACTION98
3.48-3.620.24881230.23881192X-RAY DIFFRACTION96
3.62-3.790.26441410.20341243X-RAY DIFFRACTION98
3.79-3.990.2451410.1771260X-RAY DIFFRACTION99
3.99-4.240.18631400.1791233X-RAY DIFFRACTION98
4.24-4.560.20151470.16751260X-RAY DIFFRACTION100
4.56-5.020.19441420.16651276X-RAY DIFFRACTION100
5.02-5.750.22351340.19211262X-RAY DIFFRACTION100
5.75-7.230.23881460.24061266X-RAY DIFFRACTION100
7.23-41.740.2711410.23941270X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -5.2359 Å / Origin y: -32.8272 Å / Origin z: 9.4138 Å
111213212223313233
T0.2534 Å20.007 Å20.0007 Å2-0.348 Å20.0208 Å2--0.2592 Å2
L1.9167 °20.8419 °2-0.8875 °2-3.1165 °2-1.1651 °2--2.8502 °2
S0.0456 Å °0.1556 Å °0.2717 Å °-0.0088 Å °0.2116 Å °0.1701 Å °-0.0623 Å °-0.1892 Å °-0.2514 Å °
Refinement TLS groupSelection details: ALL

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