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- PDB-6ocg: Crystal structure of VASH1-SVBP complex bound with EpoY -

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Basic information

Entry
Database: PDB / ID: 6ocg
TitleCrystal structure of VASH1-SVBP complex bound with EpoY
Components
  • Small vasohibin-binding protein
  • Tubulinyl-Tyr carboxypeptidase 1
Keywordshydrolase/hydrolase inhibitor / carboxypeptidase / tubulin detyrosination / VASH1-SVBP complex / microtubule modification / CYTOSOLIC PROTEIN / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / Carboxyterminal post-translational modifications of tubulin / regulation of cellular senescence / negative regulation of lymphangiogenesis / peptidase activator activity / negative regulation of endothelial cell migration / labyrinthine layer blood vessel development / axon development ...regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / Carboxyterminal post-translational modifications of tubulin / regulation of cellular senescence / negative regulation of lymphangiogenesis / peptidase activator activity / negative regulation of endothelial cell migration / labyrinthine layer blood vessel development / 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 / microtubule binding / angiogenesis / cytoskeleton / regulation of cell cycle / 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
Chem-BJL / Tubulinyl-Tyr carboxypeptidase 1 / Small vasohibin-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.833 Å
AuthorsLi, F. / Luo, X. / Yu, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)RP150583-P2 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2019
Title: Structural basis of tubulin detyrosination by vasohibins.
Authors: Li, F. / Hu, Y. / Qi, S. / Luo, X. / Yu, H.
History
DepositionMar 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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 1
B: Small vasohibin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2565
Polymers31,8032
Non-polymers4533
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-26 kcal/mol
Surface area13920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.671, 126.454, 46.082
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Tubulinyl-Tyr carboxypeptidase 1 / / Tubulin carboxypeptidase 1 / Tyrosine carboxypeptidase 1 / TTCP 1 / Vasohibin-1


Mass: 28665.246 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 BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q7L8A9, tubulinyl-Tyr carboxypeptidase
#2: Protein/peptide Small vasohibin-binding protein / Coiled coil domain-containing protein 23


Mass: 3137.525 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 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8N300

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Non-polymers , 4 types, 341 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-BJL / N-[(3R)-4-ethoxy-3-hydroxy-4-oxobutanoyl]-L-tyrosine


Mass: 325.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C15H19NO7
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 3.22 Å3/Da / Density % sol: 61.75 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 5% (v/v) TacsimateTM, 0.1 M HEPES, pH 7.0, and 10% (w/v) polyethylene glycol monomethyl ether 5,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 37002 / % possible obs: 99.6 % / Redundancy: 13.1 % / Biso Wilson estimate: 19.01 Å2 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.016 / Rrim(I) all: 0.058 / Χ2: 0.952 / Net I/σ(I): 50.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.83-1.8613.33.54118110.6170.9943.6810.90399.8
1.86-1.913.52.46918020.710.6892.5650.93799.7
1.9-1.9313.41.91318360.7760.5361.9880.97599.8
1.93-1.9713.41.44818160.8680.4061.5050.94899.5
1.97-2.0113.21.1118230.9060.3131.1550.93399.6
2.01-2.06130.82218160.9540.2330.8550.95799.9
2.06-2.1112.80.57318390.9730.1660.5970.99799.9
2.11-2.1711.90.40318310.9770.1210.4210.9999.3
2.17-2.2312.70.31117910.9880.0890.3240.99398.5
2.23-2.3113.60.26418450.9940.0740.2741.09399.8
2.31-2.3913.60.17318300.9950.0480.180.97899.6
2.39-2.4813.50.13918430.9960.0390.1450.96999.7
2.48-2.613.40.10618530.9970.030.110.93899.7
2.6-2.7312.90.0818490.9980.0230.0830.948100
2.73-2.912.20.06418600.9980.0190.0670.94199.6
2.9-3.1313.80.05218590.9990.0150.0540.95799.8
3.13-3.4413.60.04418710.9990.0120.0460.95399.7
3.44-3.9412.80.0418770.9990.0110.0410.95699.4
3.94-4.9712.50.03419110.9990.010.0350.85999.3
4.97-5012.20.03120390.9980.0090.0320.81599.5

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OCF

6ocf


Resolution: 1.833→47.121 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.29
RfactorNum. reflection% reflection
Rfree0.2187 1662 5 %
Rwork0.1771 --
obs0.1792 33223 89.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.38 Å2 / Biso mean: 30.3425 Å2 / Biso min: 6.9 Å2
Refinement stepCycle: final / Resolution: 1.833→47.121 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2238 0 30 338 2606
Biso mean--47.91 39.28 -
Num. residues----273
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8329-1.88680.3062550.26551035109036
1.8868-1.94770.2764890.25581690177959
1.9477-2.01740.25891280.24972441256984
2.0174-2.09810.2841500.2262859300998
2.0981-2.19360.25441500.2012847299798
2.1936-2.30930.24461520.190828743026100
2.3093-2.45390.2391530.179729093062100
2.4539-2.64340.23111540.185429323086100
2.6434-2.90940.25381540.180629273081100
2.9094-3.33030.20561550.167629473102100
3.3303-4.19540.19611570.14312981313899
4.1954-47.13660.16211650.154731193284100
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)
11.14822.50960.24435.5981-0.10163.84640.1009-0.09550.63040.4128-0.16750.1372-0.6051-0.50970.05460.24040.09560.02820.1582-0.01730.3093-43.383434.419-21.3594
22.2016-1.0350.83382.09520.0833.8119-0.07890.71850.6446-0.49230.029-0.3848-0.4248-0.1260.0080.20380.03360.05450.3180.1330.2795-37.338532.5504-35.0751
31.19290.46280.38351.1788-0.80971.0404-0.0218-0.1904-0.1830.08210.02540.19830.0207-0.1181-0.0840.1222-0.06190.10780.05680.00150.1833-35.072515.1155-16.1024
43.20321.2504-0.44771.914-0.40051.22480.0808-0.44060.15590.378-0.07350.09220.004-0.0404-0.0620.2005-0.02020.0810.2124-0.0050.0899-25.135419.1002-5.1007
52.6696-0.1447-0.23651.2565-0.19452.4220.0055-0.94520.01920.72880.0954-0.0247-0.00930.0076-0.00890.6526-0.00010.00140.6114-0.01650.1421-20.761518.92377.7991
66.97361.4032-0.37886.1998-0.18015.1453-0.00830.38270.0278-0.34450.0134-0.0147-0.0033-0.1628-0.03150.09540.02150.03130.03940.02030.0938-38.391526.2423-29.4141
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 59 through 84 )A59 - 84
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 105 )A85 - 105
3X-RAY DIFFRACTION3chain 'A' and (resid 106 through 180 )A106 - 180
4X-RAY DIFFRACTION4chain 'A' and (resid 181 through 277 )A181 - 277
5X-RAY DIFFRACTION5chain 'A' and (resid 278 through 305 )A278 - 305
6X-RAY DIFFRACTION6chain 'B' and (resid 26 through 51 )B26 - 51

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