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- PDB-6ocf: The crystal structure of VASH1-SVBP complex -

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Basic information

Entry
Database: PDB / ID: 6ocf
TitleThe crystal structure of VASH1-SVBP complex
Components
  • Small vasohibin-binding protein
  • Tubulinyl-Tyr carboxypeptidase 1
KeywordsHYDROLASE/PROTEIN BINDING / tubulin carboxypeptidases / microtubule modification / tubulin detyrosination / VASH1-SVBP complex / HYDROLASE-PROTEIN BINDING 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 / SAD / Resolution: 2.102 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)RP150538-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 1.4Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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)35,2194
Polymers35,0912
Non-polymers1282
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-23 kcal/mol
Surface area16680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.558, 100.558, 206.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-518-

HOH

21A-633-

HOH

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Components

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


Mass: 29092.645 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: 5998.477 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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.72 Å3/Da / Density % sol: 66.96 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M sodium citrate tribasic dihydrate, pH 5.0, and 18% (w/v) PEG20000

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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: Mar 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 48368 / % possible obs: 99.6 % / Redundancy: 24.5 % / Biso Wilson estimate: 24.27 Å2 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.018 / Rrim(I) all: 0.09 / Χ2: 1.072 / Net I/σ(I): 42.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.1420.42.56814760.5470.5282.6250.91997
2.14-2.1821.32.34615130.6050.4782.3970.93997.9
2.18-2.2222.11.94115110.6910.3991.9840.9599
2.22-2.2623.11.62715190.8060.3271.6610.94699.3
2.26-2.3123.41.41115560.8390.2851.440.93799.8
2.31-2.37241.09415410.910.2211.1170.92999.9
2.37-2.4224.40.93715220.9390.190.9560.934100
2.42-2.4922.50.75815450.9570.1620.7760.93899.9
2.49-2.5625.20.64415580.9680.1290.6570.941100
2.56-2.6526.40.51615440.980.10.5260.96100
2.65-2.7426.30.35415500.990.0690.360.96799.9
2.74-2.8526.30.28315560.9930.0550.2880.99299.9
2.85-2.9826.10.20215420.9950.040.2051.00999.9
2.98-3.1425.30.15315710.9970.0310.1561.034100
3.14-3.3323.80.11515500.9970.0240.1181.09599.8
3.33-3.5927.20.08715850.9980.0170.0891.265100
3.59-3.9526.70.0715690.9990.0140.0711.399100
3.95-4.5225.50.05615920.9990.0110.0571.35100
4.52-5.724.80.05116150.9990.010.0521.25299.9
5.7-5024.40.04117210.9990.0090.0421.48899.7

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Coot1.13_2998model building
HKL-3000data reduction
HKL-3000data collection
AutoSolphasing
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.102→45.214 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.71
RfactorNum. reflection% reflection
Rfree0.222 2405 4.97 %
Rwork0.1958 --
obs0.1972 48368 82.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 149.8 Å2 / Biso mean: 41.7347 Å2 / Biso min: 9.12 Å2
Refinement stepCycle: final / Resolution: 2.102→45.214 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2438 0 15 168 2621
Biso mean--37.96 44.98 -
Num. residues----297
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1022-2.14510.3193440.306484989326
2.1451-2.19170.3768670.30481244131138
2.1917-2.24270.335820.29271578166048
2.2427-2.29880.3429940.27561875196957
2.2988-2.3610.23621130.26912185229867
2.361-2.43040.29561290.25122517264676
2.4304-2.50890.29771560.24982939309589
2.5089-2.59850.26491670.23883152331996
2.5985-2.70260.24721750.22573295347099
2.7026-2.82550.23291710.211132673438100
2.8255-2.97450.22851770.196732923469100
2.9745-3.16080.2021740.189133153489100
3.1608-3.40480.2261720.183332613433100
3.4048-3.74730.22281760.167333133489100
3.7473-4.28910.14781700.152232753445100
4.2891-5.40240.17621680.157733043472100
5.4024-45.22420.22351700.190433023472100
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)
14.22691.52732.7132.1670.92583.57850.1155-0.32990.02330.28550.0053-0.2752-0.10190.10170.00830.18640.0302-0.09350.3293-0.19740.1783119.4676113.970621.2871
29.04874.9805-4.94153.8954-4.91936.88960.11170.398-0.98870.08470.2418-0.48590.5781-0.057-0.37590.25920.0821-0.04920.2460.02530.206288.193896.81746.4894
30.9421-0.7598-0.04473.29080.16341.08760.3418-0.1153-0.1156-0.08530.0215-0.31780.08990.1935-0.08460.2670.0052-0.06560.4727-0.18510.2302123.9703114.800319.9969
40.8993-0.1565-0.10190.97660.32060.38630.0914-0.1661-0.1165-0.07220.1498-0.7582-0.02580.33430.0083-0.10730.0119-0.06510.3753-0.15520.4296127.731697.52656.2367
58.08111.3680.52284.85671.06722.97810.14680.3351-0.5592-0.19510.0909-0.34250.49780.631-0.22960.53290.12850.10150.4825-0.25130.699130.598185.3276-7.0656
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 18 through 61 )B18 - 61
2X-RAY DIFFRACTION2chain 'B' and (resid 62 through 66 )B62 - 66
3X-RAY DIFFRACTION3chain 'A' and (resid 58 through 117 )A58 - 117
4X-RAY DIFFRACTION4chain 'A' and (resid 118 through 286 )A118 - 286
5X-RAY DIFFRACTION5chain 'A' and (resid 287 through 305 )A287 - 305

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