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- PDB-6j8o: Structure of a hypothetical protease -

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Basic information

Entry
Database: PDB / ID: 6j8o
TitleStructure of a hypothetical protease
Components
  • 8-mer peptide
  • Small vasohibin-binding protein
  • Tubulinyl-Tyr carboxypeptidase 1
KeywordsPEPTIDE BINDING PROTEIN/HYDROLASE / protease / complex / PEPTIDE BINDING PROTEIN / PEPTIDE BINDING PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / Post-chaperonin tubulin folding pathway / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / regulation of cellular senescence / negative regulation of lymphangiogenesis / peptidase activator activity ...regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / Post-chaperonin tubulin folding pathway / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / regulation of cellular senescence / negative regulation of lymphangiogenesis / peptidase activator activity / cytoskeleton-dependent intracellular transport / Intraflagellar transport / Sealing of the nuclear envelope (NE) by ESCRT-III / Gap junction assembly / Formation of tubulin folding intermediates by CCT/TriC / COPI-independent Golgi-to-ER retrograde traffic / Kinesins / Assembly and cell surface presentation of NMDA receptors / negative regulation of endothelial cell migration / COPI-dependent Golgi-to-ER retrograde traffic / labyrinthine layer blood vessel development / axon development / negative regulation of endothelial cell proliferation / Recycling pathway of L1 / negative regulation of blood vessel endothelial cell migration / RHOH GTPase cycle / protein secretion / RHO GTPases activate IQGAPs / Hedgehog 'off' state / regulation of angiogenesis / cytoplasmic microtubule / metallocarboxypeptidase activity / microtubule-based process / COPI-mediated anterograde transport / Activation of AMPK downstream of NMDARs / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / negative regulation of protein ubiquitination / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / cellular response to interleukin-4 / negative regulation of angiogenesis / RHO GTPases Activate Formins / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / PKR-mediated signaling / structural constituent of cytoskeleton / microtubule cytoskeleton organization / Aggrephagy / response to wounding / HCMV Early Events / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / double-stranded RNA binding / apical part of cell / mitotic cell cycle / actin binding / microtubule binding / angiogenesis / microtubule / cytoskeleton / regulation of cell cycle / cell cycle / cell division / GTPase activity / ubiquitin protein ligase binding / GTP binding / structural molecule activity / 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 / 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-1B chain / Tubulinyl-Tyr carboxypeptidase 1 / Small vasohibin-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.855 Å
AuthorsLiao, S. / Gao, J. / Xu, C.
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: To Be Published
Title: Structure of a hypothetical protease
Authors: Liao, S. / Gao, J. / Xu, C.
History
DepositionJan 20, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 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
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Small vasohibin-binding protein
B: Tubulinyl-Tyr carboxypeptidase 1
C: 8-mer peptide


Theoretical massNumber of molelcules
Total (without water)34,2603
Polymers34,2603
Non-polymers00
Water6,900383
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-11 kcal/mol
Surface area14190 Å2
Unit cell
Length a, b, c (Å)69.641, 127.360, 44.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-661-

HOH

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Components

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


Mass: 5667.565 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-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: 27652.031 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-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q7L8A9, tubulinyl-Tyr carboxypeptidase
#3: Protein/peptide 8-mer peptide


Mass: 940.862 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68363*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.87 Å3/Da / Density % sol: 57.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M BIS-TRIS pH 6.5, 16% polyethylene glycol 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 34141 / % possible obs: 99.9 % / Redundancy: 8.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.031 / Net I/σ(I): 22.3
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 8 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3364 / CC1/2: 0.739 / Rpim(I) all: 0.315 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: 000)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIX(1.14_3260: 000)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: a low resolution SeMet structure from our group

Resolution: 1.855→44.31 Å / SU ML: 0.16 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 18.59
RfactorNum. reflection% reflection
Rfree0.1945 2000 5.92 %
Rwork0.177 --
obs0.1781 33784 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.855→44.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2216 0 0 383 2599
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042275
X-RAY DIFFRACTIONf_angle_d0.7443067
X-RAY DIFFRACTIONf_dihedral_angle_d9.5561889
X-RAY DIFFRACTIONf_chiral_restr0.045328
X-RAY DIFFRACTIONf_plane_restr0.004395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8548-1.90120.27021230.23751967X-RAY DIFFRACTION87
1.9012-1.95260.21771380.20732187X-RAY DIFFRACTION97
1.9526-2.01010.21781420.19722258X-RAY DIFFRACTION99
2.0101-2.07490.23421420.19642252X-RAY DIFFRACTION100
2.0749-2.14910.23451410.18712252X-RAY DIFFRACTION100
2.1491-2.23510.22211440.18112284X-RAY DIFFRACTION100
2.2351-2.33690.2191430.18262277X-RAY DIFFRACTION100
2.3369-2.460.19311440.18492286X-RAY DIFFRACTION100
2.46-2.61420.21381430.17852284X-RAY DIFFRACTION100
2.6142-2.8160.20261450.18242294X-RAY DIFFRACTION100
2.816-3.09930.18891440.1792291X-RAY DIFFRACTION100
3.0993-3.54760.19111470.1672332X-RAY DIFFRACTION100
3.5476-4.46890.15211490.14922362X-RAY DIFFRACTION100
4.4689-44.32260.17751550.17492458X-RAY DIFFRACTION99

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