[English] 日本語
Yorodumi
- PDB-6j4o: Structural basis of tubulin detyrosination by vasohibins-SVBP enz... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6j4o
TitleStructural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications
Components
  • Small vasohibin-binding protein
  • Tubulinyl-Tyr carboxypeptidase 2
KeywordsHYDROLASE / carboxypeptidase / tubulin / microtubule
Function / homology
Function and homology information


cell-cell fusion / regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / syncytium formation by plasma membrane fusion / Carboxyterminal post-translational modifications of tubulin / negative regulation of endothelial cell migration / labyrinthine layer blood vessel development / peptidase activator activity / axon development ...cell-cell fusion / regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / syncytium formation by plasma membrane fusion / Carboxyterminal post-translational modifications of tubulin / negative regulation of endothelial cell migration / labyrinthine layer blood vessel development / peptidase activator activity / axon development / protein secretion / regulation of angiogenesis / metallocarboxypeptidase activity / positive regulation of endothelial cell proliferation / negative regulation of protein ubiquitination / 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
PHOSPHATE ION / Tubulinyl-Tyr carboxypeptidase 2 / Small vasohibin-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsWang, N. / Huang, H.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2018YFC1004500 China
National Natural Science Foundation of Chinathe Thousand Young Talents Program China
National Natural Science Foundation of ChinaK18221002 China
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2019
Title: Structural basis of tubulin detyrosination by the vasohibin-SVBP enzyme complex.
Authors: Wang, N. / Bosc, C. / Ryul Choi, S. / Boulan, B. / Peris, L. / Olieric, N. / Bao, H. / Krichen, F. / Chen, L. / Andrieux, A. / Olieric, V. / Moutin, M.J. / Steinmetz, M.O. / Huang, H.
History
DepositionJan 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 13, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tubulinyl-Tyr carboxypeptidase 2
B: Small vasohibin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,64010
Polymers37,8952
Non-polymers7458
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-31 kcal/mol
Surface area14580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.140, 123.248, 195.171
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-520-

HOH

21A-559-

HOH

31A-606-

HOH

-
Components

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


Mass: 29932.059 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: VASH2, VASHL / Plasmid: RSFduet / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-RIL / References: UniProt: Q86V25, tubulinyl-Tyr carboxypeptidase
#2: Protein Small vasohibin-binding protein / Coiled coil domain-containing protein 23


Mass: 7962.624 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 / Plasmid: RSFduet / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-RIL / References: UniProt: Q8N300
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 63.45 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 8.2 / Details: 1.6 M sodium/potassium phosphate, pH 8.2 / PH range: 8.2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 25255 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.058 / Rrim(I) all: 0.146 / Net I/σ(I): 12.2
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1 / Num. unique obs: 1254 / CC1/2: 0.691 / Rpim(I) all: 0.459 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→47.31 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.28
RfactorNum. reflection% reflection
Rfree0.2239 1795 8.32 %
Rwork0.1842 --
obs0.1874 21587 96.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→47.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2306 0 45 232 2583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012400
X-RAY DIFFRACTIONf_angle_d1.0473227
X-RAY DIFFRACTIONf_dihedral_angle_d11.4351444
X-RAY DIFFRACTIONf_chiral_restr0.051338
X-RAY DIFFRACTIONf_plane_restr0.006405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.36220.31231120.25741231X-RAY DIFFRACTION79
2.3622-2.43170.29981230.23731373X-RAY DIFFRACTION88
2.4317-2.51020.23871260.23261437X-RAY DIFFRACTION91
2.5102-2.59990.2591350.21931520X-RAY DIFFRACTION97
2.5999-2.7040.29431400.21191531X-RAY DIFFRACTION98
2.704-2.82710.27661420.2071562X-RAY DIFFRACTION99
2.8271-2.97610.24581440.19571574X-RAY DIFFRACTION100
2.9761-3.16250.24391430.19531567X-RAY DIFFRACTION100
3.1625-3.40660.24551430.17491570X-RAY DIFFRACTION99
3.4066-3.74930.19861450.161588X-RAY DIFFRACTION100
3.7493-4.29160.16611440.14261580X-RAY DIFFRACTION100
4.2916-5.40570.18521460.14681604X-RAY DIFFRACTION100
5.4057-47.32030.20941520.20431655X-RAY DIFFRACTION98
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)
14.3142-3.61981.59093.9456-0.31341.70010.0354-0.0342-0.2117-0.0108-0.18120.1630.2434-0.2860.23910.2896-0.04170.06790.5103-0.01190.305442.281528.088590.1731
22.99493.0305-1.27693.7797-0.61632.7088-0.0443-0.6873-0.2634-0.0896-0.0368-0.84860.36310.30780.03250.2324-0.01850.00360.65320.00750.29756.831829.019691.168
33.3005-0.71613.49560.53940.72068.50460.00890.1028-0.2659-0.1412-0.0099-0.0161-0.32190.093-0.06570.2458-0.03270.03770.230.00460.166150.317731.653561.1911
44.4442-2.2513.24423.4895-1.13986.0688-0.0083-0.3713-0.3070.01210.10050.5720.1864-0.615-0.0850.2236-0.09320.03370.27970.00780.256838.430926.606977.6449
54.17472.58164.89352.39452.72876.29310.3840.2942-0.02850.3101-0.36310.22890.3708-0.19260.03510.37390.00820.050.30840.00170.419837.825135.906471.554
62.7010.43710.6780.89711.11271.42240.1601-0.1389-0.21080.1601-0.09390.03190.23-0.123-0.04910.2028-0.0309-0.01110.098-0.00690.17439.284920.927367.412
73.33380.37111.04685.7725-2.2874.30630.1494-0.0845-0.2711-0.08240.0361-0.22690.45780.3767-0.17090.21240.02720.02310.1693-0.02020.276945.130213.161762.0735
82.6705-0.06060.09974.2855-0.67862.22810.01420.0418-0.1445-0.03120.03440.48750.1817-0.3481-0.03510.1824-0.0356-0.01520.2028-0.00850.295130.567316.4764.3635
96.1142-1.75050.13565.8519-1.2197.3511-0.01890.6677-0.0603-1.1767-0.13161.0466-0.0468-0.6261-0.04170.4153-0.0494-0.10990.4076-0.04560.406530.791510.353553.1687
107.0421-2.55640.43418.07280.94896.03460.0236-0.3014-0.30160.4193-0.0841-0.04060.14260.62510.08180.1745-0.06820.00660.36210.02530.143452.43626.870383.8956
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 49 through 73 )
2X-RAY DIFFRACTION2chain 'A' and (resid 74 through 94 )
3X-RAY DIFFRACTION3chain 'A' and (resid 95 through 121 )
4X-RAY DIFFRACTION4chain 'A' and (resid 122 through 138 )
5X-RAY DIFFRACTION5chain 'A' and (resid 139 through 152 )
6X-RAY DIFFRACTION6chain 'A' and (resid 153 through 200 )
7X-RAY DIFFRACTION7chain 'A' and (resid 201 through 239 )
8X-RAY DIFFRACTION8chain 'A' and (resid 240 through 275 )
9X-RAY DIFFRACTION9chain 'A' and (resid 276 through 294 )
10X-RAY DIFFRACTION10chain 'B' and (resid 24 through 59 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more