[English] 日本語
Yorodumi
- PDB-6j7b: Crystal structure of VASH1-SVBP in complex with epoY -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6j7b
TitleCrystal structure of VASH1-SVBP in complex with epoY
Components
  • Small vasohibin-binding protein
  • Tubulinyl-Tyr carboxypeptidase 1
KeywordsHYDROLASE / carboxypeptidase / tubulin / microtubule / inhibitor / epoY
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: 1.618 Å
AuthorsWang, N. / Bao, H. / Huang, H. / Wu, B.
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: Cell Res. / Year: 2019
Title: Molecular basis of vasohibins-mediated detyrosination and its impact on spindle function and mitosis.
Authors: Liao, S. / Rajendraprasad, G. / Wang, N. / Eibes, S. / Gao, J. / Yu, H. / Wu, G. / Tu, X. / Huang, H. / Barisic, M. / Xu, C.
History
DepositionJan 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tubulinyl-Tyr carboxypeptidase 1
B: Small vasohibin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3593
Polymers35,0342
Non-polymers3251
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-14 kcal/mol
Surface area14510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.310, 70.920, 128.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-1280-

HOH

-
Components

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


Mass: 28878.480 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 (E. coli) / References: UniProt: Q7L8A9, tubulinyl-Tyr carboxypeptidase
#2: Protein Small vasohibin-binding protein / Coiled coil domain-containing protein 23


Mass: 6155.090 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 (E. coli) / References: UniProt: Q8N300
#3: Chemical ChemComp-BJL / N-[(3R)-4-ethoxy-3-hydroxy-4-oxobutanoyl]-L-tyrosine


Mass: 325.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H19NO7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.19 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 6 / Details: 20%PEG6000, 1M lithium chloride, 0.1M MES pH6.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.62→70.92 Å / Num. obs: 52501 / % possible obs: 100 % / Redundancy: 12 % / CC1/2: 0.998 / Rpim(I) all: 0.039 / Net I/σ(I): 12.8
Reflection shellResolution: 1.62→1.71 Å / Rmerge(I) obs: 1.326 / Num. unique obs: 7575 / CC1/2: 0.686 / Rpim(I) all: 0.39

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
iMOSFLMdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J4O

6j4o


Resolution: 1.618→47.54 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.197 2589 4.94 %
Rwork0.178 --
obs0.1789 52398 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.618→47.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2295 0 23 382 2700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072373
X-RAY DIFFRACTIONf_angle_d0.9043201
X-RAY DIFFRACTIONf_dihedral_angle_d14.0571450
X-RAY DIFFRACTIONf_chiral_restr0.053342
X-RAY DIFFRACTIONf_plane_restr0.005413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.618-1.64910.27231600.24142743X-RAY DIFFRACTION100
1.6491-1.68280.26521070.2332713X-RAY DIFFRACTION100
1.6828-1.71940.26681380.23362745X-RAY DIFFRACTION100
1.7194-1.75940.3161450.2292707X-RAY DIFFRACTION100
1.7594-1.80340.26191530.22922723X-RAY DIFFRACTION100
1.8034-1.85210.20961390.20232761X-RAY DIFFRACTION100
1.8521-1.90660.2451430.21712726X-RAY DIFFRACTION100
1.9066-1.96820.23711180.21042764X-RAY DIFFRACTION100
1.9682-2.03850.1971470.17612740X-RAY DIFFRACTION100
2.0385-2.12010.18871630.16832718X-RAY DIFFRACTION100
2.1201-2.21660.17531460.16742786X-RAY DIFFRACTION100
2.2166-2.33350.23421270.18692738X-RAY DIFFRACTION99
2.3335-2.47970.16751390.16482772X-RAY DIFFRACTION100
2.4797-2.67110.16591520.16842743X-RAY DIFFRACTION100
2.6711-2.93990.19781510.1722804X-RAY DIFFRACTION100
2.9399-3.36520.21011380.1682814X-RAY DIFFRACTION100
3.3652-4.23940.17661630.15522818X-RAY DIFFRACTION100
4.2394-47.56050.17511600.17382994X-RAY DIFFRACTION100
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)
15.51914.62814.23285.59724.97324.5194-0.0152-0.6578-0.74860.42960.088-0.67730.02180.4661-0.43150.29590.0228-0.05650.31950.0590.262550.737562.688931.0957
23.9093-0.88890.24562.24760.28984.9589-0.1509-0.9234-0.39670.67940.0125-0.20240.03310.4459-0.06120.3039-0.0401-0.0280.39250.13670.212743.411763.671337.5449
33.97470.43420.36133.0275-0.2010.72580.1538-0.34670.21650.3889-0.0640.2870.0074-0.3036-0.02660.24-0.00980.05890.31250.02680.268232.666968.647633.6256
41.43740.6844-2.30811.1251-1.25164.1358-0.04030.15760.0489-0.16590.04760.0465-0.0145-0.3364-0.05890.20270.0278-0.0180.18340.00050.166847.373876.84387.5652
52.442-0.5881-0.78080.72760.28631.274-0.0172-0.1518-0.09260.0530.0018-0.10030.18230.06830.01180.1689-0.0057-0.00710.14260.02260.162252.361266.757321.7047
61.1148-0.06260.16191.3980.60211.9324-0.003-0.04890.00010.02110.0321-0.0199-0.0128-0.0064-0.0260.13680.0168-0.01030.1207-0.01180.14659.344175.678915.9218
71.0604-0.50330.09671.73551.64432.2223-0.067-0.25420.04030.36390.2136-0.01110.10190.0492-0.06240.18340.0322-0.01160.1958-0.01230.154460.585680.098624.4562
85.64791.094-2.64883.0184-0.50695.10840.3239-0.30940.28610.202-0.06040.2298-0.6664-0.1129-0.32520.21860.012-0.00610.1768-0.01750.176355.450883.719518.0691
92.768-0.5486-0.21361.48921.38043.1535-0.0417-0.03220.279-0.06510.08650.0087-0.2715-0.0403-0.05670.20290.0097-0.00560.1259-0.00760.192860.261389.067318.3843
101.024-0.0130.11821.77340.59231.85690.0453-0.0853-0.06910.01040.1544-0.26410.03550.2164-0.25070.14150.0252-0.0240.1647-0.00180.186265.816973.901918.4747
113.97350.38670.47385.00450.65716.2259-0.13990.44720.3459-0.13520.0712-0.565-0.20680.9878-0.04560.1292-0.0376-0.01920.3060.01480.322574.456284.595318.3017
123.8059-0.0468-0.54243.96511.09913.8248-0.0847-0.0047-0.3405-0.274-0.02740.07450.2306-0.1580.00550.1864-0.03470.02830.19820.02710.167737.98863.91725.5342
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 57 through 70 )
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 84 )
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 105 )
4X-RAY DIFFRACTION4chain 'A' and (resid 106 through 132 )
5X-RAY DIFFRACTION5chain 'A' and (resid 133 through 170 )
6X-RAY DIFFRACTION6chain 'A' and (resid 171 through 197 )
7X-RAY DIFFRACTION7chain 'A' and (resid 198 through 211 )
8X-RAY DIFFRACTION8chain 'A' and (resid 212 through 226 )
9X-RAY DIFFRACTION9chain 'A' and (resid 227 through 250 )
10X-RAY DIFFRACTION10chain 'A' and (resid 251 through 277 )
11X-RAY DIFFRACTION11chain 'A' and (resid 278 through 305 )
12X-RAY DIFFRACTION12chain 'B' and (resid 20 through 52 )

+
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