[English] 日本語
Yorodumi
- PDB-6j8f: Crystal structure of SVBP-VASH1 with peptide mimic the C-terminal... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6j8f
TitleCrystal structure of SVBP-VASH1 with peptide mimic the C-terminal of alpha-tubulin
Components
  • 8-mer peptide
  • Small vasohibin-binding protein
  • Tubulinyl-Tyr carboxypeptidase 1
KeywordsPEPTIDE BINDING PROTEIN/HYDROLASE / protease / complex / PEPTIDE BINDING PROTEIN / Structural Genomics / PSI-2 / Protein Structure Initiative / Structural Genomics Consortium / SGC / 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 / axonemal microtubule / negative regulation of lymphangiogenesis / Cilium Assembly / regulation of cellular senescence / cytoskeleton-dependent intracellular transport / organelle transport along microtubule ...regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / Post-chaperonin tubulin folding pathway / axonemal microtubule / negative regulation of lymphangiogenesis / Cilium Assembly / regulation of cellular senescence / cytoskeleton-dependent intracellular transport / organelle transport along microtubule / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Carboxyterminal post-translational modifications of tubulin / forebrain morphogenesis / Intraflagellar transport / Sealing of the nuclear envelope (NE) by ESCRT-III / cerebellar cortex morphogenesis / Formation of tubulin folding intermediates by CCT/TriC / glial cell differentiation / dentate gyrus development / neuron projection arborization / flagellated sperm motility / Gap junction assembly / Prefoldin mediated transfer of substrate to CCT/TriC / Kinesins / COPI-independent Golgi-to-ER retrograde traffic / Assembly and cell surface presentation of NMDA receptors / response to L-glutamate / pyramidal neuron differentiation / negative regulation of endothelial cell migration / centrosome cycle / labyrinthine layer blood vessel development / peptidase activator activity / COPI-dependent Golgi-to-ER retrograde traffic / smoothened signaling pathway / regulation of synapse organization / axon development / negative regulation of endothelial cell proliferation / startle response / motor behavior / response to tumor necrosis factor / Recycling pathway of L1 / locomotory exploration behavior / microtubule polymerization / negative regulation of blood vessel endothelial cell migration / protein secretion / regulation of angiogenesis / response to mechanical stimulus / sperm flagellum / RHO GTPases activate IQGAPs / microtubule-based process / Hedgehog 'off' state / COPI-mediated anterograde transport / Activation of AMPK downstream of NMDARs / condensed chromosome / metallocarboxypeptidase activity / negative regulation of protein ubiquitination / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / MHC class II antigen presentation / homeostasis of number of cells within a tissue / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / cellular response to calcium ion / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Resolution of Sister Chromatid Cohesion / negative regulation of angiogenesis / AURKA Activation by TPX2 / adult locomotory behavior / Translocation of SLC2A4 (GLUT4) to the plasma membrane / neuromuscular junction / intracellular protein transport / RHO GTPases Activate Formins / recycling endosome / synapse organization / cerebral cortex development / PKR-mediated signaling / visual learning / structural constituent of cytoskeleton / response to wounding / microtubule cytoskeleton organization / memory / cytoplasmic ribonucleoprotein granule / neuron migration / apical part of cell / HCMV Early Events / Aggrephagy / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / mitotic cell cycle / microtubule cytoskeleton / actin binding / neuron apoptotic process / angiogenesis / microtubule binding / gene expression / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
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-1A chain / Tubulinyl-Tyr carboxypeptidase 1 / Small vasohibin-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.283 Å
AuthorsLiao, S. / Gao, J. / Xu, C. / Structural Genomics Consortium (SGC)
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: 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 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Mar 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 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,9933
Polymers33,9933
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-17 kcal/mol
Surface area13830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.950, 108.377, 46.896
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

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


Mass: 5410.277 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: 27668.096 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
#3: Protein/peptide 8-mer peptide


Mass: 914.891 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q71U36*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M Na citrate tribasic dihydrate pH 5.0, 18% PEG 20000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.28→54.19 Å / Num. obs: 16147 / % possible obs: 99.9 % / Redundancy: 12.5 % / Net I/σ(I): 10.9
Reflection shellResolution: 2.28→2.41 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2322 / CC1/2: 0.726 / Rpim(I) all: 0.491 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIX(1.14_3260: ???)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: low resolution SeMet structure

Resolution: 2.283→54.188 Å / SU ML: 0.25 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 27.74
RfactorNum. reflection% reflection
Rfree0.2369 828 5.14 %
Rwork0.1995 --
obs0.2015 16109 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.283→54.188 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2141 0 0 44 2185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032176
X-RAY DIFFRACTIONf_angle_d0.6852936
X-RAY DIFFRACTIONf_dihedral_angle_d5.7411325
X-RAY DIFFRACTIONf_chiral_restr0.043314
X-RAY DIFFRACTIONf_plane_restr0.004378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2825-2.42550.32661410.28172488X-RAY DIFFRACTION100
2.4255-2.61280.33911380.2632518X-RAY DIFFRACTION100
2.6128-2.87570.28061320.22592496X-RAY DIFFRACTION100
2.8757-3.29180.22591300.20192538X-RAY DIFFRACTION100
3.2918-4.14710.21241250.18122567X-RAY DIFFRACTION100
4.1471-54.20380.21111620.17772674X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 26.5379 Å / Origin y: 19.938 Å / Origin z: 10.6746 Å
111213212223313233
T0.2786 Å20.022 Å2-0.0092 Å2-0.2648 Å2-0.0144 Å2--0.2899 Å2
L0.956 °2-0.3296 °2-0.0942 °2-1.0518 °2-0.2592 °2--0.5915 °2
S0.0031 Å °-0.0061 Å °0.0053 Å °0.0271 Å °-0.0067 Å °-0.0436 Å °-0.0849 Å °-0.0281 Å °-0.0002 Å °
Refinement TLS groupSelection details: all

+
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