6WSL Protein Binding date May 01, 2020
title Cryo-Em Structure Of Vash1-Svbp Bound To Microtubules
authors F.Li, Y.Li, H.Yu
compound source
Molecule: Tubulin Alpha-1a Chain
Chain: A, E
Synonym: Alpha-Tubulin 3,Tubulin B-Alpha-1,Tubulin Alpha-3
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tuba1a, Tuba3
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111

Molecule: Tubulin Beta-3 Chain
Chain: B, F
Synonym: Tubulin Beta-4 Chain,Tubulin Beta-III
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tubb3, Tubb4
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111

Molecule: Tubulinyl-Tyr Carboxypeptidase 1
Chain: C, G
Synonym: Tubulin Carboxypeptidase 1,Tyrosine Carboxypeptida 1,Vasohibin-1;
Ec: 3.4.17.17
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Vash1, Kiaa1036, Vash
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Small Vasohibin-Binding Protein
Chain: D, H
Synonym: Coiled Coil Domain-Containing Protein 23
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Svbp, Ccdc23
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 3.10 Å
ligand G2P, GTP enzyme Hydrolase E.C.3.4.17.17 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, E


F, B
  • netrin receptor binding


    • H, D


    Primary referenceCryo-EM structure of VASH1-SVBP bound to microtubules., Li F, Li Y, Ye X, Gao H, Shi Z, Luo X, Rice LM, Yu H, Elife. 2020 Aug 10;9. pii: 58157. doi: 10.7554/eLife.58157. PMID:32773040
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (358 Kb) [Save to disk]
  • Biological Unit Coordinates (6wsl.pdb1.gz) 352 Kb
  • LPC: Ligand-Protein Contacts for 6WSL
  • CSU: Contacts of Structural Units for 6WSL
  • Retrieve 6WSL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6WSL from S2C, [Save to disk]
    • View 6WSL in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 6WSL
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6wsl_D] [6wsl_H] [6wsl_G] [6wsl_E] [6wsl_A] [6wsl_F] [6wsl_C] [6wsl_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6WSL
  • Community annotation for 6WSL at PDBWiki (http://pdbwiki.org)

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