6N4Q Membrane Protein date Nov 20, 2018
title Cryoem Structure Of Nav1.7 Vsd2 (Actived State) In Complex W Gating Modifier Toxin Protx2
authors H.Xu, A.Rohou, C.P.Arthur, A.Estevez, C.Ciferri, J.Payandeh, C.M.K
compound source
Molecule: Nav1.7 Vsd2-Navab Chimera
Chain: A, B, C, D
Synonym: Neuroendocrine Sodium Channel,Hne-Na,Peripheral So Channel 1,Pn1,Sodium Channel Protein Type Ix Subunit Alpha, Gated Sodium Channel Subunit Alpha Nav1.7;
Engineered: Yes
Organism_scientific: Arcobacter Butzleri (Strain Rm4018), H Sapiens;
Organism_common: Human
Organism_taxid: 367737, 9606
Strain: Rm4018
Gene: Abu_1752, Scn9a, Nena
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_vector_type: Baculovirus

Molecule: Betaomega-Theraphotoxin-Tp2a
Chain: E, F, G, H
Synonym: Betaomega-Trtx-Tp2a,Protx-II,Pt-II,Protoxin-2,Pro
Engineered: Yes

Synthetic: Yes
Organism_scientific: Thrixopelma Pruriens
Organism_common: Peruvian Green Velvet Tarantula
Organism_taxid: 213387

Molecule: Fab Light Chain
Chain: I, K

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090

Molecule: Fab Heavy Chain
Chain: J, L

Organism_scientific: Mus Musculus
Organism_taxid: 10090
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 3.60 Å
Gene
Ontology
ChainFunctionProcessComponent
A, B, C, D


F, E, H, G


Primary referenceStructural Basis of Nav1.7 Inhibition by a Gating-Modifier Spider Toxin., Xu H, Li T, Rohou A, Arthur CP, Tzakoniati F, Wong E, Estevez A, Kugel C, Franke Y, Chen J, Ciferri C, Hackos DH, Koth CM, Payandeh J, Cell. 2019 Feb 7;176(4):702-715.e14. doi: 10.1016/j.cell.2018.12.018. Epub 2019, Jan 17. PMID:30661758
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (301 Kb) [Save to disk]
  • Biological Unit Coordinates (6n4q.pdb1.gz) 296 Kb
  • CSU: Contacts of Structural Units for 6N4Q
  • Retrieve 6N4Q in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6N4Q from S2C, [Save to disk]
  • View 6N4Q 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 6N4Q
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6n4q from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6n4q_G] [6n4q_L] [6n4q_B] [6n4q_E] [6n4q_I] [6n4q_H] [6n4q_A] [6n4q_C] [6n4q_D] [6n4q_K] [6n4q_J] [6n4q_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6N4Q
  • Community annotation for 6N4Q at PDBWiki (http://pdbwiki.org)

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