5NVK Translation date May 04, 2017
title Crystal Structure Of The Human 4ehp-Gigyf1 Complex
authors D.Peter, E.Valkov
compound source
Molecule: Eukaryotic Translation Initiation Factor 4e Type
Chain: A, C, E, G
Synonym: Eif4e Type 2,Eukaryotic Translation Initiation Fac Homologous Protein,Eukaryotic Translation Initiation Factor 3,Eif4e-Like Protein 4e-Lp,Mrna Cap-Binding Protein 4ehp,H4 Cap-Binding Protein Type 3;
Engineered: Yes
Other_details: The First Residue Of The Coordinate Sequence G Belongs To The Expression Tag;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Eif4e2, Eif4el3
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Star

Molecule: Grb10-Interacting Gyf Protein 1
Chain: B, D, F, H
Synonym: Perq Amino Acid-Rich With Gyf Domain-Containing Pr
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gigyf1, Cds2, Perq1, Pp3360
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Star
symmetry Space Group: P 42
R_factor 0.204 R_Free 0.254
crystal
cell
length a length b length c angle alpha angle beta angle gamma
135.320 135.320 60.910 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.90 Å
Gene
Ontology
ChainFunctionProcessComponent
A, C, G, E


Primary referenceGIGYF1/2 proteins use auxiliary sequences to selectively bind to 4EHP and repress target mRNA expression., Peter D, Weber R, Sandmeir F, Wohlbold L, Helms S, Bawankar P, Valkov E, Igreja C, Izaurralde E, Genes Dev. 2017 Jun 1;31(11):1147-1161. doi: 10.1101/gad.299420.117. Epub 2017, Jul 11. PMID:28698298
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (486 Kb) [Save to disk]
  • Biological Unit Coordinates (5nvk.pdb1.gz) 121 Kb
  • Biological Unit Coordinates (5nvk.pdb2.gz) 125 Kb
  • Biological Unit Coordinates (5nvk.pdb3.gz) 120 Kb
  • Biological Unit Coordinates (5nvk.pdb4.gz) 121 Kb
  • CSU: Contacts of Structural Units for 5NVK
  • Structure Factors (230 Kb)
  • Retrieve 5NVK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5NVK from S2C, [Save to disk]
  • Re-refined 5nvk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5NVK 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 5NVK
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5nvk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5nvk_G] [5nvk_H] [5nvk_C] [5nvk_E] [5nvk_B] [5nvk_F] [5nvk_A] [5nvk_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5NVK
  • Community annotation for 5NVK at PDBWiki (http://pdbwiki.org)

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