5F1B Viral Protein Transport Protein date Nov 30, 2015
title Structural Basis Of Ebola Virus Entry: Viral Glycoprotein Bo Endosomal Receptor Niemann-Pick C1
authors H.Wang, Y.Shi, J.Song, J.Qi, G.Lu, J.Yan, G.F.Gao
compound source
Molecule: Gp1
Chain: A
Fragment: Unp Residues 32-188
Synonym: Gp1,2,Gp
Engineered: Yes
Organism_scientific: Zaire Ebolavirus
Organism_common: Zebov
Organism_taxid: 128951
Strain: Kikwit-95
Gene: Gp
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111
Expression_system_cell_line: High Five Cells
Expression_system_vector_type: Baculovirus
Expression_system_vector: Pfastbac1

Molecule: Gp2
Chain: B
Fragment: Unp Residues 509-598
Synonym: Gp1,2,Gp
Engineered: Yes

Organism_scientific: Zaire Ebolavirus
Organism_common: Zebov
Organism_taxid: 128951
Strain: Kikwit-95
Gene: Gp
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111
Expression_system_cell_line: High Five Cells
Expression_system_vector_type: Baculovirus
Expression_system_vector: Pfastbac1

Molecule: Niemann-Pick C1 Protein
Chain: C
Fragment: Unp Residues 374-620
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Npc1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 63
R_factor 0.181 R_Free 0.230
crystal
cell
length a length b length c angle alpha angle beta angle gamma
107.261 107.261 93.777 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.30 Å
ligand NAG enzyme
Primary referenceEbola Viral Glycoprotein Bound to Its Endosomal Receptor Niemann-Pick C1., Wang H, Shi Y, Song J, Qi J, Lu G, Yan J, Gao GF, Cell. 2016 Jan 14;164(1-2):258-68. doi: 10.1016/j.cell.2015.12.044. PMID:26771495
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (162 Kb) [Save to disk]
  • Biological Unit Coordinates (5f1b.pdb1.gz) 155 Kb
  • LPC: Ligand-Protein Contacts for 5F1B
  • CSU: Contacts of Structural Units for 5F1B
  • Structure Factors (463 Kb)
  • Retrieve 5F1B in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5F1B from S2C, [Save to disk]
  • Re-refined 5f1b structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5F1B 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 5F1B
  • 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 5f1b from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5f1b] [5f1b_C] [5f1b_A] [5f1b_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5F1B
  • Community annotation for 5F1B at PDBWiki (http://pdbwiki.org)

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