3D12 Hydrolase Membrane Protein date May 02, 2008
title Crystal Structures Of Nipah Virus G Attachment Glycoprotein With Its Receptor Ephrin-B3
authors K.Xu, K.R.Rajashankar, Y.P.Chan, P.Himanen, C.C.Broder, D.B.Nikol
compound source
Molecule: Hemagglutinin-Neuraminidase
Chain: A, D
Fragment: Unp Residues 176-602
Ec: 3.2.1.18
Engineered: Yes
Organism_scientific: Nipah Virus
Organism_taxid: 121791
Gene: Hn
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_strain: Hi5
Expression_system_plasmid: Pacgp67

Molecule: Ephrin-B3
Chain: B, E
Fragment: Unp Residues 29-169
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Efnb3
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_plasmid: Pacgp67
symmetry Space Group: P 65 2 2
R_factor 0.221 R_Free 0.265
crystal
cell
length a length b length c angle alpha angle beta angle gamma
189.492 189.492 277.052 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.01 Å
ligand BGC, BMA, GL0, GLC, GXL, LXB, LXZ, MAN, NAG, NGA, NGZ, SO4 enzyme Hydrolase E.C.3.2.1.18 BRENDA
note 3D12 is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
A, D


E, B


Primary referenceHost cell recognition by the henipaviruses: crystal structures of the Nipah G attachment glycoprotein and its complex with ephrin-B3., Xu K, Rajashankar KR, Chan YP, Himanen JP, Broder CC, Nikolov DB, Proc Natl Acad Sci U S A. 2008 Jul 22;105(29):9953-8. Epub 2008 Jul 16. PMID:18632560
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (202 Kb) [Save to disk]
  • Biological Unit Coordinates (3d12.pdb1.gz) 192 Kb
  • Biological Unit Coordinates (3d12.pdb2.gz) 98 Kb
  • Biological Unit Coordinates (3d12.pdb3.gz) 98 Kb
  • LPC: Ligand-Protein Contacts for 3D12
  • CSU: Contacts of Structural Units for 3D12
  • Likely Quarternary Molecular Structure file(s) for 3D12
  • Structure Factors (305 Kb)
  • Retrieve 3D12 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3D12 from S2C, [Save to disk]
  • Re-refined 3d12 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3D12 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 3D12
  • 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
  • 3D motif for 3D12, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3d12_D] [3d12_B] [3d12_E] [3d12] [3d12_A]
  • SWISS-PROT database: [O35393] [Q9IH62]
  • Domain organization of [EFNB3_MOUSE] [GLYCP_NIPAV] by SWISSPFAM
  • Other resources with information on 3D12
  • Community annotation for 3D12 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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