3CSY

Crystal structure of the trimeric prefusion Ebola virus glycoprotein in complex with a neutralizing antibody from a human survivor

Structural Biology Knowledgebase: 3CSY SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.302
  • R-Value Work: 0.261

Literature

Macromolecules
Sequence Display for 3CSY

Classification: IMMUNE SYSTEM / VIRAL PROTEIN

Total Structure Weight: 406073.88

Macromolecule Entities
Molecule Chains Length Organism Details
Fab KZ52 heavy chain A, C, E, G 226 Homo sapiens Fragment: heavy chain
Fab KZ52 light chain B, D, F, H 217 Homo sapiens Fragment: light chain
Envelope glycoprotein GP1 I, K, M, O 334 Zaire ebolavirus Fragment: deletion of residues 312-463
Mutation: T42V, T230V
Details: Weak or discontinuous electron density is observed in the outer regions of the glycoprotein (residues 268-278 and 299-310) and these residues are tentatively assigned
Gene Name(s): GP
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Envelope glycoprotein GP2 J, L, N, P 131 Zaire ebolavirus Fragment: deletion of residues 633-676
Gene Name(s): GP

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

I, J, K, L, M, N, O, P N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

I, J, L, M, N, O, P BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

J, L, N, P ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B, C, D, E, F, G, H L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.302
  • R-Value Work: 0.261
  • Space Group: H 3 2

Unit Cell:

Length (Å) Angle (°)
a = 273.71 α = 90.00
b = 273.71 β = 90.00
c = 409.43 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-04-10
  • Released Date: 2008-07-08
  • Deposition author(s): Lee, J.E., Fusco, M.L., Hessell, A.J., Oswald, W.B., Burton, D.R., Saphire, E.O.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update