1L9L

GRANULYSIN FROM HUMAN CYTOLYTIC T LYMPHOCYTES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.92 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.137 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Granulysin Crystal Structure and a Structure-Derived Lytic Mechanism

Anderson, D.H.Sawaya, M.R.Cascio, D.Ernst, W.Modlin, R.Krensky, A.Eisenberg, D.

(2002) J.Mol.Biol. 325: 355-365


  • PubMed Abstract: 
  • Our crystal structure of granulysin suggests a mechanism for lysis of bacterial membranes by granulysin, a 74-residue basic protein from human cytolytic T lymphocyte and natural killer cells. We determined the initial crystal structure of selenomethi ...

    Our crystal structure of granulysin suggests a mechanism for lysis of bacterial membranes by granulysin, a 74-residue basic protein from human cytolytic T lymphocyte and natural killer cells. We determined the initial crystal structure of selenomethionyl granulysin by MAD phasing at 2A resolution. We present the structure model refined using native diffraction data to 0.96A resolution. The five-helical bundle of granulysin resembles other "saposin folds" (such as NK-lysin). Positive charges distribute in a ring around the granulysin molecule, and one face has net positive charge. Sulfate ions bind near the segment of the molecule identified as most membrane-lytic and of highest hydrophobic moment. The ion locations may indicate granulysin's orientation of initial approach towards the membrane. The crystal packing reveals one way to pack a sheet of granulysin molecules at the cell surface for a concerted lysis effort. The energy of binding granulysin charges to the bacterial membrane could drive the subsequent lytic processes. The loosely packed core facilitates a hinge or scissors motion towards exposure of hydrophobic surface that we propose tunnels the granulysin into the fracturing target membrane.


    Organizational Affiliation

    Howard Hughes Medical Institute, 5-748 MacDonald, Box 951662, Los Angeles, CA 90095-1662, USA. dha@mbi.ucla.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Granulysin
A
74Homo sapiensMutation(s): 0 
Gene Names: GNLY (LAG2, NKG5, TLA519)
Find proteins for P22749 (Homo sapiens)
Go to Gene View: GNLY
Go to UniProtKB:  P22749
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MPO
Query on MPO

Download SDF File 
Download CCD File 
A
3[N-MORPHOLINO]PROPANE SULFONIC ACID
C7 H15 N O4 S
DVLFYONBTKHTER-UHFFFAOYSA-N
 Ligand Interaction
EOH
Query on EOH

Download SDF File 
Download CCD File 
A
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.92 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.137 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 23.265α = 90.00
b = 60.436β = 90.99
c = 23.591γ = 90.00
Software Package:
Software NamePurpose
SHELXL-97refinement
SHELXDphasing
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
DENZOdata reduction
SCALEPACKdata scaling
DMphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-11-06
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-09-13
    Type: Refinement description