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 
  • R-Value Observed: 0.138 

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

  • DOI: 10.1016/s0022-2836(02)01234-2
  • Primary Citation of Related Structures:  
    1L9L

  • 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 selenomethionyl granulysin by MAD phasing at 2A resolution ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GranulysinA74Homo sapiensMutation(s): 0 
Gene Names: GNLYLAG2NKG5TLA519
UniProt & NIH Common Fund Data Resources
Find proteins for P22749 (Homo sapiens)
Explore P22749 
Go to UniProtKB:  P22749
PHAROS:  P22749
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.92 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.138 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 23.265α = 90
b = 60.436β = 90.99
c = 23.591γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
SHELXL-97refinement
DMphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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