3NSJ | pdb_00003nsj

The X-ray crystal structure of lymphocyte perforin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 
    0.215 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

The structural basis for membrane binding and pore formation by lymphocyte perforin.

Law, R.H.Lukoyanova, N.Voskoboinik, I.Caradoc-Davies, T.T.Baran, K.Dunstone, M.A.D'Angelo, M.E.Orlova, E.V.Coulibaly, F.Verschoor, S.Browne, K.A.Ciccone, A.Kuiper, M.J.Bird, P.I.Trapani, J.A.Saibil, H.R.Whisstock, J.C.

(2010) Nature 468: 447-451

  • DOI: https://doi.org/10.1038/nature09518
  • Primary Citation Related Structures: 
    3NSJ

  • PubMed Abstract: 

    Natural killer cells and cytotoxic T lymphocytes accomplish the critically important function of killing virus-infected and neoplastic cells. They do this by releasing the pore-forming protein perforin and granzyme proteases from cytoplasmic granules into the cleft formed between the abutting killer and target cell membranes. Perforin, a 67-kilodalton multidomain protein, oligomerizes to form pores that deliver the pro-apoptopic granzymes into the cytosol of the target cell. The importance of perforin is highlighted by the fatal consequences of congenital perforin deficiency, with more than 50 different perforin mutations linked to familial haemophagocytic lymphohistiocytosis (type 2 FHL). Here we elucidate the mechanism of perforin pore formation by determining the X-ray crystal structure of monomeric murine perforin, together with a cryo-electron microscopy reconstruction of the entire perforin pore. Perforin is a thin 'key-shaped' molecule, comprising an amino-terminal membrane attack complex perforin-like (MACPF)/cholesterol dependent cytolysin (CDC) domain followed by an epidermal growth factor (EGF) domain that, together with the extreme carboxy-terminal sequence, forms a central shelf-like structure. A C-terminal C2 domain mediates initial, Ca(2+)-dependent membrane binding. Most unexpectedly, however, electron microscopy reveals that the orientation of the perforin MACPF domain in the pore is inside-out relative to the subunit arrangement in CDCs. These data reveal remarkable flexibility in the mechanism of action of the conserved MACPF/CDC fold and provide new insights into how related immune defence molecules such as complement proteins assemble into pores.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, Monash University, Clayton, Melbourne, Victoria 3800, Australia.

Macromolecule Content 

  • Total Structure Weight: 61.96 kDa 
  • Atom Count: 4,373 
  • Modeled Residue Count: 530 
  • Deposited Residue Count: 540 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Perforin-1540Mus musculusMutation(s): 1 
Gene Names: Prf1Pfp
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P10820 (Mus musculus)
Explore P10820 
Go to UniProtKB:  P10820
IMPC:  MGI:97551
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10820
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P10820-1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
M [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
IOD

Query on IOD



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
I [auth A],
J [auth A]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL

Query on GOL



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
K [auth A],
L [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free:  0.215 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.64α = 90
b = 109.8β = 90
c = 141.03γ = 90
Software Package:
Software NamePurpose
SCALAdata processing
SHARPphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction
SCALAdata scaling
BUSTERrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Structure summary
  • Version 1.4: 2024-10-16
    Changes: Structure summary