Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 50.02 kDa 
• Atom Count: 3406 
• Modelled Residue Count: 434 
• Deposited Residue Count: 448 
• Unique protein chains: 1

3B4R

Site-2 Protease from Methanocaldococcus jannaschii

• PDB DOI: 10.2210/pdb3B4R/pdb

• Classification: HYDROLASE
• Organism(s): Methanocaldococcus jannaschii
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2007-10-24 Released: 2008-01-15 
• Deposition Author(s): Jeffrey, P.D., Feng, L., Yan, H., Wu, Z., Yan, N., Wang, Z., Shi, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.318 
• R-Value Work: 0.251 
• R-Value Observed: 0.251 

Literature

Structure of a site-2 protease family intramembrane metalloprotease.

Feng, L., Yan, H., Wu, Z., Yan, N., Wang, Z., Jeffrey, P.D., Shi, Y.

(2007) Science 318: 1608-1612

• PubMed: 18063795 
• DOI: 10.1126/science.1150755
• Primary Citation of Related Structures:  
  3B4R


• PubMed Abstract: 
  

Regulated intramembrane proteolysis by members of the site-2 protease (S2P) family is an important signaling mechanism conserved from bacteria to humans. Here we report the crystal structure of the transmembrane core domain of an S2P metalloprotease from Methanocaldococcus jannaschii. The protease consists of six transmembrane segments, with the catalytic zinc atom coordinated by two histidine residues and one aspartate residue approximately 14 angstroms into the lipid membrane surface. The protease exhibits two distinct conformations in the crystals. In the closed conformation, the active site is surrounded by transmembrane helices and is impermeable to substrate peptide; water molecules gain access to zinc through a polar, central channel that opens to the cytosolic side. In the open conformation, transmembrane helices alpha1 and alpha6 separate from each other by 10 to 12 angstroms, exposing the active site to substrate entry. The structure reveals how zinc embedded in an integral membrane protein can catalyze peptide cleavage.

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Organizational Affiliation: 

Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ 08544, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative zinc metalloprotease MJ0392	A, B	224	Methanocaldococcus jannaschii	Mutation(s): 0  EC: 3.4.24 Membrane Entity: Yes
UniProt
Find proteins for Q57837 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q57837  Go to UniProtKB:  Q57837

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.318 
• R-Value Work: 0.251 
• R-Value Observed: 0.251 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.42	α = 90
b = 124.42	β = 90
c = 136.72	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
DENZO	data reduction
SCALEPACK	data scaling
SHELXS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-10-24 
• Released Date: 2008-01-15 
Deposition Author(s): Jeffrey, P.D., Feng, L., Yan, H., Wu, Z., Yan, N., Wang, Z., Shi, Y.

Revision History  

• Version 1.0: 2008-01-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance