Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 37.51 kDa 
• Atom Count: 2791 
• Modelled Residue Count: 314 
• Deposited Residue Count: 332 
• Unique protein chains: 2

4NZL

Extracellular proteins of Staphylococcus aureus inhibit the neutrophil serine proteases

• PDB DOI: 10.2210/pdb4NZL/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens, Staphylococcus aureus subsp. aureus Mu50
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-12-12 Released: 2014-08-20 
• Deposition Author(s): Stapels, D.A.C., von Koeckritz-Blickwede, M., Ramyar, K.X., Bischoff, M., Milder, F., Ruyken, M., Scheepmaker, L., McWhorter, W.J., Herrmann, M., van Kessel, K.P.M., Geisbrecht, B.V., Rooijakkers, S.H.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.207 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 

Literature

Staphylococcus aureus secretes a unique class of neutrophil serine protease inhibitors.

Stapels, D.A., Ramyar, K.X., Bischoff, M., von Kockritz-Blickwede, M., Milder, F.J., Ruyken, M., Eisenbeis, J., McWhorter, W.J., Herrmann, M., van Kessel, K.P., Geisbrecht, B.V., Rooijakkers, S.H.

(2014) Proc Natl Acad Sci U S A 111: 13187-13192

• PubMed: 25161283 
• DOI: 10.1073/pnas.1407616111
• Primary Citation of Related Structures:  
  4NZL


• PubMed Abstract: 
  

Neutrophils are indispensable for clearing infections with the prominent human pathogen Staphylococcus aureus. Here, we report that S. aureus secretes a family of proteins that potently inhibits the activity of neutrophil serine proteases (NSPs): neutrophil elastase (NE), proteinase 3, and cathepsin G. The NSPs, but not related serine proteases, are specifically blocked by the extracellular adherence protein (Eap) and the functionally orphan Eap homologs EapH1 and EapH2, with inhibitory-constant values in the low-nanomolar range. Eap proteins are together essential for NSP inhibition by S. aureus in vitro and promote staphylococcal infection in vivo. The crystal structure of the EapH1/NE complex showed that Eap molecules constitute a unique class of noncovalent protease inhibitors that occlude the catalytic cleft of NSPs. These findings increase our insights into the complex pathogenesis of S. aureus infections and create opportunities to design novel treatment strategies for inflammatory conditions related to excessive NSP activity.

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Organizational Affiliation: 

Medical Microbiology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands; [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutrophil elastase	A	218	Homo sapiens	Mutation(s): 0  Gene Names: ELANE, ELA2 EC: 3.4.21.37
UniProt & NIH Common Fund Data Resources
Find proteins for P08246 (Homo sapiens) Explore P08246  Go to UniProtKB:  P08246
PHAROS:  P08246 GTEx:  ENSG00000197561

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	B	114	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 0  Gene Names: SAV2205
UniProt
Find proteins for A0A0H3K0M1 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore A0A0H3K0M1  Go to UniProtKB:  A0A0H3K0M1

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86566TX GlyCosmos:  G86566TX GlyGen:  G86566TX

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.207 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.952	α = 90
b = 94.952	β = 90
c = 84.162	γ = 120

Software Package:

Software Name	Purpose
MAR345	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-12-12 
• Released Date: 2014-08-20 
Deposition Author(s): Stapels, D.A.C., von Koeckritz-Blickwede, M., Ramyar, K.X., Bischoff, M., Milder, F., Ruyken, M., Scheepmaker, L., McWhorter, W.J., Herrmann, M., van Kessel, K.P.M., Geisbrecht, B.V., Rooijakkers, S.H.M.

Revision History  

• Version 1.0: 2014-08-20
  Type: Initial release
  
• Version 1.1: 2014-10-01
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Advisory, Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary