[English] 日本語
Yorodumi- PDB-4zjg: Crystal structure of native alpha-2-macroglobulin from Escherichi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zjg | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of native alpha-2-macroglobulin from Escherichia coli spanning domains MG0-NIE-MG1. | ||||||||||||
Components | alpha-2-Macroglobulin | ||||||||||||
Keywords | MEMBRANE PROTEIN / Bacterial pan-proteinase inhibitor | ||||||||||||
Function / homology | Function and homology information endopeptidase inhibitor activity / protein homodimerization activity / extracellular space / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||||||||
Authors | Garcia-Ferrer, I. / Arede, P. / Gomez-Blanco, J. / Luque, D. / Duquerroy, S. / Caston, J.R. / Goulas, T. / Gomis-Ruth, X.F. | ||||||||||||
Funding support | Spain, 3items
| ||||||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2015 Title: Structural and functional insights into Escherichia coli α2-macroglobulin endopeptidase snap-trap inhibition. Authors: Irene Garcia-Ferrer / Pedro Arêde / Josué Gómez-Blanco / Daniel Luque / Stephane Duquerroy / José R Castón / Theodoros Goulas / F Xavier Gomis-Rüth / Abstract: The survival of commensal bacteria requires them to evade host peptidases. Gram-negative bacteria from the human gut microbiome encode a relative of the human endopeptidase inhibitor, α2- ...The survival of commensal bacteria requires them to evade host peptidases. Gram-negative bacteria from the human gut microbiome encode a relative of the human endopeptidase inhibitor, α2-macroglobulin (α2M). Escherichia coli α2M (ECAM) is a ∼ 180-kDa multidomain membrane-anchored pan-peptidase inhibitor, which is cleaved by host endopeptidases in an accessible bait region. Structural studies by electron microscopy and crystallography reveal that this cleavage causes major structural rearrangement of more than half the 13-domain structure from a native to a compact induced form. It also exposes a reactive thioester bond, which covalently traps the peptidase. Subsequently, peptidase-laden ECAM is shed from the membrane and may dimerize. Trapped peptidases are still active except against very large substrates, so inhibition potentially prevents damage of large cell envelope components, but not host digestion. Mechanistically, these results document a novel monomeric "snap trap." | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4zjg.cif.gz | 135.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4zjg.ent.gz | 111 KB | Display | PDB format |
PDBx/mmJSON format | 4zjg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/4zjg ftp://data.pdbj.org/pub/pdb/validation_reports/zj/4zjg | HTTPS FTP |
---|
-Related structure data
Related structure data | 3016C 3017C 3018C 4ziqC 4ziuC 4zjhC 5a42C C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 38490.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Gene: yfhM, b2520, JW2504 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P76578 |
---|
-Non-polymers , 6 types, 49 molecules
#2: Chemical | ChemComp-PG4 / | ||
---|---|---|---|
#3: Chemical | ChemComp-PGE / | ||
#4: Chemical | ChemComp-1PE / | ||
#5: Chemical | ChemComp-PEG / | ||
#6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.77 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 30% [v/v] PEG400 100mM Tris-HCl / PH range: 9.0-10.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792, 0.9795, 0.9688 | ||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2014 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
| ||||||||||||
Reflection | Resolution: 2.3→63.8 Å / Num. all: 17299 / Num. obs: 17299 / % possible obs: 99.9 % / Redundancy: 25.4 % / Biso Wilson estimate: 58.95 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 22.9 | ||||||||||||
Reflection shell | Resolution: 2.3→2.44 Å / Redundancy: 24.3 % / Rmerge(I) obs: 1.083 / Mean I/σ(I) obs: 3.4 / % possible all: 99.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.3→63.8 Å / Cor.coef. Fo:Fc: 0.9109 / Cor.coef. Fo:Fc free: 0.9077 / SU R Cruickshank DPI: 0.285 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.291 / SU Rfree Blow DPI: 0.223 / SU Rfree Cruickshank DPI: 0.224
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 77.18 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.427 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.3→63.8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.44 Å / Total num. of bins used: 9
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|