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- PDB-1ezx: CRYSTAL STRUCTURE OF A SERPIN:PROTEASE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1ezx
TitleCRYSTAL STRUCTURE OF A SERPIN:PROTEASE COMPLEX
Components
  • (ALPHA-1-ANTITRYPSIN) x 2
  • TRYPSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / protease-inhibitor complex / serpin / alpha-1-antitrypsin / trypsin / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


Cargo concentration in the ER / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / acute-phase response ...Cargo concentration in the ER / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / acute-phase response / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / protease binding / : / endopeptidase activity / ficolin-1-rich granule lumen / endoplasmic reticulum lumen / serine-type endopeptidase activity / intracellular membrane-bounded organelle / Neutrophil degranulation / endoplasmic reticulum / Golgi apparatus / proteolysis / extracellular space / extracellular exosome / extracellular region / metal ion binding / identical protein binding
Similarity search - Function
Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily ...Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / : / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Roll / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Serine protease 1 / Alpha-1-antitrypsin
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsHuntington, J.A. / Carrell, R.W.
CitationJournal: Nature / Year: 2000
Title: Structure of a serpin-protease complex shows inhibition by deformation.
Authors: Huntington, J.A. / Read, R.J. / Carrell, R.W.
History
DepositionMay 12, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-1-ANTITRYPSIN
B: ALPHA-1-ANTITRYPSIN
C: TRYPSIN


Theoretical massNumber of molelcules
Total (without water)67,2783
Polymers67,2783
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.234, 171.295, 145.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein ALPHA-1-ANTITRYPSIN


Mass: 37692.922 Da / Num. of mol.: 1
Fragment: N-TERMINAL FRAGMENT OF PROTEOLYTIC CLEAVAGE AT MET358-SER359
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Tissue fraction: PLASMA / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: P01009
#2: Protein/peptide ALPHA-1-ANTITRYPSIN


Mass: 4139.938 Da / Num. of mol.: 1
Fragment: C-TERMINAL FRAGMENT OF PROTEOLYTIC CLEAVAGE AT MET358-SER359
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Tissue fraction: PLASMA / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: P01009
#3: Protein TRYPSIN


Mass: 25444.717 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: P00760, trypsin
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 3350, sodium citrate , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
220 mMNa acetate1drop
30.2 MNa citrate1reservoir
420 %PEG33501reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 14, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 24803 / Num. obs: 24548 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Biso Wilson estimate: 58.9 Å2 / Rmerge(I) obs: 0.158 / Net I/σ(I): 12
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 8 % / Rmerge(I) obs: 0.833 / Num. unique all: 3524 / % possible all: 99
Reflection
*PLUS
Num. measured all: 190117
Reflection shell
*PLUS
% possible obs: 99 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementResolution: 2.6→30 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood target of Pannu and Read, 1996
RfactorNum. reflection% reflectionSelection details
Rfree0.2388 1042 -random
Rwork0.2049 ---
all-24803 --
obs-24548 99 %-
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3903 0 0 81 3984
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0064
X-RAY DIFFRACTIONc_angle_deg1.37

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