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- PDB-5syt: Crystal Structure of ZMPSTE24 -

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Basic information

Entry
Database: PDB / ID: 5syt
TitleCrystal Structure of ZMPSTE24
ComponentsCAAX prenyl protease 1 homolog
KeywordsHYDROLASE / MEMBRANE PROTEIN / CaaX protease / zinc metalloprotease / STE24 / isoprenylation / Structural Genomics / PSI-2 / Protein Structure Initiative / Membrane Protein Structural Biology Consortium / MPSBC
Function / homology
Function and homology information


prenylated protein catabolic process / regulation of stress-activated protein kinase signaling cascade / regulation of mitotic cell cycle DNA replication / regulation of termination of RNA polymerase I transcription / Ste24 endopeptidase / CAAX-box protein processing / inflammatory cell apoptotic process / regulation of hormone metabolic process / response to DNA damage checkpoint signaling / kidney morphogenesis ...prenylated protein catabolic process / regulation of stress-activated protein kinase signaling cascade / regulation of mitotic cell cycle DNA replication / regulation of termination of RNA polymerase I transcription / Ste24 endopeptidase / CAAX-box protein processing / inflammatory cell apoptotic process / regulation of hormone metabolic process / response to DNA damage checkpoint signaling / kidney morphogenesis / cellular lipid metabolic process / cardiac ventricle development / maintenance of rDNA / growth plate cartilage development / nuclear envelope organization / regulation of fibroblast proliferation / calcium ion import into sarcoplasmic reticulum / regulation of cellular senescence / ventricular cardiac muscle tissue development / CAMKK-AMPK signaling cascade / cardiac conduction / regulation of TOR signaling / positive regulation of gene expression via chromosomal CpG island demethylation / regulation of defense response to virus / metalloexopeptidase activity / regulation of bone mineralization / regulation of ventricular cardiac muscle cell membrane repolarization / adult walking behavior / cardiac muscle cell development / negative regulation of miRNA processing / nuclear inner membrane / regulation of DNA damage response, signal transduction by p53 class mediator / neuromuscular process / bone mineralization / protein maturation / regulation of lipid metabolic process / regulation of multicellular organism growth / regulation of glucose metabolic process / hair follicle development / heart morphogenesis / thymus development / liver development / regulation of autophagy / determination of adult lifespan / multicellular organism growth / cellular response to gamma radiation / metalloendopeptidase activity / late endosome membrane / regulation of cell shape / early endosome membrane / double-stranded DNA binding / endopeptidase activity / DNA repair / endoplasmic reticulum membrane / protein-containing complex / proteolysis / extracellular exosome / membrane / metal ion binding
Similarity search - Function
CAAX prenyl protease 1 / CAAX prenyl protease 1, N-terminal / CAAX prenyl protease N-terminal, five membrane helices / Peptidase M48 / Peptidase family M48
Similarity search - Domain/homology
PENTAETHYLENE GLYCOL MONODECYL ETHER / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DI(HYDROXYETHYL)ETHER / CAAX prenyl protease 1 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsClark, K. / Jenkins, J.L. / Fedoriw, N. / Dumont, M.E. / Membrane Protein Structural Biology Consortium (MPSBC)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54 GM094611 United States
CitationJournal: Protein Sci. / Year: 2017
Title: Human CaaX protease ZMPSTE24 expressed in yeast: Structure and inhibition by HIV protease inhibitors.
Authors: Clark, K.M. / Jenkins, J.L. / Fedoriw, N. / Dumont, M.E.
History
DepositionAug 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: CAAX prenyl protease 1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,95924
Polymers55,3311
Non-polymers5,62823
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8930 Å2
ΔGint-90 kcal/mol
Surface area24710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.455, 84.560, 76.885
Angle α, β, γ (deg.)90.000, 119.070, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CAAX prenyl protease 1 homolog / Farnesylated proteins-converting enzyme 1 / FACE-1 / Prenyl protein-specific endoprotease 1 / Zinc ...Farnesylated proteins-converting enzyme 1 / FACE-1 / Prenyl protein-specific endoprotease 1 / Zinc metalloproteinase Ste24 homolog


Mass: 55331.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZMPSTE24, FACE1, STE24 / Details (production host): pSGP46 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BJ5460 / References: UniProt: O75844, Ste24 endopeptidase

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Non-polymers , 9 types, 181 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#4: Chemical ChemComp-CXE / PENTAETHYLENE GLYCOL MONODECYL ETHER


Mass: 378.544 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H42O6
#5: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

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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: 3.83 Å3/Da / Density % sol: 67.87 % / Description: Thin rods up to 400 microns long
Crystal growTemperature: 286 K / Method: vapor diffusion / pH: 7.5
Details: 24% PEG3350, 170 mM ammonium sulfate, 15% glycerol, 50 mM HEPES, pH 7.5
Temp details: Crystals were transferred to 277 K before cryoprotection.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 27, 2016
RadiationMonochromator: cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→33.601 Å / Num. obs: 56449 / % possible obs: 99.6 % / Redundancy: 14.7 % / Biso Wilson estimate: 22.44 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.439 / Net I/σ(I): 6.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2-2.0514.83.4951.60.574197.8
8.94-33.6150.1220.996194.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLM7.21data reduction
Aimless0.5.9data scaling
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4AW6

4aw6


Resolution: 2→33.601 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.78
RfactorNum. reflection% reflection
Rfree0.249 2007 3.56 %
Rwork0.218 --
obs0.2191 56380 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 135.07 Å2 / Biso mean: 41.6363 Å2 / Biso min: 14.19 Å2
Refinement stepCycle: final / Resolution: 2→33.601 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3561 0 655 160 4376
Biso mean--55.71 39.47 -
Num. residues----444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123923
X-RAY DIFFRACTIONf_angle_d1.3315234
X-RAY DIFFRACTIONf_chiral_restr0.055564
X-RAY DIFFRACTIONf_plane_restr0.008613
X-RAY DIFFRACTIONf_dihedral_angle_d21.752304
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.36391470.371138453992100
2.05-2.10540.42451310.345538774008100
2.1054-2.16740.29841530.316738514004100
2.1674-2.23730.291410.287738744015100
2.2373-2.31730.28231490.248938824031100
2.3173-2.410.26611370.230638934030100
2.41-2.51970.28431410.21638614002100
2.5197-2.65250.28911450.204338984043100
2.6525-2.81860.23231410.191238714012100
2.8186-3.03610.24281390.192538994038100
3.0361-3.34140.23321430.195538884031100
3.3414-3.82430.23061460.181938994045100
3.8243-4.81590.18351450.175139224067100
4.8159-33.60560.22921490.20873913406298

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