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- PDB-6bh8: Crystal structure of ZMPSTE24 in complex with phosphoramidon -

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Basic information

Entry
Database: PDB / ID: 6bh8
TitleCrystal structure of ZMPSTE24 in complex with phosphoramidon
ComponentsCAAX prenyl protease 1 homolog
KeywordsHYDROLASE / Integral Membrane Protein / Zinc Metalloprotease / Inhibitor Complex
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 / kidney morphogenesis / response to DNA damage checkpoint signaling ...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 / kidney morphogenesis / response to DNA damage checkpoint signaling / cardiac ventricle development / nuclear envelope organization / growth plate cartilage development / maintenance of rDNA / 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 / regulation of defense response to virus / positive regulation of gene expression via chromosomal CpG island demethylation / metalloexopeptidase activity / regulation of bone mineralization / regulation of ventricular cardiac muscle cell membrane repolarization / negative regulation of miRNA processing / nuclear inner membrane / cardiac muscle cell development / adult walking behavior / regulation of DNA damage response, signal transduction by p53 class mediator / neuromuscular process / bone mineralization / regulation of lipid metabolic process / regulation of glucose metabolic process / regulation of multicellular organism growth / hair follicle development / heart morphogenesis / protein maturation / liver development / thymus development / determination of adult lifespan / cellular response to gamma radiation / multicellular organism growth / metalloendopeptidase activity / lipid metabolic process / late endosome membrane / regulation of cell shape / double-stranded DNA binding / early endosome membrane / endopeptidase activity / regulation of autophagy / DNA repair / endoplasmic reticulum membrane / protein-containing complex / proteolysis / extracellular exosome / metal ion binding / membrane
Similarity search - Function
CAAX prenyl protease 1 / CAAX prenyl protease 1, N-terminal / CAAX prenyl protease N-terminal, five membrane helices / Metalloproteases ("zincins"), catalytic domain / Peptidase M48 / Peptidase family M48 / Zincin-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHORAMIDON / Chem-RDF / CAAX prenyl protease 1 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.85 Å
AuthorsGoblirsch, B.R. / Arachea, B.T. / Wiener, M.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM108612 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Phosphoramidon inhibits the integral membrane protein zinc metalloprotease ZMPSTE24.
Authors: Goblirsch, B.R. / Arachea, B.T. / Councell, D.J. / Wiener, M.C.
History
DepositionOct 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CAAX prenyl protease 1 homolog
B: CAAX prenyl protease 1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,2608
Polymers111,4292
Non-polymers1,8316
Water00
1
A: CAAX prenyl protease 1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6304
Polymers55,7151
Non-polymers9153
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CAAX prenyl protease 1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6304
Polymers55,7151
Non-polymers9153
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.329, 84.661, 132.017
Angle α, β, γ (deg.)90.000, 96.260, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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: 55714.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZMPSTE24, FACE1, STE24 / Plasmid: pSGP47 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BJ5460 / References: UniProt: O75844, Ste24 endopeptidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Zn
#3: Chemical ChemComp-RDF / N-ALPHA-L-RHAMNOPYRANOSYLOXY(HYDROXYPHOSPHINYL)-L-LEUCYL-L-TRYPTOPHAN / PHOSPHORAMIDON


Type: peptide-like, Glycopeptide / Class: Enzyme inhibitor / Mass: 543.504 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H34N3O10P / Feature type: SUBJECT OF INVESTIGATION / References: PHOSPHORAMIDON / Comment: inhibitor*YM
#4: Chemical ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
Sequence detailsThe deposited sequence is derived from NCBI GenBank entry BC037283.1

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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: 4.64 Å3/Da / Density % sol: 73.48 % / Description: Long needle-like morphology
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Glycerol, Ammonium Sulfate, PEG 3350, Hepes/NaOH pH 7.5
Temp details: Crystallization set-ups at 296 and then immediately moved to 277

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 1, 2017
RadiationMonochromator: Double crystal Monochromator, Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.85→47.03 Å / Num. obs: 19383 / % possible obs: 97.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 111.68 Å2 / CC1/2: 0.761 / Rmerge(I) obs: 0.5105 / Rpim(I) all: 0.3347 / Rrim(I) all: 0.6127 / Net I/σ(I): 2.21
Reflection shellResolution: 3.85→3.99 Å / Redundancy: 3.3 % / Rmerge(I) obs: 2.291 / Mean I/σ(I) obs: 0.54 / Num. unique obs: 187 / CC1/2: 0.326 / Rpim(I) all: 1.468 / Rrim(I) all: 2.729 / % possible all: 97.38

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5SYT

5syt


Resolution: 3.85→47.028 Å / SU ML: 0.87 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 45.21
RfactorNum. reflection% reflection
Rfree0.3713 1909 9.92 %
Rwork0.3376 --
obs0.3409 19241 97.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 373.37 Å2 / Biso mean: 143.7474 Å2 / Biso min: 10.17 Å2
Refinement stepCycle: final / Resolution: 3.85→47.028 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6383 0 186 0 6569
Biso mean--135.55 --
Num. residues----781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136691
X-RAY DIFFRACTIONf_angle_d1.1549045
X-RAY DIFFRACTIONf_chiral_restr0.0551003
X-RAY DIFFRACTIONf_plane_restr0.0081089
X-RAY DIFFRACTIONf_dihedral_angle_d15.0962379
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.85-3.94630.44881360.38371230136698
3.9463-4.05290.38951340.38921225135998
4.0529-4.17210.38241340.36871226136099
4.1721-4.30670.40071390.37061247138699
4.3067-4.46050.44521380.34661260139899
4.4605-4.63890.43861350.32731224135998
4.6389-4.84980.35081380.30661247138599
4.8498-5.10520.37061360.30671240137699
5.1052-5.42470.31051380.31571256139499
5.4247-5.84280.35861400.322512641404100
5.8428-6.42950.3791380.31361251138999
6.4295-7.35680.38741390.32121257139699
7.3568-9.25710.30231370.31411246138397
9.2571-47.03110.36241270.36151159128688

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