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- PDB-8q26: HsNMT1 in complex with both MyrCoA and GNCFSKPR inhibitor peptide -

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Basic information

Entry
Database: PDB / ID: 8q26
TitleHsNMT1 in complex with both MyrCoA and GNCFSKPR inhibitor peptide
Components
  • Glycylpeptide N-tetradecanoyltransferase 1
  • MYR-GLY-ASN-CYS-PHE-SER-LYS-PRO-ARG
KeywordsTRANSFERASE / E-MYRISTOYLATION / NMT / MYRISTOYLTRANSFERASE TYPE1 / ACYLTRANSFERASE / GNAT / GCN5-RELATED N-ACETYLTRANSFERASES
Function / homology
Function and homology information


myristoyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / peptidyl-lysine N6-myristoyltransferase activity / Late Phase of HIV Life Cycle / ketone metabolic process / regulation of opsin-mediated signaling pathway / Activation, myristolyation of BID and translocation to mitochondria / positive regulation of establishment of protein localization to mitochondrion / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity ...myristoyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / peptidyl-lysine N6-myristoyltransferase activity / Late Phase of HIV Life Cycle / ketone metabolic process / regulation of opsin-mediated signaling pathway / Activation, myristolyation of BID and translocation to mitochondria / positive regulation of establishment of protein localization to mitochondrion / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / protein localization to membrane / eNOS activation / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Inactivation, recovery and regulation of the phototransduction cascade / in utero embryonic development / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Glycylpeptide N-tetradecanoyltransferase, conserved site / Myristoyl-CoA:protein N-myristoyltransferase signature 1. / Myristoyl-CoA:protein N-myristoyltransferase signature 2. / Glycylpeptide N-tetradecanoyltransferase / Glycylpeptide N-tetradecanoyltransferase, N-terminal / Glycylpeptide N-tetradecanoyltransferase, C-terminal / Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain / Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
COENZYME A / MYRISTIC ACID / Glycylpeptide N-tetradecanoyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDian, C. / Giglione, C. / Meinnel, T.
Funding support France, 4items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-20-CE44-0013 France
Agence Nationale de la Recherche (ANR)ANR-2010-BLAN-1611-01 France
Fondation ARCARCPJA32020060002137 France
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INSB-05-01 France
CitationJournal: Structure / Year: 2024
Title: Novel, tightly structurally related N-myristoyltransferase inhibitors display equally potent yet distinct inhibitory mechanisms.
Authors: Riviere, F. / Dian, C. / Dutheil, R.F. / Monassa, P. / Giglione, C. / Meinnel, T.
History
DepositionAug 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Feb 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycylpeptide N-tetradecanoyltransferase 1
B: Glycylpeptide N-tetradecanoyltransferase 1
E: MYR-GLY-ASN-CYS-PHE-SER-LYS-PRO-ARG
F: MYR-GLY-ASN-CYS-PHE-SER-LYS-PRO-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,74812
Polymers94,6374
Non-polymers2,1118
Water14,052780
1
A: Glycylpeptide N-tetradecanoyltransferase 1
E: MYR-GLY-ASN-CYS-PHE-SER-LYS-PRO-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3746
Polymers47,3182
Non-polymers1,0564
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-29 kcal/mol
Surface area16450 Å2
2
B: Glycylpeptide N-tetradecanoyltransferase 1
F: MYR-GLY-ASN-CYS-PHE-SER-LYS-PRO-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3746
Polymers47,3182
Non-polymers1,0564
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-29 kcal/mol
Surface area16690 Å2
Unit cell
Length a, b, c (Å)79.220, 177.870, 57.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABEF

#1: Protein Glycylpeptide N-tetradecanoyltransferase 1


Mass: 46408.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NMT1 / Production host: Escherichia coli (E. coli) / References: UniProt: P30419
#2: Protein/peptide MYR-GLY-ASN-CYS-PHE-SER-LYS-PRO-ARG


Mass: 910.053 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 788 molecules

#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 780 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.16 Å3/Da / Density % sol: 42.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MgCl2, 0.2 M NaCl, 0.1 M sodium citrate pH 5.6, and 18-24% (w/v) PEG 6K or 8K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.96112 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96112 Å / Relative weight: 1
ReflectionResolution: 1.9→48.54 Å / Num. obs: 64915 / % possible obs: 99.6 % / Redundancy: 4.7 % / Biso Wilson estimate: 20.49 Å2 / CC1/2: 0.999 / Net I/σ(I): 20.3
Reflection shellResolution: 1.9→1.95 Å / Num. unique obs: 4487 / Rpim(I) all: 0.037 / Rsym value: 0.077

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→47.47 Å / SU ML: 0.1854 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.3646
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.206 3241 5 %
Rwork0.1613 61575 -
obs0.1636 64816 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.07 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6473 0 100 780 7353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00596813
X-RAY DIFFRACTIONf_angle_d0.83989280
X-RAY DIFFRACTIONf_chiral_restr0.05391008
X-RAY DIFFRACTIONf_plane_restr0.00581173
X-RAY DIFFRACTIONf_dihedral_angle_d18.17732513
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.24931310.23632495X-RAY DIFFRACTION92.33
1.93-1.960.27261350.22062552X-RAY DIFFRACTION97.85
1.96-1.990.25431390.20052662X-RAY DIFFRACTION99.79
1.99-2.030.28221380.18972628X-RAY DIFFRACTION99.96
2.03-2.070.25871400.17472657X-RAY DIFFRACTION99.96
2.07-2.10.21741390.17552655X-RAY DIFFRACTION99.93
2.1-2.150.24591410.17032677X-RAY DIFFRACTION99.93
2.15-2.190.21511390.17292641X-RAY DIFFRACTION99.86
2.19-2.250.23771400.1662662X-RAY DIFFRACTION100
2.25-2.30.23911400.17072660X-RAY DIFFRACTION99.93
2.3-2.360.21011390.172639X-RAY DIFFRACTION99.89
2.36-2.430.22481420.17152692X-RAY DIFFRACTION99.96
2.43-2.510.23881410.17342681X-RAY DIFFRACTION99.96
2.51-2.60.24351400.17442658X-RAY DIFFRACTION100
2.6-2.710.18531420.17172693X-RAY DIFFRACTION99.96
2.71-2.830.19491410.17572678X-RAY DIFFRACTION100
2.83-2.980.21271420.16822707X-RAY DIFFRACTION100
2.98-3.160.20911420.16742689X-RAY DIFFRACTION100
3.16-3.410.21371430.14872720X-RAY DIFFRACTION100
3.41-3.750.19021430.14362712X-RAY DIFFRACTION99.93
3.75-4.290.15191440.12672732X-RAY DIFFRACTION99.97
4.29-5.410.1631460.12872787X-RAY DIFFRACTION99.9
5.41-47.470.19421540.16532898X-RAY DIFFRACTION99.51

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