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- PDB-8q3t: HsNMT1 in complex with both MyrCoA and GNCFSKPRVPTK inhibitor peptide -

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Basic information

Entry
Database: PDB / ID: 8q3t
TitleHsNMT1 in complex with both MyrCoA and GNCFSKPRVPTK inhibitor peptide
Components
  • Glycylpeptide N-tetradecanoyltransferase 1
  • MYR-GLY-ASN-CYS-PHE-SER-LYS-PRO-ARG-VAL-PRO
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 / cytosol / cytoplasm
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: 1.96 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 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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
C: MYR-GLY-ASN-CYS-PHE-SER-LYS-PRO-ARG-VAL-PRO
D: MYR-GLY-ASN-CYS-PHE-SER-LYS-PRO-ARG-VAL-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,36813
Polymers95,0294
Non-polymers2,3399
Water16,376909
1
A: Glycylpeptide N-tetradecanoyltransferase 1
C: MYR-GLY-ASN-CYS-PHE-SER-LYS-PRO-ARG-VAL-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7668
Polymers47,5152
Non-polymers1,2516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-34 kcal/mol
Surface area16870 Å2
2
B: Glycylpeptide N-tetradecanoyltransferase 1
D: MYR-GLY-ASN-CYS-PHE-SER-LYS-PRO-ARG-VAL-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6035
Polymers47,5152
Non-polymers1,0883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-7 kcal/mol
Surface area16840 Å2
Unit cell
Length a, b, c (Å)79.610, 178.580, 58.130
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 ABCD

#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-VAL-PRO


Mass: 1106.298 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: N-myristoylated GNCFSKPRVPTK peptide (last two residues are not seen)
Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 918 molecules

#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#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.: 909 / 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: 2.15 Å3/Da / Density % sol: 42.68 %
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: 1.96→48.72 Å / Num. obs: 59629 / % possible obs: 99.6 % / Redundancy: 7.4 % / Biso Wilson estimate: 17.82 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.026 / Rsym value: 0.067 / Net I/σ(I): 22.7
Reflection shellResolution: 1.96→2.02 Å / Redundancy: 7 % / Mean I/σ(I) obs: 6.1 / Num. unique obs: 4200 / CC1/2: 0.961 / Rpim(I) all: 0.136 / Rsym value: 0.367 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→47.67 Å / SU ML: 0.1753 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.0769
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1957 2979 5 %
Rwork0.1512 56562 -
obs0.1535 59541 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.3 Å2
Refinement stepCycle: LAST / Resolution: 1.96→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6659 0 0 909 7568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00646939
X-RAY DIFFRACTIONf_angle_d0.87319442
X-RAY DIFFRACTIONf_chiral_restr0.05411018
X-RAY DIFFRACTIONf_plane_restr0.00571194
X-RAY DIFFRACTIONf_dihedral_angle_d18.09732584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-20.24191340.19972531X-RAY DIFFRACTION93.21
2-2.030.20131370.16352612X-RAY DIFFRACTION98.96
2.03-2.070.21881410.15672668X-RAY DIFFRACTION99.15
2.07-2.110.24241390.15552646X-RAY DIFFRACTION99.08
2.11-2.150.22951400.15972673X-RAY DIFFRACTION98.81
2.15-2.20.20031400.15642641X-RAY DIFFRACTION99.68
2.2-2.250.23421390.15342647X-RAY DIFFRACTION98.83
2.25-2.310.23661410.15822675X-RAY DIFFRACTION99.93
2.31-2.370.211400.15722668X-RAY DIFFRACTION99.15
2.37-2.440.22361410.15912675X-RAY DIFFRACTION99.26
2.44-2.520.22481420.16062697X-RAY DIFFRACTION99.96
2.52-2.610.20711410.16292679X-RAY DIFFRACTION99.58
2.61-2.710.2231420.16292696X-RAY DIFFRACTION99.61
2.71-2.830.20161420.1572698X-RAY DIFFRACTION99.72
2.83-2.980.2231420.15272696X-RAY DIFFRACTION99.79
2.98-3.170.16811420.15552715X-RAY DIFFRACTION99.86
3.17-3.410.18821450.14152749X-RAY DIFFRACTION99.83
3.41-3.760.16321430.13662718X-RAY DIFFRACTION99.9
3.76-4.30.14621460.12782767X-RAY DIFFRACTION99.97
4.3-5.420.14511470.1282804X-RAY DIFFRACTION99.9
5.42-47.670.21281550.17242907X-RAY DIFFRACTION99.09

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