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- PDB-7owq: HsNMT1 in complex with both MyrCoA and peptide N-Methylated-GNCFSKPR -

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Basic information

Entry
Database: PDB / ID: 7owq
TitleHsNMT1 in complex with both MyrCoA and peptide N-Methylated-GNCFSKPR
Components
  • Glycylpeptide N-tetradecanoyltransferase 1
  • MGY-ASN-CYS-PHE-SER-LYS-PRO-ARG
KeywordsTRANSFERASE / N-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
TETRADECANOYL-COA / Glycylpeptide N-tetradecanoyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDian, C. / Giglione, C. / Meinnel, T.
Funding support France, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-20-CE44-0013 France
Fondation ARCARCPJA32020060002137 France
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INSB-05-01 France
CitationJournal: J.Mol.Biol. / Year: 2022
Title: Structural and Large-scale Analysis Unveil the Intertwined Paths Promoting NMT-catalyzed Lysine and Glycine Myristoylation.
Authors: Riviere, F. / Dian, C. / Dutheil, R.F. / Monassa, P. / Giglione, C. / Meinnel, T.
History
DepositionJun 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn
Item: _pdbx_entry_details.has_protein_modification

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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
D: MGY-ASN-CYS-PHE-SER-LYS-PRO-ARG
F: MGY-ASN-CYS-PHE-SER-LYS-PRO-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7356
Polymers94,7794
Non-polymers1,9562
Water00
1
A: Glycylpeptide N-tetradecanoyltransferase 1
D: MGY-ASN-CYS-PHE-SER-LYS-PRO-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3673
Polymers47,3892
Non-polymers9781
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-27 kcal/mol
Surface area17310 Å2
MethodPISA
2
B: Glycylpeptide N-tetradecanoyltransferase 1
F: MGY-ASN-CYS-PHE-SER-LYS-PRO-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3673
Polymers47,3892
Non-polymers9781
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-28 kcal/mol
Surface area16870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.655, 58.876, 154.207
Angle α, β, γ (deg.)90.000, 92.062, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Glycylpeptide N-tetradecanoyltransferase 1 / Myristoyl-CoA:protein N-myristoyltransferase 1 / Type I N-myristoyltransferase / Peptide N- ...Myristoyl-CoA:protein N-myristoyltransferase 1 / Type I N-myristoyltransferase / Peptide N-myristoyltransferase 1


Mass: 46465.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NMT1, NMT / Details (production host): pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): ROSETTA2 PLYSS
References: UniProt: P30419, glycylpeptide N-tetradecanoyltransferase
#2: Protein/peptide MGY-ASN-CYS-PHE-SER-LYS-PRO-ARG


Mass: 924.079 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: N-acetylated-Glycine-peptide / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-MYA / TETRADECANOYL-COA / MYRISTOYL-COA


Mass: 977.890 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H62N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 21% PEG 8K, 0.1M sodum citrate, 0.1 M MgCl2, 0.2M NaCl

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.96775 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Feb 8, 2016
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96775 Å / Relative weight: 1
ReflectionResolution: 3→47.69 Å / Num. obs: 32321 / % possible obs: 98.6 % / Redundancy: 6.3 % / Biso Wilson estimate: 49.82 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.058 / Rsym value: 0.134 / Net I/σ(I): 11.2
Reflection shellResolution: 3→3.18 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 3 / Num. unique obs: 2710 / CC1/2: 0.856 / Rpim(I) all: 0.265 / Rsym value: 0.601 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O9V

5o9v


Resolution: 3→47.69 Å / SU ML: 0.4087 / Cross valid method: FREE R-VALUE / σ(F): 0.37 / Phase error: 27.5367
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2551 1753 5.42 %
Rwork0.2105 30568 -
obs0.213 32321 97.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.33 Å2
Refinement stepCycle: LAST / Resolution: 3→47.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6330 0 126 0 6456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00286637
X-RAY DIFFRACTIONf_angle_d0.70039049
X-RAY DIFFRACTIONf_chiral_restr0.04911003
X-RAY DIFFRACTIONf_plane_restr0.0061140
X-RAY DIFFRACTIONf_dihedral_angle_d16.1741023
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.080.39491130.33042385X-RAY DIFFRACTION96.22
3.08-3.170.39861510.3112273X-RAY DIFFRACTION97.9
3.17-3.270.33431660.2792388X-RAY DIFFRACTION98.08
3.27-3.390.30661330.25662306X-RAY DIFFRACTION98.11
3.39-3.530.2951690.24622318X-RAY DIFFRACTION98.26
3.53-3.690.3125990.23342479X-RAY DIFFRACTION98.4
3.69-3.880.29141220.20812288X-RAY DIFFRACTION98.41
3.88-4.120.21481580.19342244X-RAY DIFFRACTION95.66
4.13-4.440.1997950.17892292X-RAY DIFFRACTION93.35
4.44-4.890.18021210.15622408X-RAY DIFFRACTION99.72
4.89-5.60.25541200.18152442X-RAY DIFFRACTION100
5.6-7.050.24921430.20742388X-RAY DIFFRACTION99.72
7.05-47.690.19811630.17912357X-RAY DIFFRACTION99.49

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