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- PDB-7owm: HsNMT1 in complex with both MyrCoA and HCPA substrate peptide GKQNSKLR -

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Basic information

Entry
Database: PDB / ID: 7owm
TitleHsNMT1 in complex with both MyrCoA and HCPA substrate peptide GKQNSKLR
Components
  • Glycylpeptide N-tetradecanoyltransferase 1
  • Neuron-specific calcium-binding protein hippocalcin
KeywordsTRANSFERASE / E-MYRISTOYLATION / NMT / MYRISTOYLTRANSFERASE TYPE1 / ACYLTRANSFERASE / GNAT / GCN5-RELATED N-ACETYLTRANSFERASES
Function / homology
Function and homology information


response to Aroclor 1254 / response to ketamine / myristoyltransferase activity / regulation of voltage-gated calcium channel activity / peptidyl-lysine N6-myristoyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / Late Phase of HIV Life Cycle / cellular ketone metabolic process / regulation of opsin-mediated signaling pathway / cellular response to electrical stimulus ...response to Aroclor 1254 / response to ketamine / myristoyltransferase activity / regulation of voltage-gated calcium channel activity / peptidyl-lysine N6-myristoyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / Late Phase of HIV Life Cycle / cellular ketone metabolic process / regulation of opsin-mediated signaling pathway / cellular response to electrical stimulus / Activation, myristolyation of BID and translocation to mitochondria / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / cellular response to L-glutamate / protein localization to membrane / regulation of postsynaptic neurotransmitter receptor internalization / neuronal cell body membrane / dendritic spine head / inner ear development / positive regulation of protein targeting to membrane / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / dendrite membrane / cellular response to calcium ion / dendrite cytoplasm / calcium-mediated signaling / kinase binding / Inactivation, recovery and regulation of the phototransduction cascade / retina development in camera-type eye / actin binding / perikaryon / in utero embryonic development / axon / glutamatergic synapse / calcium ion binding / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Recoverin family / 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 / EF hand ...Recoverin family / 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 / EF hand / Acyl-CoA N-acyltransferase / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
TETRADECANOYL-COA / Glycylpeptide N-tetradecanoyltransferase 1 / Neuron-specific calcium-binding protein hippocalcin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycylpeptide N-tetradecanoyltransferase 1
B: Glycylpeptide N-tetradecanoyltransferase 1
C: Neuron-specific calcium-binding protein hippocalcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1889
Polymers93,8643
Non-polymers2,3246
Water18,1231006
1
A: Glycylpeptide N-tetradecanoyltransferase 1
C: Neuron-specific calcium-binding protein hippocalcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4684
Polymers47,3992
Non-polymers1,0702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-22 kcal/mol
Surface area16510 Å2
MethodPISA
2
B: Glycylpeptide N-tetradecanoyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7205
Polymers46,4651
Non-polymers1,2544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-17 kcal/mol
Surface area16910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.879, 178.380, 58.255
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

#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 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): ROSETTA2 PLYSS
References: UniProt: P30419, glycylpeptide N-tetradecanoyltransferase
#2: Protein/peptide Neuron-specific calcium-binding protein hippocalcin / Calcium-binding protein BDR-2


Mass: 933.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P84074
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1006 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.31 Å3/Da / Density % sol: 46.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20% PEG8K, 100mM Sodium Citrate pH 5.6, 100mM MgCl2, 100mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.984 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 18, 2019 / Details: K/B mirrors
RadiationMonochromator: silicium Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.5→48.773 Å / Num. obs: 128545 / % possible obs: 98.4 % / Redundancy: 13.9 % / Biso Wilson estimate: 16.7 Å2 / CC1/2: 0.9978 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.032 / Net I/σ(I): 12.2
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 8.9 % / Rmerge(I) obs: 1.532 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 6425 / CC1/2: 0.6483 / Rpim(I) all: 0.541 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
STARANISOdata scaling
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O9T

5o9t


Resolution: 1.5→48.77 Å / SU ML: 0.1589 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.1827
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1958 6514 5.07 %
Rwork0.1544 122017 -
obs0.1564 128531 96.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.18 Å2
Refinement stepCycle: LAST / Resolution: 1.5→48.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6297 0 213 1006 7516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00596840
X-RAY DIFFRACTIONf_angle_d0.87379325
X-RAY DIFFRACTIONf_chiral_restr0.05971021
X-RAY DIFFRACTIONf_plane_restr0.00511171
X-RAY DIFFRACTIONf_dihedral_angle_d20.57482684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.27931630.23192974X-RAY DIFFRACTION71.43
1.52-1.530.29151880.22173143X-RAY DIFFRACTION75.45
1.53-1.550.25571910.2023254X-RAY DIFFRACTION78.98
1.55-1.570.22741780.1933487X-RAY DIFFRACTION82.16
1.57-1.590.25922060.19123607X-RAY DIFFRACTION86.72
1.59-1.620.24642210.18513787X-RAY DIFFRACTION90.97
1.62-1.640.22242190.17993973X-RAY DIFFRACTION95.16
1.64-1.660.27292430.17264183X-RAY DIFFRACTION99.15
1.66-1.690.24181980.16314165X-RAY DIFFRACTION99.98
1.69-1.720.24792240.16634220X-RAY DIFFRACTION100
1.72-1.750.20832400.16214191X-RAY DIFFRACTION99.98
1.75-1.780.21512240.17154196X-RAY DIFFRACTION100
1.78-1.810.21012380.16854201X-RAY DIFFRACTION100
1.81-1.850.22172310.16674157X-RAY DIFFRACTION100
1.85-1.890.21342200.15494242X-RAY DIFFRACTION100
1.89-1.930.21142320.15424192X-RAY DIFFRACTION99.98
1.93-1.980.19622200.1524234X-RAY DIFFRACTION100
1.98-2.040.1912220.1454217X-RAY DIFFRACTION100
2.04-2.10.18772120.1434230X-RAY DIFFRACTION100
2.1-2.160.20122330.14654249X-RAY DIFFRACTION99.98
2.16-2.240.19862030.14634275X-RAY DIFFRACTION100
2.24-2.330.18032250.15214196X-RAY DIFFRACTION100
2.33-2.440.18992200.15194260X-RAY DIFFRACTION100
2.44-2.560.20482490.15754222X-RAY DIFFRACTION100
2.56-2.730.22272140.16164263X-RAY DIFFRACTION100
2.73-2.940.19592190.15884306X-RAY DIFFRACTION100
2.94-3.230.18132000.1574318X-RAY DIFFRACTION100
3.23-3.70.16092180.14194336X-RAY DIFFRACTION100
3.7-4.660.15732210.12444373X-RAY DIFFRACTION99.96
4.66-48.770.19222420.16424566X-RAY DIFFRACTION99.81

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