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- PDB-7owu: HsNMT1 in complex with both CoA and Myr-ANCFSKPR peptide -

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Basic information

Entry
Database: PDB / ID: 7owu
TitleHsNMT1 in complex with both CoA and Myr-ANCFSKPR peptide
Components
  • ALA-ASN-CYS-PHE-SER-LYS-PRO-ARG
  • Glycylpeptide N-tetradecanoyltransferase 1
KeywordsTRANSFERASE / N-MYRISTOYLATION / NMT / MYRISTOYLTRANSFERASE TYPE1 / ACYLTRANSFERASE / GNAT / GCN5-RELATED N-ACETYLTRANSFERASES
Function / homology
Function and homology information


myristoyltransferase 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 / Activation, myristolyation of BID and translocation to mitochondria / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / protein localization to membrane ...myristoyltransferase 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 / Activation, myristolyation of BID and translocation to mitochondria / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / protein localization to membrane / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 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: ALA-ASN-CYS-PHE-SER-LYS-PRO-ARG
D: ALA-ASN-CYS-PHE-SER-LYS-PRO-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,23113
Polymers94,7794
Non-polymers2,4529
Water9,458525
1
A: Glycylpeptide N-tetradecanoyltransferase 1
C: ALA-ASN-CYS-PHE-SER-LYS-PRO-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5706
Polymers47,3892
Non-polymers1,1804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-9 kcal/mol
Surface area16710 Å2
MethodPISA
2
B: Glycylpeptide N-tetradecanoyltransferase 1
D: ALA-ASN-CYS-PHE-SER-LYS-PRO-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6627
Polymers47,3892
Non-polymers1,2725
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-8 kcal/mol
Surface area17000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.296, 58.076, 156.053
Angle α, β, γ (deg.)90.000, 90.160, 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

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

#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 ALA-ASN-CYS-PHE-SER-LYS-PRO-ARG


Mass: 924.079 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 534 molecules

#3: Chemical ChemComp-COA / COENZYME A / Coenzyme A


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


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


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


Mass: 18.015 Da / Num. of mol.: 525 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.24 Å3/Da / Density % sol: 45.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 21% PEG 8K, 100mM Sodium Acetate 4.6

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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-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 1, 2016
RadiationMonochromator: 0.966 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.08→46.9 Å / Num. obs: 166966 / % possible obs: 99.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 24.96 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.038 / Rsym value: 0.06 / Net I/σ(I): 13
Reflection shellResolution: 2.08→2.14 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 4.3 / Num. unique obs: 12891 / CC1/2: 0.937 / Rpim(I) all: 0.167 / Rsym value: 0.259 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C2Y

4c2y


Resolution: 2.08→46.86 Å / SU ML: 0.2468 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 24.1769
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2233 4660 4.94 %
Rwork0.1787 89670 -
obs0.1809 94330 96.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.27 Å2
Refinement stepCycle: LAST / Resolution: 2.08→46.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6490 0 141 525 7156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00446851
X-RAY DIFFRACTIONf_angle_d0.79149319
X-RAY DIFFRACTIONf_chiral_restr0.04871008
X-RAY DIFFRACTIONf_plane_restr0.00541176
X-RAY DIFFRACTIONf_dihedral_angle_d20.76792525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.10.32431470.23453025X-RAY DIFFRACTION97.12
2.1-2.130.32231570.22942918X-RAY DIFFRACTION96.88
2.13-2.150.26371630.21593057X-RAY DIFFRACTION96.96
2.15-2.180.25651610.22222970X-RAY DIFFRACTION95.52
2.18-2.210.27111460.20532803X-RAY DIFFRACTION92.94
2.21-2.240.27111690.20853011X-RAY DIFFRACTION96.54
2.24-2.270.28641850.2092947X-RAY DIFFRACTION97
2.27-2.310.29511630.19912972X-RAY DIFFRACTION97.3
2.31-2.340.28251520.20513017X-RAY DIFFRACTION97.36
2.34-2.380.31781320.20753021X-RAY DIFFRACTION97.68
2.38-2.420.22711510.20393053X-RAY DIFFRACTION97.77
2.42-2.470.28761250.20213033X-RAY DIFFRACTION97.53
2.47-2.510.31461130.20063063X-RAY DIFFRACTION97.84
2.51-2.560.25021820.20022981X-RAY DIFFRACTION97.56
2.56-2.620.27751410.2032994X-RAY DIFFRACTION97.21
2.62-2.680.27981610.20152970X-RAY DIFFRACTION97.12
2.68-2.750.261290.19663067X-RAY DIFFRACTION97.29
2.75-2.820.28191210.19193006X-RAY DIFFRACTION97.35
2.82-2.910.23161640.19163016X-RAY DIFFRACTION97.1
2.91-30.23821880.18572933X-RAY DIFFRACTION96.93
3-3.110.23811820.18212864X-RAY DIFFRACTION94.6
3.11-3.230.23361560.17453012X-RAY DIFFRACTION95.08
3.23-3.380.2131710.16382945X-RAY DIFFRACTION96.74
3.38-3.560.19171890.16292949X-RAY DIFFRACTION98.25
3.56-3.780.18251470.15883028X-RAY DIFFRACTION97.57
3.78-4.070.17881450.15243003X-RAY DIFFRACTION97.79
4.07-4.480.14481410.14323100X-RAY DIFFRACTION97.74
4.48-5.130.17021360.13972932X-RAY DIFFRACTION95.37
5.13-6.460.21241540.18372950X-RAY DIFFRACTION95.71
6.46-46.860.17441890.16883030X-RAY DIFFRACTION99.02

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