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- PDB-8q3s: HsNMT1 in complex with both MyrCoA and GNCFSKAR inhibitor peptide -

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Basic information

Entry
Database: PDB / ID: 8q3s
TitleHsNMT1 in complex with both MyrCoA and GNCFSKAR inhibitor peptide
Components
  • GLY-ASN-CYS-PHE-SER-LYS-ALA-ARG
  • Glycylpeptide N-tetradecanoyltransferase 1
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)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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 1.1Nov 13, 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: GLY-ASN-CYS-PHE-SER-LYS-ALA-ARG
D: GLY-ASN-CYS-PHE-SER-LYS-ALA-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,01614
Polymers94,5854
Non-polymers2,43110
Water11,367631
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.900, 179.170, 58.200
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 GLY-ASN-CYS-PHE-SER-LYS-ALA-ARG


Mass: 884.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: synthetic construct (others)

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Non-polymers , 5 types, 641 molecules

#3: Chemical ChemComp-COA / 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


Mass: 92.094 Da / Num. of mol.: 4 / 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 631 / 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: 2.2 Å3/Da / Density % sol: 44.15 %
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: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.78→47.84 Å / Num. obs: 80129 / % possible obs: 99.3 % / Redundancy: 7.4 % / Biso Wilson estimate: 24.11 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.039 / Rsym value: 0.1 / Net I/σ(I): 12.5
Reflection shellResolution: 1.78→1.83 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5568 / CC1/2: 0.782 / Rpim(I) all: 0.0475 / Rsym value: 1.166 / % possible all: 94

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→47.84 Å / SU ML: 0.2138 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.4398
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2123 4001 5 %
Rwork0.1792 76019 -
obs0.1808 80020 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.84 Å2
Refinement stepCycle: LAST / Resolution: 1.78→47.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6434 0 152 631 7217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00656856
X-RAY DIFFRACTIONf_angle_d0.84379323
X-RAY DIFFRACTIONf_chiral_restr0.05481010
X-RAY DIFFRACTIONf_plane_restr0.00551174
X-RAY DIFFRACTIONf_dihedral_angle_d18.24522537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.80.39431220.34632333X-RAY DIFFRACTION89.05
1.8-1.830.32941360.312584X-RAY DIFFRACTION98.05
1.83-1.850.3161350.27192547X-RAY DIFFRACTION99.78
1.85-1.870.30461350.24412592X-RAY DIFFRACTION98.77
1.87-1.90.25511370.232595X-RAY DIFFRACTION99.27
1.9-1.930.24591370.2152594X-RAY DIFFRACTION99.71
1.93-1.950.2651360.2082589X-RAY DIFFRACTION98.7
1.95-1.980.26211370.20882598X-RAY DIFFRACTION99.93
1.98-2.020.24861370.20252611X-RAY DIFFRACTION98.78
2.02-2.050.22251370.20242591X-RAY DIFFRACTION99.89
2.05-2.090.21781350.19222575X-RAY DIFFRACTION99.01
2.09-2.130.23981380.18262624X-RAY DIFFRACTION99.93
2.13-2.170.21881370.17622588X-RAY DIFFRACTION99.34
2.17-2.220.21361380.17342629X-RAY DIFFRACTION100
2.22-2.270.22321370.16832597X-RAY DIFFRACTION99.53
2.27-2.330.20261380.17332633X-RAY DIFFRACTION99.57
2.33-2.390.22121380.17742603X-RAY DIFFRACTION99.93
2.39-2.460.19651380.17742627X-RAY DIFFRACTION99.78
2.46-2.540.22241390.17622644X-RAY DIFFRACTION99.78
2.54-2.630.22571390.1822635X-RAY DIFFRACTION99.96
2.63-2.740.25441380.18122633X-RAY DIFFRACTION99.86
2.74-2.860.21831400.17812648X-RAY DIFFRACTION100
2.86-3.010.20011390.172650X-RAY DIFFRACTION99.96
3.01-3.20.19281410.17742680X-RAY DIFFRACTION99.96
3.2-3.450.20371400.16522662X-RAY DIFFRACTION100
3.45-3.80.18391410.15862674X-RAY DIFFRACTION99.89
3.8-4.350.17831420.14452688X-RAY DIFFRACTION99.93
4.35-5.470.17621430.15542739X-RAY DIFFRACTION99.52
5.48-47.840.20921510.19962856X-RAY DIFFRACTION99.37

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