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- PDB-8q24: HsNMT1 in complex with both MyrCoA and (DAB)SFSKPR inhibitor peptide -

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Basic information

Entry
Database: PDB / ID: 8q24
TitleHsNMT1 in complex with both MyrCoA and (DAB)SFSKPR inhibitor peptide
Components
  • DAB-SER-PHE-SER-LYS-PRO-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 / 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: 1.9 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 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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
E: DAB-SER-PHE-SER-LYS-PRO-ARG
C: DAB-SER-PHE-SER-LYS-PRO-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,06413
Polymers94,5774
Non-polymers2,4879
Water8,773487
1
A: Glycylpeptide N-tetradecanoyltransferase 1
C: DAB-SER-PHE-SER-LYS-PRO-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5217
Polymers47,2882
Non-polymers1,2335
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-49 kcal/mol
Surface area16620 Å2
2
B: Glycylpeptide N-tetradecanoyltransferase 1
E: DAB-SER-PHE-SER-LYS-PRO-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5436
Polymers47,2882
Non-polymers1,2544
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-26 kcal/mol
Surface area16730 Å2
Unit cell
Length a, b, c (Å)78.739, 177.986, 58.266
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 ABEC

#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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): ROSETTA2 PLYSS
References: UniProt: P30419, glycylpeptide N-tetradecanoyltransferase
#2: Protein/peptide DAB-SER-PHE-SER-LYS-PRO-ARG


Mass: 822.952 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 496 molecules

#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
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / 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: 2.11 Å3/Da / Density % sol: 41.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 22% PEG6K, 100mM Sodium Citrate pH 5.6, 0.1 M MgCL2, 0.1 M 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 2 / Wavelength: 0.97563 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 15, 2020 / Details: KB mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97563 Å / Relative weight: 1
ReflectionResolution: 1.9→48.75 Å / Num. obs: 124527 / % possible obs: 100 % / Redundancy: 13.8 % / Biso Wilson estimate: 29.5 Å2 / CC1/2: 1 / Rpim(I) all: 0.023 / Rsym value: 0.057 / Net I/σ(I): 25
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 13.1 % / Mean I/σ(I) obs: 4.5 / Num. unique obs: 4176 / CC1/2: 0.973 / Rpim(I) all: 0.233 / Rsym value: 0.584 / % 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: 5O9T

5o9t


Resolution: 1.9→48.75 Å / SU ML: 0.1939 / Cross valid method: FREE R-VALUE / σ(F): 0.46 / Phase error: 23.5369
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.215 6180 4.96 %
Rwork0.1719 118347 -
obs0.174 124527 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6555 0 2 487 7044
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00676825
X-RAY DIFFRACTIONf_angle_d0.94299291
X-RAY DIFFRACTIONf_chiral_restr0.08351015
X-RAY DIFFRACTIONf_plane_restr0.00541169
X-RAY DIFFRACTIONf_dihedral_angle_d21.58272639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.30862130.23573998X-RAY DIFFRACTION99.81
1.92-1.940.24431800.23123900X-RAY DIFFRACTION99.8
1.94-1.970.26392080.21993983X-RAY DIFFRACTION99.9
1.97-1.990.28592680.21243870X-RAY DIFFRACTION99.64
1.99-2.020.24931960.20933941X-RAY DIFFRACTION99.98
2.02-2.050.22072050.19343926X-RAY DIFFRACTION99.61
2.05-2.080.24931850.18763986X-RAY DIFFRACTION99.62
2.08-2.110.20751780.19513969X-RAY DIFFRACTION99.88
2.11-2.140.25042090.19533959X-RAY DIFFRACTION99.55
2.14-2.170.27242030.19023922X-RAY DIFFRACTION99.85
2.17-2.210.24122390.19053872X-RAY DIFFRACTION99.9
2.21-2.250.22732250.1953961X-RAY DIFFRACTION99.76
2.25-2.30.24772140.19893867X-RAY DIFFRACTION99.8
2.3-2.340.23182160.18673999X-RAY DIFFRACTION99.86
2.34-2.390.23692060.18623929X-RAY DIFFRACTION99.9
2.39-2.450.25042250.18553948X-RAY DIFFRACTION99.95
2.45-2.510.23721910.19183963X-RAY DIFFRACTION99.86
2.51-2.580.2352190.19523916X-RAY DIFFRACTION99.95
2.58-2.650.23972140.1933956X-RAY DIFFRACTION99.95
2.65-2.740.25381960.1843941X-RAY DIFFRACTION99.98
2.74-2.840.25911900.1923946X-RAY DIFFRACTION100
2.84-2.950.25662070.18863969X-RAY DIFFRACTION100
2.95-3.090.21212010.183960X-RAY DIFFRACTION100
3.09-3.250.21082090.17193948X-RAY DIFFRACTION99.95
3.25-3.450.19671720.16433981X-RAY DIFFRACTION99.98
3.45-3.720.20071960.15313945X-RAY DIFFRACTION99.95
3.72-4.090.1692230.14343940X-RAY DIFFRACTION100
4.09-4.680.1752160.12683937X-RAY DIFFRACTION99.86
4.68-5.90.19311880.15463961X-RAY DIFFRACTION99.98
5.9-48.750.18881880.17223954X-RAY DIFFRACTION99.45

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