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- PDB-8q2z: HsNMT1 in complex with both MyrCoA and GNLLSKFR peptide -

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Basic information

Entry
Database: PDB / ID: 8q2z
TitleHsNMT1 in complex with both MyrCoA and GNLLSKFR peptide
Components
  • GNLLSKFR
  • 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: 1.88 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 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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: GNLLSKFR
D: GNLLSKFR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,14415
Polymers94,6894
Non-polymers2,45511
Water10,899605
1
A: Glycylpeptide N-tetradecanoyltransferase 1
C: GNLLSKFR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6209
Polymers47,3442
Non-polymers1,2757
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-42 kcal/mol
Surface area16570 Å2
2
B: Glycylpeptide N-tetradecanoyltransferase 1
D: GNLLSKFR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5256
Polymers47,3442
Non-polymers1,1804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-8 kcal/mol
Surface area16530 Å2
Unit cell
Length a, b, c (Å)79.870, 178.300, 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 GNLLSKFR


Mass: 936.111 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 , 6 types, 616 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 605 / 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: 2.19 Å3/Da / Density % sol: 43.79 %
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: Jan 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.88→47.73 Å / Num. obs: 67320 / % possible obs: 99 % / Redundancy: 6 % / Biso Wilson estimate: 21.1 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.037 / Rsym value: 0.084 / Net I/σ(I): 14.7
Reflection shellResolution: 1.88→1.93 Å / Mean I/σ(I) obs: 3.4 / Num. unique obs: 4806 / CC1/2: 0.878 / Rpim(I) all: 0.243 / Rsym value: 0.527 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→47.68 Å / SU ML: 0.1661 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.7215
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.193 3359 5 %
Rwork0.1572 63878 -
obs0.159 67237 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.2 Å2
Refinement stepCycle: LAST / Resolution: 1.88→47.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6465 0 138 605 7208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00646877
X-RAY DIFFRACTIONf_angle_d0.85069365
X-RAY DIFFRACTIONf_chiral_restr0.05591018
X-RAY DIFFRACTIONf_plane_restr0.00531180
X-RAY DIFFRACTIONf_dihedral_angle_d16.92712533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.910.27251330.24662563X-RAY DIFFRACTION96.67
1.91-1.940.26011380.19962604X-RAY DIFFRACTION96.89
1.94-1.970.24271350.1892598X-RAY DIFFRACTION99.6
1.97-20.20571390.17082626X-RAY DIFFRACTION97.67
2-2.040.19351380.16472621X-RAY DIFFRACTION99.32
2.04-2.070.21331380.16092625X-RAY DIFFRACTION98.22
2.07-2.110.20541390.15282636X-RAY DIFFRACTION99.36
2.11-2.160.19461380.14952638X-RAY DIFFRACTION97.95
2.16-2.20.22111400.15262656X-RAY DIFFRACTION99.89
2.2-2.250.21321380.16022623X-RAY DIFFRACTION98.4
2.25-2.310.21681400.16332647X-RAY DIFFRACTION99.79
2.31-2.370.21851390.16042647X-RAY DIFFRACTION98.79
2.37-2.440.1921400.16472652X-RAY DIFFRACTION98.73
2.44-2.520.21051400.16522665X-RAY DIFFRACTION99.47
2.52-2.610.21841410.16732670X-RAY DIFFRACTION99.36
2.61-2.720.19911400.17682673X-RAY DIFFRACTION99.12
2.72-2.840.20871400.17342656X-RAY DIFFRACTION98.83
2.84-2.990.21231410.16662686X-RAY DIFFRACTION99.12
2.99-3.180.21831420.16152684X-RAY DIFFRACTION99.33
3.18-3.420.15871420.15132708X-RAY DIFFRACTION99.16
3.42-3.770.15281420.13952684X-RAY DIFFRACTION99.26
3.77-4.310.15441430.12752728X-RAY DIFFRACTION99.07
4.31-5.430.15321450.12962745X-RAY DIFFRACTION98.13
5.43-47.680.21131480.17452843X-RAY DIFFRACTION97.27

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