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- PDB-8q3d: HsNMT1 in complex with both MyrCoA and GNCFSKPR(NH2) inhibitor peptide -

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Basic information

Entry
Database: PDB / ID: 8q3d
TitleHsNMT1 in complex with both MyrCoA and GNCFSKPR(NH2) inhibitor peptide
Components
  • (Glycylpeptide N-tetradecanoyltransferase ...) x 2
  • GNCFSKPR(NH2) inhibitor peptide
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
COENZYME A / MYRISTIC ACID / Glycylpeptide N-tetradecanoyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 2.0Feb 26, 2025Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / citation / citation_author / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entry_details / pdbx_modification_feature / pdbx_poly_seq_scheme / pdbx_validate_rmsd_bond / struct_conn / struct_ref_seq
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _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 / _entity.formula_weight / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end

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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: GNCFSKPR(NH2) inhibitor peptide
D: GNCFSKPR(NH2) inhibitor peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,09815
Polymers94,6324
Non-polymers2,46711
Water10,539585
1
A: Glycylpeptide N-tetradecanoyltransferase 1
C: GNCFSKPR(NH2) inhibitor peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5327
Polymers47,3162
Non-polymers1,2165
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-21 kcal/mol
Surface area16520 Å2
2
B: Glycylpeptide N-tetradecanoyltransferase 1
D: GNCFSKPR(NH2) inhibitor peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5668
Polymers47,3152
Non-polymers1,2516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-34 kcal/mol
Surface area16590 Å2
Unit cell
Length a, b, c (Å)79.800, 178.340, 58.260
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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Glycylpeptide N-tetradecanoyltransferase ... , 2 types, 2 molecules AB

#1: Protein Glycylpeptide N-tetradecanoyltransferase 1


Mass: 46408.363 Da / Num. of mol.: 1
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 Glycylpeptide N-tetradecanoyltransferase 1


Mass: 46407.375 Da / Num. of mol.: 1
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

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Protein/peptide , 1 types, 2 molecules CD

#3: Protein/peptide GNCFSKPR(NH2) inhibitor peptide


Mass: 908.060 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, 596 molecules

#4: Chemical ChemComp-COA / COENZYME A


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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-MYR / MYRISTIC ACID


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


Mass: 18.015 Da / Num. of mol.: 585 / 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: 43.84 %
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
PH range: 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Feb 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.15→48.78 Å / Num. obs: 45961 / % possible obs: 99.4 % / Redundancy: 17 % / Biso Wilson estimate: 18.73 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.02 / Rsym value: 0.082 / Net I/σ(I): 29.3
Reflection shellResolution: 2.15→2.21 Å / Mean I/σ(I) obs: 13 / Num. unique obs: 3507 / CC1/2: 0.984 / Rpim(I) all: 0.066 / Rsym value: 0.262 / % possible all: 94.5

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→47.67 Å / SU ML: 0.1781 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 17.351
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1867 2294 5 %
Rwork0.1424 43584 -
obs0.1446 45878 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.61 Å2
Refinement stepCycle: LAST / Resolution: 2.15→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6429 0 153 585 7167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00686838
X-RAY DIFFRACTIONf_angle_d0.85379311
X-RAY DIFFRACTIONf_chiral_restr0.05271010
X-RAY DIFFRACTIONf_plane_restr0.00561174
X-RAY DIFFRACTIONf_dihedral_angle_d19.3722509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20.22481340.15392541X-RAY DIFFRACTION95.37
2.2-2.250.19541430.14272711X-RAY DIFFRACTION99.96
2.25-2.30.22061400.14912672X-RAY DIFFRACTION99.93
2.3-2.370.21441420.14522700X-RAY DIFFRACTION100
2.37-2.440.22651440.15012722X-RAY DIFFRACTION100
2.44-2.510.2151420.15152699X-RAY DIFFRACTION100
2.51-2.60.19881410.15542688X-RAY DIFFRACTION100
2.6-2.710.21521430.1522721X-RAY DIFFRACTION100
2.71-2.830.2111440.1532733X-RAY DIFFRACTION100
2.83-2.980.1911430.15192720X-RAY DIFFRACTION100
2.98-3.170.18941440.15362727X-RAY DIFFRACTION100
3.17-3.410.20281450.14532761X-RAY DIFFRACTION99.97
3.41-3.760.15751420.13292682X-RAY DIFFRACTION98.12
3.76-4.30.16531440.1212748X-RAY DIFFRACTION98.6
4.3-5.410.14161480.11782812X-RAY DIFFRACTION99.97
5.42-47.670.17031550.15882947X-RAY DIFFRACTION99.74

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