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- PDB-6sjz: HsNMT1 in complex with both MyrCoA and Acetylated-GNCFSKPR substrates -

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Basic information

Entry
Database: PDB / ID: 6sjz
TitleHsNMT1 in complex with both MyrCoA and Acetylated-GNCFSKPR substrates
Components
  • Apoptosis-inducing factor 3
  • Glycylpeptide N-tetradecanoyltransferase 1
KeywordsTRANSFERASE / 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 / Oxidoreductases / protein localization to membrane / oxidoreductase activity, acting on NAD(P)H / execution phase of apoptosis / eNOS activation / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / 2 iron, 2 sulfur cluster binding / Inactivation, recovery and regulation of the phototransduction cascade / in utero embryonic development / mitochondrial inner membrane / endoplasmic reticulum / mitochondrion / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Reductase, C-terminal / Reductase C-terminal / : / Aminopeptidase - #170 / 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 ...Reductase, C-terminal / Reductase C-terminal / : / Aminopeptidase - #170 / 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 / FAD/NAD-linked reductase, dimerisation domain superfamily / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Acyl-CoA N-acyltransferase / Aminopeptidase / FAD/NAD(P)-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TETRADECANOYL-COA / Glycylpeptide N-tetradecanoyltransferase 1 / Apoptosis-inducing factor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.995 Å
AuthorsDian, C. / Riviere, F.B. / Asensio, T. / Giglione, C. / Meinnel, T.
Funding support France, 3items
OrganizationGrant numberCountry
French National Research AgencyANR-2010-BLAN-1611-01 France
French National Research AgencyANR-10-LABX-0040-SPS France
French National Research AgencyFRISBI ANR-10-INSB-05-01 France
CitationJournal: Nat Commun / Year: 2020
Title: High-resolution snapshots of human N-myristoyltransferase in action illuminate a mechanism promoting N-terminal Lys and Gly myristoylation.
Authors: Dian, C. / Perez-Dorado, I. / Riviere, F. / Asensio, T. / Legrand, P. / Ritzefeld, M. / Shen, M. / Cota, E. / Meinnel, T. / Tate, E.W. / Giglione, C.
History
DepositionAug 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
E: Apoptosis-inducing factor 3
F: Apoptosis-inducing factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,19812
Polymers94,8034
Non-polymers2,3958
Water10,737596
1
A: Glycylpeptide N-tetradecanoyltransferase 1
F: Apoptosis-inducing factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5996
Polymers47,4022
Non-polymers1,1984
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-40 kcal/mol
Surface area16310 Å2
MethodPISA
2
B: Glycylpeptide N-tetradecanoyltransferase 1
E: Apoptosis-inducing factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5996
Polymers47,4022
Non-polymers1,1984
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-40 kcal/mol
Surface area16190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.908, 178.900, 58.379
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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

#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 derivative / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta2 pLysS
References: UniProt: P30419, glycylpeptide N-tetradecanoyltransferase
#2: Protein/peptide Apoptosis-inducing factor 3 / Apoptosis-inducing factor-like protein


Mass: 936.090 Da / Num. of mol.: 2 / Mutation: G3N, P8R / Source method: obtained synthetically / Details: Acetylated peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96NN9, Oxidoreductases

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Non-polymers , 4 types, 604 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 596 / 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: 44.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 22% PEG6K, 100mM Sodium Citrate pH 5.5, 100mM MgCl2, 100mM NaCl.

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 K cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 8, 2016
RadiationMonochromator: Laue [110] diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.99→48.89 Å / Num. obs: 115590 / % possible obs: 99.5 % / Redundancy: 8 % / Biso Wilson estimate: 21.32 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.038 / Rrim(I) all: 0.11 / Net I/σ(I): 14.4
Reflection shellResolution: 1.99→2.05 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.509 / Num. unique obs: 3937 / CC1/2: 0.897 / Rpim(I) all: 0.203 / Rrim(I) all: 0.55 / % possible all: 93.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.36
Highest resolutionLowest resolution
Rotation48.89 Å2.2 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O9V

5o9v


Resolution: 1.995→48.888 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 19.4
RfactorNum. reflection% reflection
Rfree0.2016 5393 4.93 %
Rwork0.1716 --
obs0.1731 109296 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.17 Å2 / Biso mean: 27.1155 Å2 / Biso min: 7.38 Å2
Refinement stepCycle: final / Resolution: 1.995→48.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6347 0 152 596 7095
Biso mean--27.89 32.43 -
Num. residues----797
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046805
X-RAY DIFFRACTIONf_angle_d0.819281
X-RAY DIFFRACTIONf_chiral_restr0.0711020
X-RAY DIFFRACTIONf_plane_restr0.0051171
X-RAY DIFFRACTIONf_dihedral_angle_d15.394131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeNum. reflection RworkRefine-IDRfactor Rfree error% reflection obs (%)
1.995-2.01750.30091222944X-RAY DIFFRACTION082
2.0175-2.04120.26151683424X-RAY DIFFRACTION0100
2.0412-2.06610.26132023451X-RAY DIFFRACTION0100
2.0661-2.09230.25061393567X-RAY DIFFRACTION0100
2.0923-2.11980.22232143383X-RAY DIFFRACTION0100
2.1198-2.14890.2111853537X-RAY DIFFRACTION0100

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