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- PDB-6sk3: C-terminal HsNMT1 deltaC3 truncation in complex with both MyrCoA ... -

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Basic information

Entry
Database: PDB / ID: 6sk3
TitleC-terminal HsNMT1 deltaC3 truncation in complex with both MyrCoA and 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 / positive regulation of establishment of protein localization to mitochondrion / Activation, myristolyation of BID and translocation to mitochondria / 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 / positive regulation of establishment of protein localization to mitochondrion / Activation, myristolyation of BID and translocation to mitochondria / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / protein localization to membrane / Oxidoreductases / oxidoreductase activity, acting on NAD(P)H / execution phase of apoptosis / 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: 2.7 Å
AuthorsDian, C. / Riviere, F.B. / Asensio, T. / Giglione, C. / Meinnel, T.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-2010-BLAN-1611-01 France
French National Research AgencyANR-10-LABX-0040-SPS 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 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Apoptosis-inducing factor 3
D: Apoptosis-inducing factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,2349
Polymers94,0704
Non-polymers2,1645
Water27015
1
A: Glycylpeptide N-tetradecanoyltransferase 1
C: Apoptosis-inducing factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1054
Polymers47,0352
Non-polymers1,0702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-25 kcal/mol
Surface area16970 Å2
MethodPISA
2
B: Glycylpeptide N-tetradecanoyltransferase 1
D: Apoptosis-inducing factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1295
Polymers47,0352
Non-polymers1,0943
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-34 kcal/mol
Surface area17240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.806, 58.074, 148.212
Angle α, β, γ (deg.)90.000, 92.250, 90.000
Int Tables number5
Space group name H-MC121

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Components

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

#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: 46124.996 Da / Num. of mol.: 2 / Mutation: V494stop
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) / Variant (production host): Rosetta2 pLysS
References: UniProt: P30419, glycylpeptide N-tetradecanoyltransferase
#2: Protein/peptide Apoptosis-inducing factor 3


Mass: 910.053 Da / Num. of mol.: 2 / Mutation: G3N, P8R / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96NN9*PLUS

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Non-polymers , 4 types, 20 molecules

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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: 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
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.1 Å3/Da / Density % sol: 41.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 19% PEG6K, 100mM Sodium Citrate pH 5.6, 100mM MgCl2, 100mM NaCl.

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100K Cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 5, 2019
RadiationMonochromator: Si (111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 2.7→49.07 Å / Num. obs: 21519 / % possible obs: 99.1 % / Redundancy: 6 % / Biso Wilson estimate: 38.84 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.074 / Rrim(I) all: 0.187 / Net I/σ(I): 7.4 / Num. measured all: 129478
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.7-2.8350.7071352527180.8420.3220.781295.8
8.96-49.076.50.05641046300.9970.0240.06121.198.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.64 Å46.87 Å
Translation4.64 Å46.87 Å

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.6.0phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→46.873 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2686 1140 5.31 %
Rwork0.2459 20342 -
obs0.2472 21482 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.54 Å2 / Biso mean: 39.0239 Å2 / Biso min: 23.28 Å2
Refinement stepCycle: final / Resolution: 2.7→46.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6360 0 139 15 6514
Biso mean--38.97 34.61 -
Num. residues----793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046679
X-RAY DIFFRACTIONf_angle_d0.7689089
X-RAY DIFFRACTIONf_chiral_restr0.051995
X-RAY DIFFRACTIONf_plane_restr0.0051144
X-RAY DIFFRACTIONf_dihedral_angle_d16.1924059
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7001-2.8230.38931290.3515243096
2.823-2.97180.3581480.3316248399
2.9718-3.1580.35431820.3137250999
3.158-3.40170.30431290.26972598100
3.4017-3.74390.28921150.24242533100
3.7439-4.28540.25361330.2215258199
4.2854-5.39780.20581520.19992577100

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