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- PDB-6sk8: DeltaC3 C-terminal truncation of HsNMT1 in complex with MyrCoA an... -

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Basic information

Entry
Database: PDB / ID: 6sk8
TitleDeltaC3 C-terminal truncation of HsNMT1 in complex with MyrCoA and GDCFSKPR 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 / peptidyl-lysine N6-myristoyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / Late Phase of HIV Life Cycle / cellular ketone metabolic process / regulation of opsin-mediated signaling pathway / Activation, myristolyation of BID and translocation to mitochondria / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / protein localization to membrane ...myristoyltransferase activity / peptidyl-lysine N6-myristoyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / Late Phase of HIV Life Cycle / cellular ketone metabolic process / regulation of opsin-mediated signaling pathway / 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 / flavin adenine dinucleotide binding / mitochondrial inner membrane / in utero embryonic development / 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 / Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain ...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] iron-sulphur domain / Rieske [2Fe-2S] 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: 1.87 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 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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)96,61613
Polymers94,0724
Non-polymers2,5449
Water15,187843
1
A: Glycylpeptide N-tetradecanoyltransferase 1
C: Apoptosis-inducing factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3267
Polymers47,0362
Non-polymers1,2905
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-37 kcal/mol
Surface area17580 Å2
MethodPISA
2
B: Glycylpeptide N-tetradecanoyltransferase 1
D: Apoptosis-inducing factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2906
Polymers47,0362
Non-polymers1,2544
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-24 kcal/mol
Surface area17030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.622, 58.256, 154.789
Angle α, β, γ (deg.)90.000, 91.260, 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: 911.038 Da / Num. of mol.: 2 / Mutation: G3D, P8R / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96NN9*PLUS

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Non-polymers , 4 types, 852 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 / Glycerol


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 843 / 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: 2.22 Å3/Da / Density % sol: 44.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 19% PEG8K, 100mM Sodium Citrate pH 5.6, 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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 6, 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: 1.87→49.31 Å / Num. obs: 68387 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 25.54 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.063 / Rrim(I) all: 0.171 / Net I/σ(I): 7.3 / Num. measured all: 507596
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
1.87-1.917.71.2193369643600.6650.4671.3071.6100
8.97-49.3170.06146496670.9950.0260.06719.899.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.64 Å49.31 Å
Translation4.64 Å49.31 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.6.0phasing
PHENIXrefinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O9V

5o9v


Resolution: 1.87→49.31 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.52
RfactorNum. reflection% reflection
Rfree0.2439 3451 5.05 %
Rwork0.2078 --
obs0.2096 68328 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.35 Å2 / Biso mean: 30.2305 Å2 / Biso min: 14.35 Å2
Refinement stepCycle: final / Resolution: 1.87→49.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6392 0 163 843 7398
Biso mean--27.67 35.56 -
Num. residues----794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036841
X-RAY DIFFRACTIONf_angle_d0.6919313
X-RAY DIFFRACTIONf_chiral_restr0.0511012
X-RAY DIFFRACTIONf_plane_restr0.0051173
X-RAY DIFFRACTIONf_dihedral_angle_d15.9244172
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.87-1.89560.30561340.31012606
1.8956-1.92270.36691530.30872528
1.9227-1.95140.35431380.30082627
1.9514-1.98190.30431590.28222513
1.9819-2.01440.31821530.28992625
2.0144-2.04910.33521570.28562479
2.0491-2.08640.35241440.26512612
2.0864-2.12650.28191320.26432575
2.1265-2.16990.28971270.25652585
2.1699-2.21710.34391230.24832594
2.2171-2.26870.29851290.24462598
2.2687-2.32540.29971230.23832601
2.3254-2.38830.3061170.23192608
2.3883-2.45860.30831150.22872601
2.4586-2.53790.25311540.23152595
2.5379-2.62860.31581480.23212591
2.6286-2.73390.25631410.21862603
2.7339-2.85830.25781640.21122519
2.8583-3.0090.23531180.19842619
3.009-3.19750.25781170.19342629
3.1975-3.44430.19971560.17262600
3.4443-3.79080.191470.16862572
3.7908-4.3390.18651470.15642621
4.339-5.46560.1795990.16082700

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