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- PDB-5o9v: HsNMT1 in complex with CoA and Myristoylated-GGCFSKPK octapeptide -

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Basic information

Entry
Database: PDB / ID: 5o9v
TitleHsNMT1 in complex with CoA and Myristoylated-GGCFSKPK octapeptide
Components
  • Apoptosis-inducing factor 3
  • Glycylpeptide N-tetradecanoyltransferase 1
KeywordsTRANSFERASE / GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE 1 N-MYRISTOYLTRANSFERASE 1 / N-MYRISTOYLTRANSFERASE TYPE1 / NMT1 / NMT / ACYLTRANSFERASE / MYR-PEPTIDE / COA / MYR-COA / MYRISTOYL / GNAT
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
COENZYME A / MYRISTIC ACID / Glycylpeptide N-tetradecanoyltransferase 1 / Apoptosis-inducing factor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.201 Å
AuthorsDian, C. / Meinnel, T. / Giglione, C.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-PalMyProt France
Fondation ARCSFI2011120111203841 France
CitationJournal: Nat. Chem. Biol. / Year: 2018
Title: Structural and genomic decoding of human and plant myristoylomes reveals a definitive recognition pattern.
Authors: Castrec, B. / Dian, C. / Ciccone, S. / Ebert, C.L. / Bienvenut, W.V. / Le Caer, J.P. / Steyaert, J.M. / Giglione, C. / Meinnel, T.
History
DepositionJun 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 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

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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)97,10415
Polymers94,5814
Non-polymers2,52311
Water8,899494
1
A: Glycylpeptide N-tetradecanoyltransferase 1
C: Apoptosis-inducing factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5988
Polymers47,2902
Non-polymers1,3086
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-25 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)48,5067
Polymers47,2902
Non-polymers1,2165
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-24 kcal/mol
Surface area17640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.130, 79.010, 178.255
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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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: 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) / Variant (production host): Rosetta2(DE3) pLysS
References: UniProt: P30419, glycylpeptide N-tetradecanoyltransferase
#2: Protein/peptide Apoptosis-inducing factor 3 / / Apoptosis-inducing factor-like protein


Mass: 824.988 Da / Num. of mol.: 2 / Fragment: UNP residues 2-9 / Source method: obtained synthetically
Details: Synthetic octapeptide GGCFSKPK modified by NMT1 to (MYR)GGCFSKPK.
Source: (synth.) Homo sapiens (human) / References: UniProt: Q96NN9, Oxidoreductases

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Non-polymers , 5 types, 505 molecules

#3: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


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


Mass: 18.015 Da / Num. of mol.: 494 / Source method: isolated from a natural source / Formula: H2O

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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: 2.16 Å3/Da / Density % sol: 43.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 22% PEG8000, 0.1M sodium citrate pH5.6, 0.1 M magnesium chloride, 0.1M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryo Oxford
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.96112 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 4, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96112 Å / Relative weight: 1
ReflectionResolution: 2.2→48.69 Å / Num. obs: 42368 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Biso Wilson estimate: 26.79 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.027 / Rsym value: 0.082 / Net I/σ(I): 24.5
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 5.6 / Num. unique obs: 4029 / CC1/2: 0.93 / Rpim(I) all: 0.136 / Rsym value: 0.378 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C2Z

4c2z


Resolution: 2.201→48.689 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2056 2141 5.05 %
Rwork0.1647 --
obs0.1667 42356 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.201→48.689 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6491 0 128 494 7113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036861
X-RAY DIFFRACTIONf_angle_d0.6759330
X-RAY DIFFRACTIONf_dihedral_angle_d15.3734076
X-RAY DIFFRACTIONf_chiral_restr0.0441003
X-RAY DIFFRACTIONf_plane_restr0.0061178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2011-2.25240.28781560.20472475X-RAY DIFFRACTION95
2.2524-2.30870.25121210.20332675X-RAY DIFFRACTION100
2.3087-2.37110.24491510.19342616X-RAY DIFFRACTION100
2.3711-2.44090.27381490.19142653X-RAY DIFFRACTION100
2.4409-2.51960.26351290.19282679X-RAY DIFFRACTION100
2.5196-2.60970.25411660.19372639X-RAY DIFFRACTION100
2.6097-2.71420.24541570.18032633X-RAY DIFFRACTION100
2.7142-2.83770.28281290.18662684X-RAY DIFFRACTION100
2.8377-2.98730.23321480.17882663X-RAY DIFFRACTION100
2.9873-3.17440.2091270.17572706X-RAY DIFFRACTION100
3.1744-3.41950.18051400.15862705X-RAY DIFFRACTION100
3.4195-3.76350.20721240.14422713X-RAY DIFFRACTION100
3.7635-4.30770.15431480.1322708X-RAY DIFFRACTION100
4.3077-5.42620.14351420.12932773X-RAY DIFFRACTION100
5.4262-48.70140.15971540.16712893X-RAY DIFFRACTION100

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