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- PDB-6qrm: HsNMT1 in complex with both MyrCoA and GNCFSKRRAA substrates -

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Basic information

Entry
Database: PDB / ID: 6qrm
TitleHsNMT1 in complex with both MyrCoA and GNCFSKRRAA substrates
Components
  • Apoptosis-inducing factor 3
  • Glycylpeptide N-tetradecanoyltransferase 1
KeywordsTRANSFERASE / 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
COENZYME A / TETRADECANOYL-COA / MYRISTIC ACID / Glycylpeptide N-tetradecanoyltransferase 1 / Apoptosis-inducing factor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
DepositionFeb 19, 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 1.2Nov 20, 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

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)97,56813
Polymers95,1554
Non-polymers2,4139
Water7,134396
1
A: Glycylpeptide N-tetradecanoyltransferase 1
C: Apoptosis-inducing factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7937
Polymers47,5782
Non-polymers1,2165
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-21 kcal/mol
Surface area16620 Å2
MethodPISA
2
B: Glycylpeptide N-tetradecanoyltransferase 1
D: Apoptosis-inducing factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7756
Polymers47,5782
Non-polymers1,1984
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-38 kcal/mol
Surface area16980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.437, 178.931, 58.412
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 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) / Strain (production host): Rosetta2 pLysS
References: UniProt: P30419, glycylpeptide N-tetradecanoyltransferase
#2: Protein/peptide Apoptosis-inducing factor 3 / Apoptosis-inducing factor-like protein


Mass: 1112.287 Da / Num. of mol.: 2 / Mutation: G3N, P8R / Source method: obtained synthetically / Details: peptide myristoylated within the crystal / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96NN9, Oxidoreductases

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Non-polymers , 6 types, 405 molecules

#3: Chemical ChemComp-COA / COENZYME A


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


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-MYA / TETRADECANOYL-COA / MYRISTOYL-COA


Mass: 977.890 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H62N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 24% PEG8K, 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-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Feb 8, 2016
RadiationMonochromator: Si (111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.3→48.91 Å / Num. obs: 75369 / % possible obs: 99.7 % / Redundancy: 9.2 % / Biso Wilson estimate: 29.09 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.051 / Rrim(I) all: 0.152 / Net I/σ(I): 12.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.669 / Num. unique obs: 3619 / CC1/2: 0.875 / Rpim(I) all: 0.226 / Rrim(I) all: 0.708 / % possible all: 99.8

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O9V

5o9v


Resolution: 2.3→48.91 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0.12 / Phase error: 21.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2033 3606 5.07 %
Rwork0.172 67559 -
obs0.1736 71165 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.07 Å2 / Biso mean: 30.6342 Å2 / Biso min: 10.95 Å2
Refinement stepCycle: final / Resolution: 2.3→48.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6451 0 137 396 6984
Biso mean--34.13 30.95 -
Num. residues----800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096786
X-RAY DIFFRACTIONf_angle_d0.9929229
X-RAY DIFFRACTIONf_chiral_restr0.0591007
X-RAY DIFFRACTIONf_plane_restr0.0061159
X-RAY DIFFRACTIONf_dihedral_angle_d15.974068
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.33030.35741250.2862259099
2.3303-2.36220.29961310.2812586100
2.3622-2.3960.28231420.2722625100
2.396-2.43170.31731250.2475261699
2.4317-2.46970.29051540.23532567100
2.4697-2.51020.30631390.2256260899
2.5102-2.55350.25761350.20812608100
2.5535-2.59990.20421360.20992596100
2.5999-2.64990.26171430.2022635100
2.6499-2.7040.25091270.19432540100
2.704-2.76280.24151370.18692658100
2.7628-2.82710.25291350.18852616100
2.8271-2.89780.24211310.18272590100
2.8978-2.97610.20421440.17692600100
2.9761-3.06370.19591700.17192606100
3.0637-3.16250.22291270.17732604100
3.1625-3.27550.18561170.15852628100
3.2755-3.40670.15861330.15642632100
3.4067-3.56170.15441260.1512618100
3.5617-3.74940.19111710.14992578100
3.7494-3.98420.18171620.14882587100
3.9842-4.29160.16181280.1282245294
4.2916-4.72320.15741340.12412620100
4.7232-5.40590.15191410.1382600100
5.4059-6.8080.21291320.18382606100
6.808-48.910.18171610.17092593100

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