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- PDB-6skj: DeltaC2 C-terminal truncation of HsNMT1 in complex with MyrCoA an... -

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Basic information

Entry
Database: PDB / ID: 6skj
TitleDeltaC2 C-terminal truncation of HsNMT1 in complex with 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 / 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 / molecular replacement / Resolution: 2.8 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 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
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

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)97,52112
Polymers94,2684
Non-polymers3,2528
Water1,62190
1
A: Glycylpeptide N-tetradecanoyltransferase 1
C: Apoptosis-inducing factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2044
Polymers47,1342
Non-polymers1,0702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-26 kcal/mol
Surface area16700 Å2
MethodPISA
2
B: Glycylpeptide N-tetradecanoyltransferase 1
D: Apoptosis-inducing factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3168
Polymers47,1342
Non-polymers2,1826
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-23 kcal/mol
Surface area16550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.965, 58.270, 154.132
Angle α, β, γ (deg.)90.000, 90.920, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-637-

HOH

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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: 46224.125 Da / Num. of mol.: 2 / Mutation: L495stop
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 / Apoptosis-inducing factor-like protein


Mass: 910.053 Da / Num. of mol.: 2 / Mutation: G3N, P8R / Source method: obtained synthetically
Details: Conformation A GNCFSKPR and MyrCoA Conformation B Tetrahedral intermediate (MYB)GNCFSKPR
Source: (synth.) Homo sapiens (human) / References: UniProt: Q96NN9, Oxidoreductases

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Non-polymers , 6 types, 98 molecules

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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: 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
#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.: 90 / 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: 2.21 Å3/Da / Density % sol: 44.47 %
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: 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: 2.6→49.371 Å / Num. obs: 22838 / % possible obs: 89.3 % / Redundancy: 5.9 % / Biso Wilson estimate: 36.12 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.059 / Rrim(I) all: 0.149 / Net I/σ(I): 9.9
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
2.6-2.675.11.918695613710.5770.872.1170.974.5
11.64-49.376.50.03620103110.9990.0160.0437.499.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.83 Å49.37 Å
Translation7.83 Å49.37 Å

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Processing

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

5o9v


Resolution: 2.8→49.371 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.75
RfactorNum. reflection% reflection
Rfree0.2188 978 5.34 %
Rwork0.189 --
obs0.1906 18321 88.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 75.63 Å2 / Biso mean: 27.2781 Å2 / Biso min: 10.57 Å2
Refinement stepCycle: final / Resolution: 2.8→49.371 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6555 0 82 90 6727
Biso mean--31.43 21.79 -
Num. residues----795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036872
X-RAY DIFFRACTIONf_angle_d0.7389361
X-RAY DIFFRACTIONf_chiral_restr0.0511017
X-RAY DIFFRACTIONf_plane_restr0.0051164
X-RAY DIFFRACTIONf_dihedral_angle_d18.0454198
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8-2.94760.3746840.272163759
2.9476-3.13230.29661260.2448211177
3.1323-3.37410.24911360.2226250089
3.3741-3.71350.25421310.1976267896
3.7135-4.25060.20591620.1685277799
4.2506-5.35430.16431580.14862779100
5.3543-49.3710.18581810.18382861100

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