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- PDB-5o9s: HsNMT1 in complex with CoA and Myristoylated-GKSNSKLK octapeptide -

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Basic information

Entry
Database: PDB / ID: 5o9s
TitleHsNMT1 in complex with CoA and Myristoylated-GKSNSKLK octapeptide
Components
  • Glycylpeptide N-tetradecanoyltransferase 1
  • Neuronal calcium sensor 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


calcium sensitive guanylate cyclase activator 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 ...calcium sensitive guanylate cyclase activator 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 / protein localization to membrane / regulation of neuron projection development / regulation of signal transduction / voltage-gated calcium channel activity / eNOS activation / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Inactivation, recovery and regulation of the phototransduction cascade / in utero embryonic development / postsynaptic density / axon / intracellular membrane-bounded organelle / calcium ion binding / dendrite / perinuclear region of cytoplasm / Golgi apparatus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Recoverin family / 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 ...Recoverin family / 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 / EF hand domain / Acyl-CoA N-acyltransferase / Aminopeptidase / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
MYRISTIC ACID / Glycylpeptide N-tetradecanoyltransferase 1 / Neuronal calcium sensor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: Neuronal calcium sensor 1
D: Neuronal calcium sensor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,59013
Polymers94,6594
Non-polymers9319
Water3,135174
1
A: Glycylpeptide N-tetradecanoyltransferase 1
C: Neuronal calcium sensor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7776
Polymers47,3292
Non-polymers4484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-10 kcal/mol
Surface area16340 Å2
MethodPISA
2
B: Glycylpeptide N-tetradecanoyltransferase 1
D: Neuronal calcium sensor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8137
Polymers47,3292
Non-polymers4835
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-23 kcal/mol
Surface area16310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.022, 80.252, 178.147
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 / Fragment: UNP residues 99-496
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 Neuronal calcium sensor 1 / NCS-1 / Frequenin homolog / Frequenin-like protein / Frequenin-like ubiquitous protein


Mass: 864.023 Da / Num. of mol.: 2 / Fragment: UNP residues 2-9 / Source method: obtained synthetically / Details: Myristoylated peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P62166

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Non-polymers , 4 types, 183 molecules

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


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


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O2 / Details: Myristoylated peptide / Source: (synth.) Homo sapiens (human)
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.18 Å3/Da / Density % sol: 43.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 22% PEG 6000, 0.1M sodium citrate pH 5.6, 0.1M magnesium chloride, 0.2M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford Cryo
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 4, 2017
Details: Be CRL lenses for vertical focusing and Rh/Pt/Si coated ellipitcal mirror for horizontal focusing
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.7→48.62 Å / Num. obs: 23547 / % possible obs: 99.3 % / Redundancy: 6.9 % / Biso Wilson estimate: 16.74 Å2 / CC1/2: 0.994 / Rpim(I) all: 0.054 / Rsym value: 0.133 / Net I/σ(I): 11.3
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 4.8 / Num. unique obs: 3050 / CC1/2: 0.934 / Rpim(I) all: 0.137 / Rsym value: 0.293 / % possible all: 98.3

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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: 2.7→48.617 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.81
RfactorNum. reflection% reflection
Rfree0.2274 1138 4.84 %
Rwork0.1751 --
obs0.1776 23496 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→48.617 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6237 0 26 174 6437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046426
X-RAY DIFFRACTIONf_angle_d0.5848730
X-RAY DIFFRACTIONf_dihedral_angle_d15.3463832
X-RAY DIFFRACTIONf_chiral_restr0.042966
X-RAY DIFFRACTIONf_plane_restr0.0041103
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.8230.29681460.2172694X-RAY DIFFRACTION98
2.823-2.97180.24451470.19672701X-RAY DIFFRACTION98
2.9718-3.15790.26581320.19582761X-RAY DIFFRACTION100
3.1579-3.40170.26531580.18052776X-RAY DIFFRACTION100
3.4017-3.74390.24321400.16652772X-RAY DIFFRACTION100
3.7439-4.28540.17321240.14732836X-RAY DIFFRACTION100
4.2854-5.3980.1931540.14732818X-RAY DIFFRACTION100
5.398-48.6250.2081370.19953000X-RAY DIFFRACTION100

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