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- PDB-5o9u: HsNMT1 in complex with CoA and Myristoylated-GCSVSKKK octapeptide -

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Basic information

Entry
Database: PDB / ID: 5o9u
TitleHsNMT1 in complex with CoA and Myristoylated-GCSVSKKK octapeptide
Components
  • Calcineurin B-like protein 4
  • 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


hypotonic salinity response / calcium-dependent protein serine/threonine phosphatase activity / myristoyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / peptidyl-lysine N6-myristoyltransferase activity / Late Phase of HIV Life Cycle / ketone metabolic process / calcineurin complex / regulation of opsin-mediated signaling pathway / Activation, myristolyation of BID and translocation to mitochondria ...hypotonic salinity response / calcium-dependent protein serine/threonine phosphatase activity / myristoyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / peptidyl-lysine N6-myristoyltransferase activity / Late Phase of HIV Life Cycle / ketone metabolic process / calcineurin complex / 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 / intracellular potassium ion homeostasis / detection of calcium ion / eNOS activation / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / calcium-mediated signaling / kinase binding / Inactivation, recovery and regulation of the phototransduction cascade / in utero embryonic development / calcium ion binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Calcineurin B-like / 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 ...Calcineurin B-like / 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 / Acyl-CoA N-acyltransferase / Aminopeptidase / EF-hand domain pair / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / MYRISTIC ACID / Calcineurin B-like protein 4 / Glycylpeptide N-tetradecanoyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Arabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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: Calcineurin B-like protein 4
D: Calcineurin B-like protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,87711
Polymers94,6094
Non-polymers2,2687
Water16,430912
1
A: Glycylpeptide N-tetradecanoyltransferase 1
C: Calcineurin B-like protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3925
Polymers47,3042
Non-polymers1,0883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-7 kcal/mol
Surface area16740 Å2
MethodPISA
2
B: Glycylpeptide N-tetradecanoyltransferase 1
D: Calcineurin B-like protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4856
Polymers47,3042
Non-polymers1,1804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-9 kcal/mol
Surface area16780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.236, 79.779, 178.751
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 pLysS
References: UniProt: P30419, glycylpeptide N-tetradecanoyltransferase
#2: Protein/peptide Calcineurin B-like protein 4 / Protein SALT OVERLY SENSITIVE 3


Mass: 839.036 Da / Num. of mol.: 2 / Fragment: UNP residues 2-9 / Source method: obtained synthetically
Details: Synthetic octapeptide GCSVSKKK modified by NMT1 to (GLM)CSVSKKK. GLM: N-Myristoyl-glycine
Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: O81223

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Non-polymers , 4 types, 919 molecules

#3: Chemical ChemComp-COA / 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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MYR / MYRISTIC ACID / Protein SALT OVERLY SENSITIVE 3 / Myristoylated-GCSVSKKK octapeptide


Mass: 228.371 Da / Num. of mol.: 2 / Fragment: UNP residues 2-9 / Source method: obtained synthetically / Formula: C14H28O2
Details: Synthetic octapeptide GCSVSKKK modified by NMT1 to (GLM)CSVSKKK. GLM: N-Myristoyl-glycine
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 912 / 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: 43.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 21% PEG 6000, 0.1M sodium citrate pH 5.6, 0.1M magnesium chloride, 0.1M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford Cryo
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 1, 2016 / Details: Compound Refractive Lens
RadiationMonochromator: Diamond (C110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.85→47.74 Å / Num. obs: 71441 / % possible obs: 99.3 % / Redundancy: 5.4 % / Biso Wilson estimate: 13.51 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.046 / Rsym value: 0.073 / Net I/σ(I): 15.1
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 5.5 / Num. unique obs: 6884 / CC1/2: 0.955 / Rpim(I) all: 0.171 / Rsym value: 0.266 / % possible all: 97.4

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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: 1.85→47.037 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.34
RfactorNum. reflection% reflection
Rfree0.1917 3542 4.96 %
Rwork0.1555 --
obs0.1573 71432 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 16.28 Å2
Refinement stepCycle: LAST / Resolution: 1.85→47.037 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6486 0 114 912 7512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076837
X-RAY DIFFRACTIONf_angle_d0.8869302
X-RAY DIFFRACTIONf_dihedral_angle_d13.7874061
X-RAY DIFFRACTIONf_chiral_restr0.0571008
X-RAY DIFFRACTIONf_plane_restr0.0051170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.87530.23751530.18112634X-RAY DIFFRACTION97
1.8753-1.90210.22711350.18322598X-RAY DIFFRACTION96
1.9021-1.93050.23811240.18012661X-RAY DIFFRACTION98
1.9305-1.96070.2351390.17492621X-RAY DIFFRACTION97
1.9607-1.99280.20891360.17312643X-RAY DIFFRACTION98
1.9928-2.02720.20811450.16542643X-RAY DIFFRACTION98
2.0272-2.06410.23231450.16392661X-RAY DIFFRACTION98
2.0641-2.10380.22831380.15812699X-RAY DIFFRACTION99
2.1038-2.14670.20931380.15832706X-RAY DIFFRACTION100
2.1467-2.19340.19571560.15562674X-RAY DIFFRACTION100
2.1934-2.24440.17341510.15052723X-RAY DIFFRACTION100
2.2444-2.30050.20751390.15542685X-RAY DIFFRACTION100
2.3005-2.36270.2131510.15862685X-RAY DIFFRACTION100
2.3627-2.43230.1941560.16162745X-RAY DIFFRACTION100
2.4323-2.51080.21831400.16312706X-RAY DIFFRACTION100
2.5108-2.60050.20741480.1612732X-RAY DIFFRACTION100
2.6005-2.70460.19641430.16782707X-RAY DIFFRACTION100
2.7046-2.82770.20551310.16512764X-RAY DIFFRACTION100
2.8277-2.97670.20751490.16462725X-RAY DIFFRACTION100
2.9767-3.16320.2021390.16112751X-RAY DIFFRACTION100
3.1632-3.40740.18261540.14662759X-RAY DIFFRACTION100
3.4074-3.75010.15011340.13932764X-RAY DIFFRACTION100
3.7501-4.29250.14511410.1292778X-RAY DIFFRACTION99
4.2925-5.40680.16591300.13262839X-RAY DIFFRACTION100
5.4068-47.05240.17051270.17252987X-RAY DIFFRACTION99

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