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- PDB-7rk3: Crystal structure of human N-myristoyltransferase 1 fragment (res... -

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Basic information

Entry
Database: PDB / ID: 7rk3
TitleCrystal structure of human N-myristoyltransferase 1 fragment (residues 109-496) bound to diacylated human Arf6 octapeptide and Coenzyme A
Components
  • ADP-ribosylation factor 6ARF6
  • Glycylpeptide N-tetradecanoyltransferase 1
KeywordsTRANSFERASE
Function / homology
Function and homology information


erythrocyte apoptotic process / maintenance of postsynaptic density structure / 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 / regulation of dendritic spine development ...erythrocyte apoptotic process / maintenance of postsynaptic density structure / 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 / regulation of dendritic spine development / establishment of epithelial cell polarity / negative regulation of receptor-mediated endocytosis / protein localization to endosome / negative regulation of dendrite development / ruffle assembly / negative regulation of protein localization to cell surface / regulation of Rac protein signal transduction / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / regulation of filopodium assembly / endocytic recycling / thioesterase binding / MET receptor recycling / protein localization to membrane / filopodium membrane / protein localization to cell surface / Flemming body / TBC/RABGAPs / cortical actin cytoskeleton organization / positive regulation of actin filament polymerization / hepatocyte apoptotic process / cleavage furrow / regulation of presynapse assembly / synaptic vesicle endocytosis / endocytic vesicle / signaling adaptor activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / vesicle-mediated transport / ruffle / cellular response to nerve growth factor stimulus / small monomeric GTPase / G protein activity / liver development / protein localization to plasma membrane / positive regulation of protein secretion / positive regulation of protein localization to plasma membrane / intracellular protein transport / positive regulation of neuron projection development / recycling endosome membrane / GDP binding / Inactivation, recovery and regulation of the phototransduction cascade / presynapse / Clathrin-mediated endocytosis / nervous system development / cell cortex / early endosome membrane / postsynapse / in utero embryonic development / cell differentiation / cell adhesion / endosome / cell cycle / cell division / focal adhesion / GTPase activity / glutamatergic synapse / GTP binding / Golgi apparatus / extracellular exosome / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
ADP-ribosylation factor 6 / 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 / small GTPase Arf family profile. ...ADP-ribosylation factor 6 / 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 / small GTPase Arf family profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Acyl-CoA N-acyltransferase / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
4'-diphospho pantetheine / HEXANOIC ACID / MYRISTIC ACID / Glycylpeptide N-tetradecanoyltransferase 1 / ADP-ribosylation factor 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsFenwick, M.K. / Lin, H.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK107868-04 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124165-01 United States
National Institutes of Health/Office of the DirectorS10OD021527
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: To Be Published
Title: Crystal structure of human N-myristoyltransferase 1 fragment (residues 109-496) bound to diacylated human Arf6 octapeptide and Coenzyme A
Authors: Fenwick, M.K. / Lin, H.
History
DepositionJul 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: ADP-ribosylation factor 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1295
Polymers46,3462
Non-polymers7833
Water7,927440
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-3 kcal/mol
Surface area15820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.984, 76.046, 106.342
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#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: 45453.348 Da / Num. of mol.: 1 / Fragment: UNP residues 29-416
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NMT1, NMT / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P30419, glycylpeptide N-tetradecanoyltransferase
#2: Protein/peptide ADP-ribosylation factor 6 / ARF6


Mass: 893.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARF6 / Production host: unidentified (others) / References: UniProt: P62330

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Non-polymers , 4 types, 443 molecules

#3: Chemical ChemComp-4PS / 4'-diphospho pantetheine / N~3~-[(2R)-2-hydroxy-4-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}-3,3-dimethylbutanoyl]-N-(2-sulfanylethyl)-beta-alaninamide


Mass: 438.328 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24N2O10P2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-6NA / HEXANOIC ACID / Caproic acid


Mass: 116.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 440 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.09 Å3/Da / Density % sol: 41.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 20% (w/v) PEG 3350, 200mM ammonium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.05→106.34 Å / Num. obs: 24871 / % possible obs: 99 % / Redundancy: 3.6 % / Biso Wilson estimate: 28.34 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.04 / Rrim(I) all: 0.078 / Net I/σ(I): 13.1 / Num. measured all: 88647
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
2.05-2.113.10.475573918330.860.310.5712.196.1
8.93-106.343.20.015120137510.010.01843.899.9

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
PHENIX1.19.1_4122phasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HsNMT1

Resolution: 2.05→61.86 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 26.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2197 1216 4.9 %
Rwork0.1585 23576 -
obs0.1616 24792 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.44 Å2 / Biso mean: 34.6862 Å2 / Biso min: 17.82 Å2
Refinement stepCycle: final / Resolution: 2.05→61.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2955 0 48 442 3445
Biso mean--38.63 43.52 -
Num. residues----360
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.130.3081380.27752483262196
2.13-2.230.28941180.22692605272399
2.23-2.350.28361350.19922576271199
2.35-2.490.26821540.17352590274499
2.49-2.690.3041350.17692568270398
2.69-2.960.2511180.17282645276399
2.96-3.380.23241360.14772637277399
3.38-4.260.15731230.1262680280399
4.26-61.860.17181590.13362792295199
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5783-0.67510.1691.33490.10322.79190.006-0.1244-0.07620.01110.0419-0.0550.07050.1328-0.04340.2319-0.023-0.01770.20490.01720.211212.5357-2.71957.4577
26.4641-4.4023-0.8155.22710.11212.2907-0.0711-0.09750.19670.27480.0533-0.20010.1625-0.1320.00760.1741-0.063-0.01040.22120.01380.13363.6075-6.55838.8748
30.58190.0866-0.02020.6436-0.24252.9912-0.0345-0.0794-0.0496-0.02720.02540.02140.2342-0.15290.01120.2597-0.0106-0.01630.2090.00920.25311.047-7.46322.594
48.78752.70086.08668.79174.45119.36730.0292-0.0563-0.1669-0.1753-0.13270.3201-0.0439-0.42040.12860.2898-0.05450.05210.2109-0.05760.23163.0093-13.1822-27.9697
50.6622-0.29320.3081.8293-0.92932.4235-0.0552-0.01690.09880.10510.1120.0211-0.3915-0.1038-0.05410.29240.0183-0.00360.24380.00460.2368-2.712911.4524-8.8911
61.39160.1385-0.19541.4544-0.41913.02780.00820.0268-0.11-0.11990.06140.10860.095-0.1799-0.07020.2651-0.0156-0.01680.18780.01430.2297-3.2951-1.9662-10.0672
77.3372-2.2373-0.76033.616-2.61923.2345-0.41680.1074-0.3962-0.57040.37240.5155-0.6964-0.17950.00010.2866-0.0705-0.01920.22450.03870.27262.3399-12.1743-9.5551
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 145 through 235 )A145 - 235
2X-RAY DIFFRACTION2chain 'A' and (resid 236 through 259 )A236 - 259
3X-RAY DIFFRACTION3chain 'A' and (resid 260 through 308 )A260 - 308
4X-RAY DIFFRACTION4chain 'A' and (resid 309 through 326 )A309 - 326
5X-RAY DIFFRACTION5chain 'A' and (resid 327 through 407 )A327 - 407
6X-RAY DIFFRACTION6chain 'A' and (resid 408 through 496 )A408 - 496
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 9 )B2 - 9

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