+Open data
-Basic information
Entry | Database: PDB / ID: 6qrm | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | HsNMT1 in complex with both MyrCoA and GNCFSKRRAA substrates | |||||||||
Components |
| |||||||||
Keywords | TRANSFERASE / Myristoyltransferase type1 / Acyltransferase / GNAT / GCN5-Related N-Acetyltransferases | |||||||||
Function / homology | Function and homology information 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 / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / protein localization to membrane ...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 / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / protein localization to membrane / Oxidoreductases / oxidoreductase activity, acting on NAD(P)H / execution phase of apoptosis / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / 2 iron, 2 sulfur cluster binding / Inactivation, recovery and regulation of the phototransduction cascade / flavin adenine dinucleotide binding / mitochondrial inner membrane / in utero embryonic development / endoplasmic reticulum / mitochondrion / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Dian, C. / Riviere, F.B. / Asensio, T. / Giglione, C. / Meinnel, T. | |||||||||
Funding support | France, 2items
| |||||||||
Citation | Journal: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6qrm.cif.gz | 190.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6qrm.ent.gz | 147.7 KB | Display | PDB format |
PDBx/mmJSON format | 6qrm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qr/6qrm ftp://data.pdbj.org/pub/pdb/validation_reports/qr/6qrm | HTTPS FTP |
---|
-Related structure data
Related structure data | 6ehjC 6sjzC 6sk2C 6sk3C 6sk8C 6skjC 5o9vS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein / Protein/peptide , 2 types, 4 molecules ABCD
#1: Protein | 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 | 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 |
---|
-Non-polymers , 6 types, 405 molecules
#3: Chemical | ChemComp-COA / | ||||||||
---|---|---|---|---|---|---|---|---|---|
#4: Chemical | ChemComp-GOL / #5: Chemical | #6: Chemical | ChemComp-MYA / | #7: Chemical | ChemComp-MYR / | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 24% PEG8K, 100mM Sodium Citrate pH 5.5, 100mM MgCl2, 100mM NaCl. |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: 100 K cryostream / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Feb 8, 2016 |
Radiation | Monochromator: Si (111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.07 Å2 / Biso mean: 30.6342 Å2 / Biso min: 10.95 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→48.91 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|