[English] 日本語
Yorodumi
- PDB-7owo: HsNMT1 in complex with both MyrCoA and N-acetylated KSFSKPR peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7owo
TitleHsNMT1 in complex with both MyrCoA and N-acetylated KSFSKPR peptide
Components
  • Glycylpeptide N-tetradecanoyltransferase 1
  • N-Acetyl-LYS-SER-PHE-SER-LYS-PRO-ARG
KeywordsTRANSFERASE / E-MYRISTOYLATION / 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 / protein localization to membrane / eNOS activation / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Inactivation, recovery and regulation of the phototransduction cascade / in utero embryonic development / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
COENZYME A / TETRADECANOYL-COA / MYRISTIC ACID / Glycylpeptide N-tetradecanoyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDian, C. / Giglione, C. / Meinnel, T.
Funding support France, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-20-CE44-0013 France
Fondation ARCARCPJA32020060002137 France
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INSB-05-01 France
CitationJournal: J.Mol.Biol. / Year: 2022
Title: Structural and Large-scale Analysis Unveil the Intertwined Paths Promoting NMT-catalyzed Lysine and Glycine Myristoylation.
Authors: Riviere, F. / Dian, C. / Dutheil, R.F. / Monassa, P. / Giglione, C. / Meinnel, T.
History
DepositionJun 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycylpeptide N-tetradecanoyltransferase 1
B: Glycylpeptide N-tetradecanoyltransferase 1
D: N-Acetyl-LYS-SER-PHE-SER-LYS-PRO-ARG
F: N-Acetyl-LYS-SER-PHE-SER-LYS-PRO-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,82310
Polymers94,6874
Non-polymers3,1366
Water12,178676
1
A: Glycylpeptide N-tetradecanoyltransferase 1
D: N-Acetyl-LYS-SER-PHE-SER-LYS-PRO-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4096
Polymers47,3432
Non-polymers2,0664
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-20 kcal/mol
Surface area16250 Å2
MethodPISA
2
B: Glycylpeptide N-tetradecanoyltransferase 1
F: N-Acetyl-LYS-SER-PHE-SER-LYS-PRO-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4134
Polymers47,3432
Non-polymers1,0702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-28 kcal/mol
Surface area16590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.315, 178.287, 58.173
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

-
Components

-
Protein / Protein/peptide , 2 types, 4 molecules ABDF

#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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): ROSETTA2 PLYSS
References: UniProt: P30419, glycylpeptide N-tetradecanoyltransferase
#2: Protein/peptide N-Acetyl-LYS-SER-PHE-SER-LYS-PRO-ARG


Mass: 878.051 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Non-polymers , 5 types, 682 molecules

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


Mass: 92.094 Da / Num. of mol.: 2 / 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 / Feature type: SUBJECT OF INVESTIGATION
#5: 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
#6: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 676 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 23% PEG 6K, 100mM NaCitrate 5.6, 100mM MgCl2, 100mM NaCl

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 4, 2020 / Details: K/B Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.7→48.72 Å / Num. obs: 79532 / % possible obs: 97.19 % / Redundancy: 13.2 % / Biso Wilson estimate: 18.17 Å2 / CC1/2: 0.9985 / Rpim(I) all: 0.031 / Rsym value: 0.11 / Net I/σ(I): 14.4
Reflection shellResolution: 1.7→1.75 Å / Redundancy: 12.31 % / Mean I/σ(I) obs: 1.872 / Num. unique obs: 3977 / CC1/2: 0.7665 / Rpim(I) all: 0.409 / Rsym value: 1.401 / % possible all: 96.5

-
Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
STARANISOdata scaling
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O9T

5o9t


Resolution: 1.7→48.72 Å / SU ML: 0.1802 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.054
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2232 3942 4.96 %
Rwork0.1829 75577 -
obs0.1848 79519 86.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.33 Å2
Refinement stepCycle: LAST / Resolution: 1.7→48.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6584 0 6 676 7266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00666885
X-RAY DIFFRACTIONf_angle_d0.89879375
X-RAY DIFFRACTIONf_chiral_restr0.0621023
X-RAY DIFFRACTIONf_plane_restr0.00571173
X-RAY DIFFRACTIONf_dihedral_angle_d20.99442651
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.351760.25141416X-RAY DIFFRACTION46.06
1.72-1.740.27881010.24061518X-RAY DIFFRACTION50.31
1.74-1.770.2783810.22811653X-RAY DIFFRACTION53.83
1.77-1.790.2973820.21991757X-RAY DIFFRACTION57.15
1.79-1.820.25971000.22481939X-RAY DIFFRACTION62.66
1.82-1.840.271240.232008X-RAY DIFFRACTION66.65
1.84-1.870.27051030.2222176X-RAY DIFFRACTION70.43
1.87-1.90.26551250.22462276X-RAY DIFFRACTION74.01
1.9-1.930.28161180.22792443X-RAY DIFFRACTION78.46
1.93-1.970.28871380.232552X-RAY DIFFRACTION83.67
1.97-2.010.2581510.21422772X-RAY DIFFRACTION89.47
2.01-2.050.24731530.20552913X-RAY DIFFRACTION95.48
2.05-2.090.2351740.20083043X-RAY DIFFRACTION98.68
2.09-2.140.26151650.20333088X-RAY DIFFRACTION99.97
2.14-2.20.20131520.19313079X-RAY DIFFRACTION100
2.2-2.250.24531760.1923081X-RAY DIFFRACTION100
2.25-2.320.24311510.19553109X-RAY DIFFRACTION100
2.32-2.40.23641580.1853103X-RAY DIFFRACTION100
2.4-2.480.22941530.18963108X-RAY DIFFRACTION100
2.48-2.580.22921620.19133109X-RAY DIFFRACTION100
2.58-2.70.22361480.18663111X-RAY DIFFRACTION100
2.7-2.840.24281610.19373142X-RAY DIFFRACTION100
2.84-3.020.22181640.18153121X-RAY DIFFRACTION100
3.02-3.250.22391780.17963136X-RAY DIFFRACTION99.97
3.25-3.580.18571570.16473160X-RAY DIFFRACTION100
3.58-4.10.1761600.1463183X-RAY DIFFRACTION100
4.1-5.160.18011610.13793208X-RAY DIFFRACTION99.97
5.16-48.720.22641700.18743373X-RAY DIFFRACTION99.61

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more