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- PDB-6pau: Structure of Human NMT2 with myristoyl-lysine peptide and CoA products -

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Basic information

Entry
Database: PDB / ID: 6pau
TitleStructure of Human NMT2 with myristoyl-lysine peptide and CoA products
Components
  • Arf6 peptide
  • Glycylpeptide N-tetradecanoyltransferase 2
KeywordsTRANSFERASE / lysine / myristoyl / myristoylation / n-myristoyl transferase
Function / homology
Function and homology information


erythrocyte apoptotic process / maintenance of postsynaptic density structure / intracellular transport of virus / peptidyl-lysine N6-myristoyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / regulation of opsin-mediated signaling pathway / regulation of dendritic spine development / negative regulation of receptor-mediated endocytosis / establishment of epithelial cell polarity / protein localization to endosome ...erythrocyte apoptotic process / maintenance of postsynaptic density structure / intracellular transport of virus / peptidyl-lysine N6-myristoyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / regulation of opsin-mediated signaling pathway / regulation of dendritic spine development / negative regulation of receptor-mediated endocytosis / establishment of epithelial cell polarity / protein localization to endosome / ruffle assembly / negative regulation of protein localization to cell surface / negative regulation of dendrite development / 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 / filopodium membrane / Flemming body / protein localization to cell surface / TBC/RABGAPs / cortical actin cytoskeleton organization / positive regulation of actin filament polymerization / hepatocyte apoptotic process / host cell / cleavage furrow / regulation of presynapse assembly / synaptic vesicle endocytosis / endocytic vesicle / signaling adaptor activity / vesicle-mediated transport / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / ruffle / Membrane binding and targetting of GAG proteins / small monomeric GTPase / cellular response to nerve growth factor stimulus / 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 / 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 / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase / Aminopeptidase / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4'-diphospho pantetheine / MYRISTIC ACID / Glycylpeptide N-tetradecanoyltransferase 2 / ADP-ribosylation factor 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsPrice, I.R. / Lin, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)1R01DK107868 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM086703-07 United States
CitationJournal: Nat Commun / Year: 2020
Title: NMT1 and NMT2 are lysine myristoyltransferases regulating the ARF6 GTPase cycle.
Authors: Kosciuk, T. / Price, I.R. / Zhang, X. / Zhu, C. / Johnson, K.N. / Zhang, S. / Halaby, S.L. / Komaniecki, G.P. / Yang, M. / DeHart, C.J. / Thomas, P.M. / Kelleher, N.L. / Christopher Fromme, J. / Lin, H.
History
DepositionJun 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycylpeptide N-tetradecanoyltransferase 2
C: Arf6 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,10815
Polymers45,4932
Non-polymers1,61613
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-19 kcal/mol
Surface area16210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.162, 46.350, 74.395
Angle α, β, γ (deg.)90.00, 114.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AC

#1: Protein Glycylpeptide N-tetradecanoyltransferase 2 / / Myristoyl-CoA:protein N-myristoyltransferase 2 / NMT 2 / Peptide N-myristoyltransferase 2 / Type II ...Myristoyl-CoA:protein N-myristoyltransferase 2 / NMT 2 / Peptide N-myristoyltransferase 2 / Type II N-myristoyltransferase


Mass: 44656.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NMT2 / Production host: Escherichia coli (E. coli)
References: UniProt: O60551, glycylpeptide N-tetradecanoyltransferase
#2: Protein/peptide Arf6 peptide


Mass: 836.073 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P62330*PLUS

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Non-polymers , 6 types, 189 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: 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
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#7: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.18 Å3/Da / Density % sol: 43.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 8 mg/mL protein in a buffer of 25 mM Tris-HCl pH 7.5, 120 mM NaCl, 1 mM DTT, 1 mM MgCl2, mixed 1:1 with well solution of 22% PEG 8000, 0.1 M Bis-Tris pH 6.5

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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: Mar 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.93→57.59 Å / Num. obs: 154166 / % possible obs: 99.49 % / Redundancy: 5.2 % / Biso Wilson estimate: 29.29 Å2 / CC1/2: 0.998 / R split: 0.04867 / Rmerge(I) obs: 0.1007 / Rrim(I) all: 0.1123 / Net I/σ(I): 11.35
Reflection shellResolution: 1.93→1.999 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.066 / Mean I/σ(I) obs: 1.54 / Num. unique obs: 15911 / CC1/2: 0.646 / % possible all: 99.56

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C2X

4c2x


Resolution: 1.93→67.831 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2177 1530 5.15 %
Rwork0.1973 --
obs0.1984 29688 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→67.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3015 0 101 176 3292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073213
X-RAY DIFFRACTIONf_angle_d0.8774342
X-RAY DIFFRACTIONf_dihedral_angle_d16.0491928
X-RAY DIFFRACTIONf_chiral_restr0.048469
X-RAY DIFFRACTIONf_plane_restr0.004540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.99230.42031480.37652519X-RAY DIFFRACTION100
1.9923-2.06360.34531170.31212566X-RAY DIFFRACTION100
2.0636-2.14620.29051160.27792562X-RAY DIFFRACTION100
2.1462-2.24390.28141280.24782584X-RAY DIFFRACTION100
2.2439-2.36220.25281280.23182545X-RAY DIFFRACTION100
2.3622-2.51020.24181510.21062539X-RAY DIFFRACTION100
2.5102-2.7040.23161390.19472524X-RAY DIFFRACTION98
2.704-2.97610.22961430.18562554X-RAY DIFFRACTION100
2.9761-3.40670.20431530.16752569X-RAY DIFFRACTION100
3.4067-4.29210.14961620.15562550X-RAY DIFFRACTION100
4.2921-67.8730.20841450.17882646X-RAY DIFFRACTION99

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