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- PDB-6sk2: HsNMT1 in complex with both MyrCoA and Acetylated-GKSFSKPR peptid... -

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Basic information

Entry
Database: PDB / ID: 6sk2
TitleHsNMT1 in complex with both MyrCoA and Acetylated-GKSFSKPR peptide reveals N-terminal Lysine Myristoylation
Components
  • Apoptosis-inducing factor 3
  • Glycylpeptide N-tetradecanoyltransferase 1
KeywordsTRANSFERASE / E-MYRISTOYLATION / NMT / 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
Reductase, C-terminal / Reductase C-terminal / 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 ...Reductase, C-terminal / Reductase C-terminal / 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 / FAD/NAD-linked reductase, dimerisation domain superfamily / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Acyl-CoA N-acyltransferase / Aminopeptidase / FAD/NAD(P)-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / TETRADECANOYL-COA / MYRISTIC ACID / Glycylpeptide N-tetradecanoyltransferase 1 / Apoptosis-inducing factor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.90000651019 Å
AuthorsDian, C. / Riviere, F.B. / Asensio, T. / Giglione, C. / Meinnel, T.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-2010-BLAN-1611-01 France
French National Research AgencyANR-10-LABX-0040-SPS France
CitationJournal: 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
DepositionAug 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.2Jan 31, 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: Glycylpeptide N-tetradecanoyltransferase 1
D: Apoptosis-inducing factor 3
F: Apoptosis-inducing factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,05110
Polymers94,8014
Non-polymers2,2506
Water13,097727
1
A: Glycylpeptide N-tetradecanoyltransferase 1
D: Apoptosis-inducing factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5816
Polymers47,4012
Non-polymers1,1804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-7 kcal/mol
Surface area16620 Å2
MethodPISA
2
B: Glycylpeptide N-tetradecanoyltransferase 1
F: Apoptosis-inducing factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4714
Polymers47,4012
Non-polymers1,0702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-29 kcal/mol
Surface area16450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.818, 178.442, 58.271
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Components on special symmetry positions
IDModelComponents
11A-613-

HOH

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Components

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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 derivative / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta2 pLysS
References: UniProt: P30419, glycylpeptide N-tetradecanoyltransferase
#2: Protein/peptide Apoptosis-inducing factor 3 / / Apoptosis-inducing factor-like protein


Mass: 935.102 Da / Num. of mol.: 2 / Mutation: G3K, C4S, P8R / Source method: obtained synthetically
Details: Epsilon myristoylation, N-terminal Lysine myristoylation in the crystal. acetylated peptide
Source: (synth.) Homo sapiens (human) / References: UniProt: Q96NN9, Oxidoreductases

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Non-polymers , 5 types, 733 molecules

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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Chemical ChemComp-MYA / TETRADECANOYL-COA / MYRISTOYL-COA


Mass: 977.890 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H62N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


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


Mass: 18.015 Da / Num. of mol.: 727 / 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: 2.16 Å3/Da / Density % sol: 43.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 22% PEG8K, 100mM Sodium Citrate pH 5.6, 100mM MgCl2, 100mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream Oxford Cryosystem / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.984002 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 23, 2019
RadiationMonochromator: Si (111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984002 Å / Relative weight: 1
ReflectionResolution: 1.9→48.79 Å / Num. obs: 131286 / % possible obs: 99.9 % / Redundancy: 14.2 % / Biso Wilson estimate: 27.4485684842 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.028 / Rrim(I) all: 0.106 / Net I/σ(I): 15.4
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.941 / Num. unique obs: 4177 / CC1/2: 0.934 / Rpim(I) all: 0.252 / Rrim(I) all: 0.975 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.72 Å48.79 Å
Translation7.72 Å48.79 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.6.0phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O9T

5o9t


Resolution: 1.90000651019→48.787531993 Å / SU ML: 0.222000257637 / Cross valid method: THROUGHOUT / σ(F): 0.373714053464 / Phase error: 24.0574383694
RfactorNum. reflection% reflection
Rfree0.219991662291 6205 4.96475464271 %
Rwork0.171966781113 --
obs0.174280163469 124981 99.8649620455 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 31.6244340982 Å2
Refinement stepCycle: LAST / Resolution: 1.90000651019→48.787531993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6406 0 144 727 7277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006271281899726881
X-RAY DIFFRACTIONf_angle_d0.8575584410959375
X-RAY DIFFRACTIONf_chiral_restr0.05600738823151014
X-RAY DIFFRACTIONf_plane_restr0.006039393795831189
X-RAY DIFFRACTIONf_dihedral_angle_d15.87790251494138
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.90000651019-1.92160.2983982615392190.2606810159353978X-RAY DIFFRACTION99.9047845751
1.9216-1.94420.2912089168291760.2529345175063940X-RAY DIFFRACTION99.2524716663
1.9442-1.96790.2843279471342020.2394161663723957X-RAY DIFFRACTION99.9519346311
1.9679-1.99280.2778316813142760.2179191282593910X-RAY DIFFRACTION99.7616777884
1.9928-2.0190.2600913512841960.2205439363363939X-RAY DIFFRACTION99.6625692938
2.019-2.04670.2678528175512070.2087188971213968X-RAY DIFFRACTION99.8087497012
2.0467-2.07590.2812725356961930.2034654610724004X-RAY DIFFRACTION99.7385931559
2.0759-2.10690.2717489760711660.2076623917983921X-RAY DIFFRACTION99.6829268293
2.1069-2.13990.2163355090112060.2067984156244020X-RAY DIFFRACTION99.9526963103
2.1399-2.17490.3116314461132150.2000487726243938X-RAY DIFFRACTION99.8557345516
2.1749-2.21240.2335922265972310.1913560744223901X-RAY DIFFRACTION99.879139473
2.2124-2.25270.2445970576562350.1867340183133959X-RAY DIFFRACTION99.8096144693
2.2527-2.2960.2825542036722120.1980035196993932X-RAY DIFFRACTION99.8554216867
2.296-2.34290.219437229492160.1799944365573998X-RAY DIFFRACTION99.786881364
2.3429-2.39380.2408470083682040.1717244617563941X-RAY DIFFRACTION99.9035912268
2.3938-2.44950.2462339856882250.1780806422463948X-RAY DIFFRACTION99.9281609195
2.4495-2.51070.285746603961950.1853795515613957X-RAY DIFFRACTION99.8797209526
2.5107-2.57860.2271421451612140.1897766833733962X-RAY DIFFRACTION100
2.5786-2.65450.2478470436152220.1891321883643942X-RAY DIFFRACTION99.9519923188
2.6545-2.74020.2828761331412020.1915420569823965X-RAY DIFFRACTION99.952026865
2.7402-2.83810.2687961663181850.1905710713853949X-RAY DIFFRACTION99.9516441006
2.8381-2.95170.2383695831292090.1850123187493986X-RAY DIFFRACTION99.9761677788
2.9517-3.0860.2155446351551990.1811402063373996X-RAY DIFFRACTION100
3.086-3.24870.2245450556722130.1678606102063956X-RAY DIFFRACTION99.9760191847
3.2487-3.45220.1865845451700.1609732126183986X-RAY DIFFRACTION100
3.4522-3.71870.1920424496841980.1492772200143958X-RAY DIFFRACTION100
3.7187-4.09270.1664345153432230.1390170135993964X-RAY DIFFRACTION100
4.0927-4.68450.1728410545492200.1281877987743946X-RAY DIFFRACTION99.9760019198
4.6845-5.90040.1975713883191860.1483767295823969X-RAY DIFFRACTION100
5.9004-48.7875319930.182560155111900.1707104084983986X-RAY DIFFRACTION99.6420901933

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