PDB-7owp: HsNMT1 in complex with both MyrCoA and ACE-G-(L-ORN)SFSKPR

ID or keywords:

Entry

Database: PDB / ID: 7owp

Title

HsNMT1 in complex with both MyrCoA and ACE-G-(L-ORN)SFSKPR

Components

ACE-GLY-ORN-SER-PHE-SER-LYS-PRO-ARG
Glycylpeptide N-tetradecanoyltransferase 1

Keywords

TRANSFERASE / 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 ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.81 Å

Authors

Dian, C. / Giglione, C. / Meinnel, T.

Funding support

France, 3items

Organization	Grant number	Country
Agence Nationale de la Recherche (ANR)	ANR-20-CE44-0013	France
Fondation ARC	ARCPJA32020060002137	France
French Infrastructure for Integrated Structural Biology (FRISBI)	ANR-10-INSB-05-01	France

Citation

Journal: 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

Deposition	Jun 18, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 21, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7owp.cif.gz	428.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7owp.ent.gz	290.8 KB	Display	PDB format
PDBx/mmJSON format	7owp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ow/7owp ftp://data.pdbj.org/pub/pdb/validation_reports/ow/7owp	HTTPS FTP

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Related structure data

Related structure data	7owmC 7ownC 7owoC 7owqC 7owrC 7owuC 5o9tS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #44 - Aug 2003 Calmodulin similarity (1) #97 - Jan 2008 Circadian Clock Proteins similarity (1) #196 - Apr 2016 Lead Poisoning similarity (1) #28 - Apr 2002 Anthrax Toxin similarity (1)

Deposited unit

A: Glycylpeptide N-tetradecanoyltransferase 1

B: Glycylpeptide N-tetradecanoyltransferase 1

E: ACE-GLY-ORN-SER-PHE-SER-LYS-PRO-ARG

D: ACE-GLY-ORN-SER-PHE-SER-LYS-PRO-ARG

hetero molecules

96.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glycylpeptide N-tetradecanoyltransferase 1

D: ACE-GLY-ORN-SER-PHE-SER-LYS-PRO-ARG

hetero molecules

defined by author&software
Evidence: native gel electrophoresis, Maldi enzymatic assay
48.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Glycylpeptide N-tetradecanoyltransferase 1

E: ACE-GLY-ORN-SER-PHE-SER-LYS-PRO-ARG

hetero molecules

defined by author&software
48.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	79.324, 178.199, 58.185
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2
Space group name Hall	P22ab
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 on special symmetry positions

ID	Model	Components
1	1	A-991- HOH

#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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): ROSETTA2 PLYSS References: UniProt: P30419, glycylpeptide N-tetradecanoyltransferase
#2: Protein/peptide	ACE-GLY-ORN-SER-PHE-SER-LYS-PRO-ARG Mass: 920.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: 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
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 790 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.23 Å³/Da / Density % sol: 45 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 18% PEG8K, 100mM Sodium Citrate pH 5.6, 100mM MgCl2, 100mM NaCl

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Data collection

Diffraction	Mean temperature: 100 K / Ambient temp details: Cryostream / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.984 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 18, 2019 / Details: KB-mirrors
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.984 Å / Relative weight: 1
Reflection	Resolution: 1.81→48.72 Å / Num. obs: 143724 / % possible obs: 99.1 % / Redundancy: 15 % / B_iso Wilson estimate: 20.87 Å² / CC_1/2: 0.999 / R_pim(I) all: 0.037 / R_sym value: 0.098 / Net I/σ(I): 16.9
Reflection shell	Resolution: 1.81→1.85 Å / Mean I/σ(I) obs: 4.8 / Num. unique obs: 4375 / CC_1/2: 0.967 / R_pim(I) all: 0.027 / R_sym value: 0.562 / % possible all: 98.2

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Processing

Software

Name	Version	Classification
PHENIX	1.17_3644	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5O9T

5o9t

Resolution: 1.81→47.55 Å / SU ML: 0.1613 / Cross valid method: FREE R-VALUE / σ(F): 0.21 / Phase error: 21.0928
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.191	7134	4.96 %
R_work	0.1552	136590	-
obs	0.157	143724	99.01 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 31.89 Å²

Refinement step

Cycle: LAST / Resolution: 1.81→47.55 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6337	0	258	790	7385

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0061	6875
X-RAY DIFFRACTION	f_angle_d	0.8615	9369
X-RAY DIFFRACTION	f_chiral_restr	0.0589	1020
X-RAY DIFFRACTION	f_plane_restr	0.0057	1186
X-RAY DIFFRACTION	f_dihedral_angle_d	19.9584	2648

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.81-1.83	0.2477	227	0.214	4472	X-RAY DIFFRACTION	96.81
1.83-1.85	0.2127	223	0.1955	4534	X-RAY DIFFRACTION	98.41
1.85-1.88	0.2289	230	0.185	4504	X-RAY DIFFRACTION	96.85
1.88-1.9	0.2256	246	0.1776	4530	X-RAY DIFFRACTION	99.52
1.9-1.92	0.2023	229	0.1834	4527	X-RAY DIFFRACTION	98.08
1.92-1.95	0.2399	264	0.1784	4454	X-RAY DIFFRACTION	97.97
1.95-1.98	0.2127	193	0.1749	4627	X-RAY DIFFRACTION	99.5
1.98-2.01	0.2172	231	0.1695	4534	X-RAY DIFFRACTION	97.09
2.01-2.04	0.2282	237	0.1671	4522	X-RAY DIFFRACTION	99.9
2.04-2.07	0.1999	231	0.1639	4491	X-RAY DIFFRACTION	97.74
2.07-2.11	0.1916	235	0.1585	4582	X-RAY DIFFRACTION	99.44
2.11-2.15	0.208	235	0.1624	4539	X-RAY DIFFRACTION	98.49
2.15-2.19	0.2461	277	0.1608	4527	X-RAY DIFFRACTION	99.19
2.19-2.23	0.1701	228	0.1515	4554	X-RAY DIFFRACTION	98.62
2.23-2.28	0.2011	239	0.1587	4551	X-RAY DIFFRACTION	99.5
2.28-2.33	0.1887	245	0.1555	4571	X-RAY DIFFRACTION	98.53
2.33-2.39	0.1879	206	0.1538	4576	X-RAY DIFFRACTION	99.96
2.39-2.46	0.2204	244	0.1612	4552	X-RAY DIFFRACTION	98.81
2.46-2.53	0.1849	257	0.1626	4554	X-RAY DIFFRACTION	99.11
2.53-2.61	0.1986	225	0.166	4568	X-RAY DIFFRACTION	99.98
2.61-2.7	0.1927	234	0.1611	4565	X-RAY DIFFRACTION	99.3
2.7-2.81	0.2211	243	0.1668	4585	X-RAY DIFFRACTION	99.44
2.81-2.94	0.1877	236	0.1659	4578	X-RAY DIFFRACTION	99.61
2.94-3.1	0.1975	245	0.1647	4551	X-RAY DIFFRACTION	99.65
3.1-3.29	0.1943	241	0.1581	4614	X-RAY DIFFRACTION	99.81
3.29-3.54	0.1954	260	0.1498	4558	X-RAY DIFFRACTION	99.85
3.54-3.9	0.1948	228	0.138	4631	X-RAY DIFFRACTION	99.88
3.9-4.46	0.1356	249	0.1205	4592	X-RAY DIFFRACTION	99.98
4.46-5.62	0.1584	253	0.1281	4569	X-RAY DIFFRACTION	99.94
5.62-47.55	0.1789	243	0.1661	4578	X-RAY DIFFRACTION	99.69

Refinement TLS params.

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

ID	L11 (°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)
1	2.24126603683	0.528565049903	1.05928570146	1.56926766071	0.536981186038	1.47145428783	0.0208356195669	-0.252676366679	-0.184113356809	0.262592813242	0.0154842029407	0.266356012903	0.481073495029	-0.510735868524	-0.00761780036057	0.375430962873	-0.09312294841	0.043004542864	0.330018067875	0.0342275949409	0.243540699404	8.48484523042	192.147665779	26.6240646348
2	0.773761055679	-0.574662855394	-0.152109788545	0.878557685791	0.195736973055	1.47740042669	0.018699437537	-0.108016646942	-0.00948292846696	0.0328315835456	0.0452800141449	-0.0780706011931	0.1354646993	0.132707324746	-0.0651174469046	0.183630812813	0.018510586094	-0.0177076008547	0.186572168581	-0.00238156706466	0.222311268507	30.3508441138	193.631978996	18.4490903211
3	0.761271326755	0.00532899418655	-0.0850561122021	0.577234580887	0.263720702696	1.48851035924	0.0285675793903	-0.0950811993095	-0.157613414387	0.062748272202	0.0300496523528	0.0198585282921	0.453058517234	-0.0826929488726	-0.0120586194505	0.283445032062	-0.000167604991624	-0.0340679744936	0.155748555551	0.0201922180873	0.204771095263	19.5404779924	186.636028373	14.097598662
4	0.366100740159	-0.521873908825	-0.0374944489882	4.29329415521	-0.785818605239	0.203145843919	0.126699258963	0.229985788451	-0.290271537039	-0.234034529172	-0.0262051481875	-0.0594729840172	0.493586650917	-0.0161505991838	0.020181748922	0.490604050712	0.0449365992416	-0.043750814312	0.225651945757	-0.0752945011673	0.319410993757	22.8421033536	182.678906281	-13.846665438
5	0.378894061063	0.182111828008	-0.143260789788	0.529642924241	-0.353732528384	1.24324503886	0.0886223759403	0.0539545846953	0.0299289797198	-0.112768803112	-0.00408073317865	-0.0169251106462	0.0184228415742	-0.0947160385808	-0.0745501002091	0.186914599488	0.0483161450174	-0.0161651940752	0.184309985933	-0.00789930256976	0.181171986959	19.2289367831	199.294551073	-3.58080593706
6	0.533122686902	-0.0114178971984	-0.132689788026	0.984912862477	0.0736219373523	1.43090107494	0.0452648359687	0.0151254502896	-0.114735458133	-0.05770316406	0.00153146157702	0.0119015980513	0.390049907289	-0.152078332434	-0.0418874588772	0.21836643394	-0.0225786380657	-0.0475200682452	0.156492292332	-0.0036033131174	0.18301064945	16.4993736535	186.052981745	0.98411324906
7	1.98416570523	-0.35615684776	-0.787771685423	1.06744996286	0.19028077563	1.01317386288	0.136568373215	0.280858891914	0.132665583755	-0.222435496099	-0.0696251886737	0.210275404025	-0.336050985663	-0.394749475885	-0.00426941775959	0.223091280699	0.100396867138	0.0177897406858	0.278518572009	0.026545656988	0.252128231251	6.59500761612	229.337404261	1.71968253625
8	1.23150823314	0.172632564894	-0.0117932156814	0.538182992024	-0.182055432379	1.41313605661	0.0210325213424	0.00268941072581	0.148991152786	0.0635694823851	-0.0247234893326	-0.0292695946446	-0.224023727442	0.0519199267951	0.00240844156958	0.157377264561	0.0210530441714	0.0079278667721	0.161153768458	-0.00839258687867	0.19662000981	23.9388904495	228.9909528	8.83694873627
9	0.692560380153	0.536778501276	-0.0664366985405	1.62812452047	0.31754851797	0.119473135506	-0.0756364350208	0.00418624421041	0.145478681092	-0.0204765975696	0.0639886975438	-0.0774611385472	-0.818163703921	0.0546378748534	0.0619917642451	0.607751817241	0.0131917235267	-0.0054013463462	0.240508140144	-0.0234728197041	0.272551979723	18.3560636973	249.532119967	29.2405740162
10	0.712758446772	-0.225884890828	0.139674123093	0.93065027194	-0.0836993866765	1.61402836435	-0.0340116741179	-0.0426737512956	0.083700486747	0.213138361638	0.0602960486404	-0.0864650454076	-0.304901172139	0.0123250606708	-0.0339370091673	0.246308589653	0.0323398143546	-0.00944931519665	0.169222867858	-0.0141592385063	0.154115806114	18.9483217559	230.150390381	34.1289524465
11	0.457310547467	0.0394344502305	0.246000829837	0.734963518311	0.260761530253	1.75763310913	-0.0116309175562	-0.0422134390469	0.0962200455016	0.0772682522923	0.00972778943059	0.0224511941189	-0.425256063768	-0.173717025796	-0.00196956645382	0.235292609613	0.0731578304543	0.0105610110443	0.192719537496	-0.0122190015137	0.184914086122	10.1073078113	234.976272282	23.508678809
12	0.154805571047	0.543807546388	0.63091690782	2.39916477047	2.75786674949	3.25043817175	0.0506472705087	0.0372022413488	0.0291836535934	-0.514292286408	0.0681484170357	0.0369575370703	0.286384974883	-0.172262726883	-0.0261476203758	0.555879801816	-0.0193573131246	-0.0400083682781	0.312952797621	0.0467491024045	0.452089848919	20.4536007718	178.708097916	8.84590791453
13	1.90080877444	1.24024591326	0.907331417793	0.820513776502	0.519263809355	2.23784859299	0.0582219783606	0.235669043923	-0.216937504258	0.327466469674	0.0931644832556	-0.0794941403429	-0.194591862479	-0.025692688118	-0.146359413614	1.10560939722	0.243556244141	-0.0982185208392	0.86404928279	-0.147626956717	0.889539043209	17.7159978009	243.68956525	20.0137262384

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 105 through 147 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 148 through 235 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 236 through 319 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 320 through 342 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 343 through 407 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 408 through 496 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 105 through 147 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 148 through 291 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 292 through 319 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 320 through 444 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 445 through 496 )
12	X-RAY DIFFRACTION	12	chain 'E' and (resid 1 through 8 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 1 through 8 )

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