PDB-4hny: Apo N-terminal acetyltransferase complex A

ID or keywords:

Entry

Database: PDB / ID: 4hny

Title

Apo N-terminal acetyltransferase complex A

Components

N-terminal acetyltransferase A complex catalytic subunit ARD1
N-terminal acetyltransferase A complex subunit NAT1

Keywords

TRANSFERASE / TPR/GNAT /

N-terminal acetyltransferase

Function / homology

Function and homology information

N-terminal protein amino acid propionylation / peptide-glutamate-alpha-N-acetyltransferase activity / N-terminal amino-acid Nalpha-acetyltransferase NatA / peptide-serine-alpha-N-acetyltransferase activity / NatA complex /

N-terminal protein amino acid acetylation /

ribosome binding /

mitochondrion / identical protein binding /

cytoplasm
Similarity search - Function

Biological species

Saccharomyces cerevisiae S288c (yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.249 Å

Authors

Neubauer, J.L. / Immormino, R.M. / Dollins, D.E. / Endo-Streeter, S.T. / Pemble IV, C.W. / York, J.D.

Citation

Journal: To be Published
Title: The Protein Complex NatA Binds Inositol Hexakisphosphate and Exhibits Conformational Flexibility
Authors: Neubauer, J.L. / Pham, T. / Immormino, R.M. / Dollins, D.E. / Endo-Streeter, S.T. / Li, S. / Pemble IV, C.W. / York, J.D.

History

Deposition	Oct 21, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 26, 2014	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4hny.cif.gz	774.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4hny.ent.gz	656.7 KB	Display	PDB format
PDBx/mmJSON format	4hny.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/hn/4hny ftp://data.pdbj.org/pub/pdb/validation_reports/hn/4hny	HTTPS FTP

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Related structure data

Related structure data	4hnwC 4hnxC C: citing same article (ref.)
Similar structure data	2p5g-2 5iud-1 2p5o-3 21693 2po4-d 3ks9-d 3k59-d 4g68-d 3lsi-d 3e3j-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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 (4) #141 - Sep 2011 O-GlcNAc Transferase similarity (2) #97 - Jan 2008 Circadian Clock Proteins similarity (4) #230 - Feb 2019 Initiation Factor eIF4E similarity (2) #166 - Oct 2013 Proteasome similarity (1)

Deposited unit

A: N-terminal acetyltransferase A complex subunit NAT1

B: N-terminal acetyltransferase A complex catalytic subunit ARD1

C: N-terminal acetyltransferase A complex subunit NAT1

D: N-terminal acetyltransferase A complex catalytic subunit ARD1

hetero molecules

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

1

A: N-terminal acetyltransferase A complex subunit NAT1

B: N-terminal acetyltransferase A complex catalytic subunit ARD1

hetero molecules

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

2

C: N-terminal acetyltransferase A complex subunit NAT1

D: N-terminal acetyltransferase A complex catalytic subunit ARD1

hetero molecules

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

Unit cell

Length a, b, c (Å)	129.416, 129.416, 171.783
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	144
Space group name H-M	P3₁

#1: Protein	N-terminal acetyltransferase A complex subunit NAT1 / NatA complex subunit NAT1 / Amino-terminal / alpha-amino / acetyltransferase 1 Mass: 100134.273 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: NAT1, AAA1, YDL040C, D2720 / Plasmid: 22b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P12945
#2: Protein	N-terminal acetyltransferase A complex catalytic subunit ARD1 / NatA complex subunit ARD1 / Arrest-defective protein 1 Mass: 28821.457 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: ARD1, YHR013C / Plasmid: 30b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P07347, EC: 2.3.1.88
#3: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol Mass: 194.226 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 986 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.22 Å³/Da / Density % sol: 61.8 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 5-25% PEG3350, 0.1 M di-ammonium hydrogen phosphate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 19, 2011
Radiation	Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.249→50 Å / Num. obs: 152807 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / R_sym value: 0.081
Reflection shell	Resolution: 2.25→2.29 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.503 / Mean I/σ(I) obs: 2.35 / % possible all: 99.7

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHENIX	(phenix.phaser: 1.7.2_869)	model building
PHENIX	(phenix.refine: 1.7.2_869)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX	1.7.2_869	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.249→30.158 Å / SU ML: 0.23 / σ(F): 0 / Phase error: 21.98 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2196	1849	1.27 %
R_work	0.1784	-	-
obs	0.179	145753	95.35 %

Solvent computation

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

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.746 Å²	-0 Å²	-0 Å²
2-	-	2.746 Å²	-0 Å²
3-	-	-	-5.492 Å²

Refinement step

Cycle: LAST / Resolution: 2.249→30.158 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14949	0	81	986	16016

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	15371
X-RAY DIFFRACTION	f_angle_d	0.964	20820
X-RAY DIFFRACTION	f_dihedral_angle_d	14.223	5523
X-RAY DIFFRACTION	f_chiral_restr	0.038	2320
X-RAY DIFFRACTION	f_plane_restr	0.005	2683

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 (%)
2.2493-2.3101	0.3004	131	0.2196	10099	X-RAY DIFFRACTION	86
2.3101-2.378	0.2589	134	0.201	10346	X-RAY DIFFRACTION	90
2.378-2.4548	0.259	123	0.1938	10524	X-RAY DIFFRACTION	91
2.4548-2.5424	0.2445	134	0.1878	10750	X-RAY DIFFRACTION	92
2.5424-2.6442	0.2293	139	0.1816	10897	X-RAY DIFFRACTION	94
2.6442-2.7644	0.2297	145	0.1836	10977	X-RAY DIFFRACTION	95
2.7644-2.9101	0.2323	145	0.1827	11192	X-RAY DIFFRACTION	96
2.9101-3.0922	0.2359	153	0.1855	11316	X-RAY DIFFRACTION	98
3.0922-3.3307	0.2314	154	0.1912	11501	X-RAY DIFFRACTION	99
3.3307-3.6654	0.2296	144	0.1741	11540	X-RAY DIFFRACTION	100
3.6654-4.1946	0.2033	147	0.1585	11593	X-RAY DIFFRACTION	100
4.1946-5.2801	0.1783	144	0.1577	11576	X-RAY DIFFRACTION	100
5.2801-30.1612	0.1971	156	0.1845	11593	X-RAY DIFFRACTION	100

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	3.5498	0.2972	1.1608	2.3988	0.24	4.8016	0.4032	0.5831	-0.177	-0.772	-0.0525	0.6498	-0.1504	-0.5447	-0.323	0.4849	0.1086	-0.1924	0.4674	0.0464	0.5987	30.8212	-54.9653	-19.0878
2	0.7606	0.0279	0.2808	0.7791	0.1118	1.1246	0.0415	-0.0435	-0.0245	0.0221	0.0121	0.0685	-0.0223	-0.0254	-0.0536	0.099	0.0242	0.0479	0.1491	0.0063	0.1589	59.4036	-38.2221	10.4774
3	1.6839	-1.4554	0.5666	1.6461	-0.3275	1.1142	-0.1772	-0.34	-0.036	0.1199	0.1839	0.1385	-0.2558	-0.5521	-0.0128	0.2022	0.1262	0.0233	0.4296	-0.0009	0.2452	30.5882	-23.6912	1.56
4	6.1028	0.1898	2.2753	6.1935	0.3887	6.3984	-0.2314	0.6865	0.3664	-0.6885	0.0507	0.3163	-0.5799	-0.0138	0.1369	0.2316	0.0079	0.0024	0.1993	0.0325	0.208	56.7685	-38.139	-0.2048
5	3.9411	0.8801	3.4642	3.6601	2.482	4.9558	0.0945	0.0524	-0.1585	-0.2415	-0.07	0.1523	-0.1975	-0.1242	0.0342	0.1722	-0.0051	0.0561	0.1227	-0.0028	0.1906	56.8349	-46.5415	-1.5967
6	5.3707	2.2299	0.2413	6.2088	-1.8783	5.9279	0.1662	-1.2224	0.5857	1.124	0.0235	0.1938	-0.7894	-0.1504	-0.152	0.4862	0.061	-0.0162	0.4114	-0.0312	0.3979	51.2459	-25.8114	8.1888
7	0.5776	-1.6005	-0.3104	5.2597	0.0693	0.9666	-0.2628	-0.7985	-0.4094	0.7033	0.3166	-0.437	-0.096	0.083	-0.1151	0.3654	0.1781	-0.07	0.4676	0.0114	0.3852	40.268	-18.7035	7.3936
8	3.8181	-0.3626	-0.5661	6.7271	1.0691	3.5854	-0.0454	0.1612	-0.1368	-0.5309	-0.0193	0.3596	-0.1712	-0.11	0.0922	0.1111	-0.0179	0.0199	0.1359	0.0526	0.1041	65.4672	-41.7103	-1.5904
9	1.2303	0.5218	-1.2788	1.3482	-1.5162	4.463	-0.0727	-0.028	-0.1741	-0.1211	-0.013	-0.2145	0.2014	0.3383	0.1134	0.1281	0.0057	0.0034	0.1325	-0.0166	0.1932	75.6793	-45.9345	-5.0311
10	9.786	4.65	-6.2561	6.4551	-6.0165	2.0223	-0.3463	-0.2371	-0.6205	0.158	-0.3668	-0.7696	0.0456	0.8879	0.7663	0.3885	0.0005	-0.0404	0.4691	0.0383	0.2799	77.3202	-50.8357	20.2418
11	2.0025	4.3111	5.6788	7.5315	0.7685	2.002	0.1609	-0.6974	-0.4608	0.8587	0.2427	-0.6985	0.1458	0.8496	-0.3181	0.4731	0.172	-0.0237	0.6316	0.0081	0.3221	74.9913	-49.4812	36.0526
12	0.8837	0.263	-0.0763	1.858	-0.2645	0.9493	0.0729	0.0735	-0.0481	0.0509	-0.0102	-0.1834	-0.0292	0.0723	-0.0628	0.1628	0.0656	0.0204	0.1922	-0.0576	0.1881	4.9819	-9.7244	44.5016
13	3.5249	-0.5805	-0.357	0.3503	0.0014	0.3864	0.0448	0.1575	-0.085	-0.0219	-0.0592	-0.0693	0.0017	0.1033	0.0126	0.1624	0.0208	-0.0146	0.1666	0.0199	0.1878	32.5537	-22.3769	46.3615
14	6.3626	1.0312	1.8453	7.2844	-2.1212	5.2036	0.0687	-0.2705	-0.0109	0.4656	-0.2107	-0.4446	-0.0963	0.3888	0.0934	0.1396	0.069	0.0567	0.2403	-0.0032	0.2049	6.2801	-4.975	47.7528
15	1.7014	2.6125	-2.2203	6.4008	-5.2981	8.8121	0.1033	-0.2309	0.0743	0.2691	-0.244	-0.2795	-0.1611	0.5185	0.1338	0.1329	0.037	0.0079	0.1561	-0.0197	0.1842	-0.5247	-9.3499	50.8667
16	7.9375	-2.8316	-2.7519	1.0052	0.9772	0.9509	0.8682	0.945	1.5083	-0.5161	-0.2861	-0.3016	-0.7454	-0.2551	-0.55	0.5024	0.0877	0.0856	0.4175	0.0445	0.5239	22.0824	-5.3609	42.0154
17	5.2398	-2.8579	0.6928	1.6251	-0.2222	0.0609	0.4129	0.6487	0.5692	-0.0991	-0.2944	-0.4358	0.002	-0.0053	-0.0964	0.1912	0.0148	0.0008	0.169	0.0139	0.24	14.5608	-7.9351	45.3216
18	1.124	-0.3647	0.2125	1.4125	1.0752	1.686	0.3745	-0.1014	0.1896	0.6422	-0.1699	0.0312	-0.6821	-0.1977	-0.1491	0.5475	-0.0053	0.0678	0.1778	0.0235	0.2249	-7.9203	5.5914	54.0874
19	9.1194	7.357	-9.5668	9.903	-9.7499	2.0058	0.0389	0.8741	0.7547	-0.4091	0.3429	0.9172	-0.4	-1.1727	-0.3852	0.3175	0.1419	-0.001	0.3954	0.0436	0.3194	-16.7878	3.3783	40.4397
20	1.0878	-0.1579	-0.775	0.5631	-1.836	7.9269	-0.1478	-0.0928	-0.0649	0.1734	0.1742	-0.0739	-0.6573	-0.467	-0.0059	0.3414	0.038	-0.0185	0.3518	0.0197	0.2372	-13.3966	5.2614	18.0226

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 54:140 )
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 141:496 )
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 497:862 )
4	X-RAY DIFFRACTION	4	(CHAIN B AND RESID 2:29 )
5	X-RAY DIFFRACTION	5	(CHAIN B AND RESID 30:50 )
6	X-RAY DIFFRACTION	6	(CHAIN B AND RESID 51:65 )
7	X-RAY DIFFRACTION	7	(CHAIN B AND RESID 66:89 )
8	X-RAY DIFFRACTION	8	(CHAIN B AND RESID 90:128 )
9	X-RAY DIFFRACTION	9	(CHAIN B AND RESID 129:204 )
10	X-RAY DIFFRACTION	10	(CHAIN B AND RESID 205:223 )
11	X-RAY DIFFRACTION	11	(CHAIN B AND RESID 224:235 )
12	X-RAY DIFFRACTION	12	(CHAIN C AND RESID 25:496 )
13	X-RAY DIFFRACTION	13	(CHAIN C AND RESID 497:862 )
14	X-RAY DIFFRACTION	14	(CHAIN D AND RESID 2:29 )
15	X-RAY DIFFRACTION	15	(CHAIN D AND RESID 30:50 )
16	X-RAY DIFFRACTION	16	(CHAIN D AND RESID 51:70 )
17	X-RAY DIFFRACTION	17	(CHAIN D AND RESID 71:100 )
18	X-RAY DIFFRACTION	18	(CHAIN D AND RESID 101:193 )
19	X-RAY DIFFRACTION	19	(CHAIN D AND RESID 194:204 )
20	X-RAY DIFFRACTION	20	(CHAIN D AND RESID 205:239 )

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