PDB-5nnr: Structure of Naa15/Naa10 bound to HypK-THB

ID or keywords:

Entry

Database: PDB / ID: 5nnr

Title

Structure of Naa15/Naa10 bound to HypK-THB

Components

HypK
N-terminal acetyltransferase-like protein
Naa10

Keywords

TRANSFERASE / N-acetylation / NATs / Naa15 / Naa10 / HypK / NatA / Nat1 / Ard1

Function / homology

Function and homology information

NatA complex / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / transferase activity / cytoplasm
Similarity search - Function

Biological species

Chaetomium thermophilum (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.1 Å

Authors

Weyer, F.A. / Gumiero, A. / Kopp, J. / Sinning, I.

Funding support

Germany, 3items

Citation

Journal: Nat Commun / Year: 2017
Title: Structural basis of HypK regulating N-terminal acetylation by the NatA complex.
Authors: Weyer, F.A. / Gumiero, A. / Lapouge, K. / Bange, G. / Kopp, J. / Sinning, I.

History

Deposition	Apr 10, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 14, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2024	Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5nnr.cif.gz	770 KB	Display	PDBx/mmCIF format
PDB format	pdb5nnr.ent.gz	638.2 KB	Display	PDB format
PDBx/mmJSON format	5nnr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5nnr_validation.pdf.gz	487.5 KB	Display	wwPDB validaton report
Full document	5nnr_full_validation.pdf.gz	515.5 KB	Display
Data in XML	5nnr_validation.xml.gz	62.7 KB	Display
Data in CIF	5nnr_validation.cif.gz	84.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nn/5nnr ftp://data.pdbj.org/pub/pdb/validation_reports/nn/5nnr	HTTPS FTP

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Related structure data

Related structure data	5nnpSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5nnp-2 5nnp-1 6vde-2 1nj2-1 4n3s-d 4ncf-d 21541 6yhh-d 4hdh-d 6iih-d 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 (3) #97 - Jan 2008 Circadian Clock Proteins similarity (4) #230 - Feb 2019 Initiation Factor eIF4E similarity (3) #166 - Oct 2013 Proteasome similarity (2)

Deposited unit

A: N-terminal acetyltransferase-like protein

B: Naa10

C: HypK

D: N-terminal acetyltransferase-like protein

E: Naa10

F: HypK

245 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: N-terminal acetyltransferase-like protein

B: Naa10

C: HypK

defined by author&software
Evidence: gel filtration, isothermal titration calorimetry, light scattering
123 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: N-terminal acetyltransferase-like protein

E: Naa10

F: HypK

defined by author&software
Evidence: gel filtration, light scattering, isothermal titration calorimetry
123 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	85.348, 85.348, 319.626
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	145
Space group name H-M	P3₂

#1: Protein	N-terminal acetyltransferase-like protein / Naa15 Mass: 85742.508 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0031530 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S4M4
#2: Protein	Naa10 Mass: 22440.535 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0063490 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SEE8
#3: Protein	HypK Mass: 14363.419 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0058830 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SCY6

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.75 Å³/Da / Density % sol: 55.22 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2 M Mg(NO3)2 20% PEG 3350 protein concentration 25 - 30 mg/ml

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978333 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 28, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978333 Å / Relative weight: 1
Reflection	Resolution: 3.1→48.35 Å / Num. obs: 47332 / % possible obs: 100 % / Redundancy: 11.7 % / R_pim(I) all: 0.065 / Net I/σ(I): 13.8
Reflection shell	Resolution: 3.1→3.21 Å / Redundancy: 11.8 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4684 / R_pim(I) all: 0.977 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.8.4_1496	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5NNP

5nnp

Resolution: 3.1→42.299 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 32.84

	R_factor	Num. reflection	% reflection
R_free	0.2717	2376	5.03 %
R_work	0.2297	-	-
obs	0.2318	47214	99.89 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 3.1→42.299 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14720	0	0	0	14720

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	15013
X-RAY DIFFRACTION	f_angle_d	1.452	20240
X-RAY DIFFRACTION	f_dihedral_angle_d	14.215	5691
X-RAY DIFFRACTION	f_chiral_restr	0.068	2207
X-RAY DIFFRACTION	f_plane_restr	0.009	2595

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 (%)
3.1003-3.1635	0.4085	138	0.3576	2704	X-RAY DIFFRACTION	100
3.1635-3.2323	0.3708	153	0.3375	2587	X-RAY DIFFRACTION	100
3.2323-3.3075	0.3592	145	0.3271	2619	X-RAY DIFFRACTION	100
3.3075-3.3901	0.3575	138	0.2975	2647	X-RAY DIFFRACTION	100
3.3901-3.4818	0.3413	127	0.3006	2632	X-RAY DIFFRACTION	100
3.4818-3.5842	0.3068	120	0.2875	2715	X-RAY DIFFRACTION	100
3.5842-3.6998	0.3528	141	0.2825	2643	X-RAY DIFFRACTION	100
3.6998-3.8319	0.3174	150	0.2711	2601	X-RAY DIFFRACTION	100
3.8319-3.9853	0.356	155	0.2563	2603	X-RAY DIFFRACTION	100
3.9853-4.1665	0.2797	140	0.2508	2597	X-RAY DIFFRACTION	100
4.1665-4.3859	0.251	152	0.2271	2639	X-RAY DIFFRACTION	100
4.3859-4.6604	0.2502	137	0.2064	2650	X-RAY DIFFRACTION	100
4.6604-5.0197	0.2443	136	0.2094	2703	X-RAY DIFFRACTION	100
5.0197-5.5239	0.2901	140	0.2132	2576	X-RAY DIFFRACTION	100
5.5239-6.3209	0.3098	127	0.2375	2645	X-RAY DIFFRACTION	100
6.3209-7.955	0.286	132	0.209	2659	X-RAY DIFFRACTION	100
7.955-42.3026	0.1714	145	0.1637	2618	X-RAY DIFFRACTION	99

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	2.6472	-0.9872	-0.595	2.4772	-0.3974	4.0617	-0.3585	-0.7895	-1.1186	-0.2767	-0.2702	0.1073	0.3283	-0.9766	0.3236	0.6699	0.6975	0.201	2.0645	0.4803	1.488	22.3774	28.3582	-45.1006
2	1.7002	-0.3785	0.2284	1.7863	-0.2709	2.1438	-0.1654	0.369	0.2179	0.5995	-0.4427	0.1753	-1.0112	0.1553	0.3618	0.6133	-0.2013	-0.0887	2.6691	-0.1883	0.8125	-15.6491	44.813	-13.5014
3	2.568	-0.9333	0.6029	1.2862	0.1224	3.4296	0.1066	-0.3204	-0.4607	0.164	-0.5988	0.1242	1.1381	0.7949	0.2911	0.3345	0.3758	0.0303	2.1334	0.2136	0.8719	-11.106	18.4824	-21.2481
4	3.0766	-0.787	-0.4412	2.7358	0.9756	1.9341	-0.484	-0.0959	0.574	-0.0649	-0.1809	0.3079	-0.5816	0.4131	0.6011	0.4394	0.0815	-0.22	1.793	0.0746	0.8007	-13.0079	41.1609	-26.6974
5	9.7469	-6.6114	5.0109	7.7856	-0.682	4.9909	-0.365	-1.0597	-1.5243	0.8424	0.5323	1.6603	0.0988	-0.6171	-0.1053	0.5524	0.2123	-0.0876	1.8022	0.0996	1.2141	-17.8921	37.1331	-18.6099
6	4.5745	-5.5628	-4.988	6.7641	6.0653	5.4387	-0.4218	-1.0005	0.774	1.434	-0.1199	-1.9334	-0.8679	1.0899	0.4143	2.2718	-0.341	-0.3362	1.6728	0.1392	1.5441	-5.1124	58.8406	-38.6132
7	3.7099	0.5987	-0.0299	4.7324	-0.9662	5.117	-0.7371	1.0033	0.6468	-0.152	0.314	0.9401	-0.7208	-0.2771	0.2823	0.6829	0.3921	-0.2876	2.1833	-0.1263	1.2503	-24.2978	45.1816	-28.8524
8	5.5388	2.3871	-0.469	3.3132	-2.0542	2.2502	-0.2127	0.2345	1.0973	0.0299	-0.266	0.2981	-1.2819	0.525	0.5399	1.2961	0.0976	-0.6335	1.6877	0.0802	1.0488	-16.8321	55.5324	-29.3039
9	6.8336	4.2181	5.7376	4.65	5.0168	5.8807	0.1531	-1.9151	-0.8346	2.3758	-0.3267	1.389	1.8494	-1.9709	0.0554	1.3414	-0.1427	-0.1041	1.8922	0.5773	1.5453	-29.7313	51.0663	-37.666
10	7.0423	0.392	1.922	2.0505	2.6003	8.9946	0.3663	0.1271	-0.4862	0.6156	0.3424	-0.028	0.8832	0.0684	-0.6372	1.5678	0.0284	-0.445	1.5326	0.2505	1.0907	-20.8425	52.7369	-43.0188
11	0.1169	-0.3905	-0.4711	1.3048	1.5742	1.899	0.049	-0.4525	0.5037	0.5994	0.161	-0.6249	-0.7004	0.5869	-0.1281	2.4421	-0.1236	-0.6251	1.711	0.3177	1.9148	-14.9555	69.6951	-21.3273
12	6.6788	-4.7902	4.1344	5.4981	-6.0654	7.2188	-1.2446	-2.9866	4.3292	2.6102	1.4777	-1.2491	-3.8021	-1.0433	-0.33	2.0237	0.2935	0.0785	2.1522	0.1669	2.3336	-5.3312	40.4854	-45.6233
13	0.9096	0.1606	-0.9377	0.0507	-0.1899	0.9923	-1.2934	-0.0364	2.4282	-0.7404	-0.276	0.9141	-0.8304	-0.7071	1.6216	2.1653	0.1681	-0.2987	2.7439	0.0481	2.2096	2.9265	46.5238	-35.9415
14	4.6108	-1.0066	-3.4217	1.0216	1.4934	3.3736	-0.0128	-0.4865	-0.8394	0.0729	0.2628	0.3388	0.7763	-0.5611	-0.1971	2.6912	-0.9134	-0.5745	2.5161	-0.0331	2.6369	25.219	55.5424	-15.3776
15	2.2606	1.602	0.1085	1.2218	-0.0372	0.1396	-0.077	-0.0083	-0.2603	0.2256	0.2117	-0.8168	0.0838	0.3196	-0.3371	1.0836	0.3935	0.1107	3.2885	0.5182	1.4225	13.7616	15.7774	-4.4512
16	1.524	-0.4488	0.9423	2.4831	-0.1663	2.6698	-0.2097	1.2084	1.0751	0.4429	-0.429	0.2248	-0.3541	-0.7725	0.3662	0.6696	-0.6581	-0.2084	2.0382	0.508	1.4294	22.4838	20.9002	54.4043
17	1.5959	-0.011	-0.6948	2.1351	0.3934	4.5372	-0.0215	0.414	-0.0997	-0.4734	-0.66	0.227	0.6941	0.3028	0.4294	0.0528	-0.0066	0.0667	2.1312	0.0075	0.7879	-15.5741	10.885	27.5504
18	1.7987	0.5129	-1.1266	2.3531	-0.0953	2.9226	0.2093	0.4527	0.311	0.476	-0.3551	0.1358	-1.1368	1.195	0.1533	0.943	-0.6326	-0.096	2.3882	0.4037	0.9919	-4.3976	40.6716	19.2217
19	6.632	2.1663	-2.6438	4.3688	0.6337	2.0411	-0.3239	0.5717	0.2796	-0.32	-0.3257	0.3119	0.3133	0.3241	0.4324	0.2574	-0.0752	0.1586	1.7991	0.0857	0.6869	-14.6202	9.4017	33.1333
20	1.9101	-0.6226	0.7556	2.7452	-2.8005	6.0327	-0.4731	-0.18	-0.4478	0.1767	-0.5412	-0.1838	1.1246	0.8634	0.7584	0.8162	-0.2143	0.3516	1.7394	0.074	0.8755	-18.2401	-0.351	41.0959
21	3.2248	-1.2755	1.2072	2.3545	-1.4805	1.3829	0.038	0.106	-1.0367	0.1984	-0.4301	0.1771	0.7308	0.5344	0.3154	1.417	-0.055	0.6244	1.7697	0.0734	1.0615	-16.8424	-6.3805	38.2295
22	1.9999	-7.0726	-7.3997	4.7928	5.0148	5.2472	0.1486	0.6767	0.039	-0.37	-0.6212	1.9357	-0.5579	-2.4443	0.3057	1.1364	0.0086	0.2042	2.0589	0.5348	1.2635	-30.0166	-1.4929	47.2431
23	4.9946	-0.8593	-1.4945	4.0682	0.2034	8.9952	0.2755	-0.2528	0.3565	-0.8761	0.505	-0.5283	-0.6895	0.211	-0.5059	1.4909	-0.0655	0.5438	1.474	0.225	1.0322	-20.9471	-3.3906	52.1793
24	0.0126	0.2356	0.2132	4.7953	4.32	3.8925	0.2488	1.0049	-0.5787	-1.5761	0.1901	-1.2082	-0.0161	0.875	-0.4636	2.6356	-0.1674	0.6982	1.9876	-0.0573	1.5407	-14.1242	-21.6731	28.2228
25	0.1399	-0.0092	-0.1016	0.0005	0.0063	0.0738	0.2293	-1.2091	1.3595	0.1279	0.2876	0.0321	0.307	0.5993	-0.478	2.6481	0.0351	-0.2573	2.863	0.5919	2.273	-4.027	6.7303	49.1938
26	4.5487	-4.2782	-2.9669	4.0256	2.8689	3.3386	0.4475	0.9856	-0.0531	-1.3412	-0.4783	-1.2212	0.5572	0.7015	0.1653	2.0291	0.4054	0.2546	2.9565	-0.3295	2.6712	23.2144	-6.3179	26.9649
27	1.3423	-0.3743	0.4508	0.2003	-0.1356	1.1045	-0.4295	-0.0874	-0.0474	0.1303	-0.5409	-0.9892	-0.276	0.7832	0.6263	1.1016	-0.2864	-0.1251	3.5467	0.6002	1.457	13.0942	33.8712	13.8002

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 90 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 91 through 420 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 421 through 743 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 2 through 46 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 47 through 69 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 70 through 78 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 79 through 95 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 96 through 122 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 123 through 134 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 135 through 161 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 162 through 175 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 26 through 32 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 33 through 58 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 59 through 68 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 69 through 125 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 4 through 89 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 90 through 571 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 572 through 742 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 2 through 69 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 70 through 95 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 96 through 122 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 123 through 134 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 135 through 161 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 162 through 179 )
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 32 through 41 )
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 42 through 68 )
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 69 through 125 )

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