PDB-6k0x: Structure of N6AMT1-TRMT112 Complex with SAM

ID or keywords:

Entry

Database: PDB / ID: 6k0x

Title

Structure of N6AMT1-TRMT112 Complex with SAM

Components

Methyltransferase N6AMT1
Multifunctional methyltransferase subunit TRM112-like protein

Keywords

GENE REGULATION /

Methylase /

Complex /

Structural Genomics /

Structural Genomics Consortium / SGC

Function / homology

Function and homology information

arsonoacetate metabolic process /

methylarsonite methyltransferase activity / histone H4K12 methyltransferase activity / eRF1 methyltransferase complex / protein-glutamine N-methyltransferase activity / tRNA N2-guanine methylation / peptidyl-glutamine methylation / rRNA (guanine-N7)-methylation / toxin metabolic process /

site-specific DNA-methyltransferase (adenine-specific) activity ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Guo, Q. / Liao, S. / Xu, C. / Structural Genomics Consortium (SGC)

Citation

Journal: To Be Published
Title: Structure of HEMK2-TRM112 Complex with SAM
Authors: Guo, Q. / Liao, S. / Xu, C.

History

Deposition	May 7, 2019	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 5, 2019	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6k0x.cif.gz	142.7 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k0/6k0x ftp://data.pdbj.org/pub/pdb/validation_reports/k0/6k0x	HTTPS FTP

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Related structure data

Related structure data	3q87S 4qtuS S: Starting model for refinement
Similar structure data	3bkz-d 6khs-d 3sc6-2 6h1d-d 4mx6-d 2g20-2 6p8s-2 4ej0-10 5ttv-d 4fkg-d 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	#60 - Dec 2004 Ubiquitin similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1)

Deposited unit

A: Methyltransferase N6AMT1

B: Multifunctional methyltransferase subunit TRM112-like protein

hetero molecules

37.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	109.607, 109.607, 130.368
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	178
Space group name H-M	P6₁22

Components on special symmetry positions

ID	Model	Components
1	1	B-247- HOH

#1: Protein	Methyltransferase N6AMT1 Mass: 23048.354 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: N6AMT1 Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: Q9Y5N5, Transferases; Transferring one-carbon groups; Methyltransferases, site-specific DNA-methyltransferase (adenine-specific)
#2: Protein	Multifunctional methyltransferase subunit TRM112-like protein Mass: 14215.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRMT112 Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: Q9UI30
#3: Chemical	ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₅H₂₂N₆O₅S / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 117 / 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: 3.03 Å³/Da / Density % sol: 59.45 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.2M ammonium acetate 0.1M sodium citrate tribasic dihydrate PH 5.6 30% Polyethylene glycol 4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 29, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.2→50 Å / Num. obs: 24031 / % possible obs: 99.8 % / Redundancy: 36.3 % / Net I/σ(I): 28
Reflection shell	Resolution: 2.2→2.24 Å / Num. unique obs: 2346

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Processing

Software

Name	Version	Classification
PHENIX	(1.14_3260: ???)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3Q87,4QTU

3q87

4qtu

Resolution: 2.2→34.05 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.35

	R_factor	Num. reflection	% reflection
R_free	0.2135	1264	5.26 %
R_work	0.1744	-	-
obs	0.1764	24031	99.8 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.2→34.05 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2405	0	27	117	2549

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2511
X-RAY DIFFRACTION	f_angle_d	0.917	3426
X-RAY DIFFRACTION	f_dihedral_angle_d	17.659	1538
X-RAY DIFFRACTION	f_chiral_restr	0.055	404
X-RAY DIFFRACTION	f_plane_restr	0.006	444

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 (%)
2.2001-2.2881	0.2428	125	0.1988	2481	X-RAY DIFFRACTION	99
2.2881-2.3922	0.3125	141	0.1945	2462	X-RAY DIFFRACTION	100
2.3922-2.5183	0.2453	137	0.1985	2484	X-RAY DIFFRACTION	100
2.5183-2.676	0.2664	127	0.2054	2509	X-RAY DIFFRACTION	100
2.676-2.8826	0.2347	142	0.2006	2504	X-RAY DIFFRACTION	100
2.8826-3.1725	0.2398	147	0.1906	2496	X-RAY DIFFRACTION	100
3.1725-3.6311	0.173	140	0.157	2549	X-RAY DIFFRACTION	100
3.6311-4.573	0.1733	146	0.1348	2577	X-RAY DIFFRACTION	100
4.573-34.0544	0.2063	159	0.18	2705	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	5.3906	0.5782	0.8112	7.8577	0.526	3.2195	0.0252	-0.2991	-0.3313	-0.0389	0.0349	-0.1816	0.3309	0.2697	-0.03	0.246	0.0894	0.028	0.3762	0.0343	0.2366	22.8142	36.5728	75.3374
2	3.9659	-0.8943	-0.75	2.5332	0.6796	2.6027	-0.0621	-0.0443	0.0543	0.1114	0.0431	-0.09	0.0569	0.1243	0.0214	0.159	0.0381	0.0002	0.1911	0.0143	0.1931	12.4032	44.5188	78.4415
3	6.8691	-0.1777	-2.4483	2.6614	0.3782	3.1492	-0.535	-0.0331	-1.1978	0.2537	0.3599	0.4448	1.0023	-0.669	0.1917	0.7313	0.0563	0.0645	0.8141	-0.0794	0.6518	9.585	27.3648	65.9344
4	3.8842	-1.2668	-0.842	2.9181	-0.0497	3.1609	0.1092	0.4332	0.0396	-0.3021	-0.1826	-0.1903	0.1091	-0.0479	0.0804	0.2466	0.0556	0.0499	0.2952	0.0289	0.2244	18.3159	40.8936	61.9016
5	3.0706	0.3387	-0.0251	5.0784	1.0374	3.6562	0.0326	0.4034	-0.0001	-0.6171	-0.0277	0.232	-0.3121	-0.1544	-0.0111	0.1863	0.0239	0.0051	0.1653	0.0009	0.184	-3.7343	50.7211	75.4032
6	2.7835	-0.1822	0.2849	5.7984	-2.2697	9.7965	0.1176	-0.371	-0.4446	0.354	0.0701	0.3276	-0.0002	-0.6898	-0.1389	0.1936	-0.0467	0.0233	0.1688	0.01	0.2102	-4.2156	46.9849	91.614
7	5.6648	-1.5637	3.8195	3.9312	-0.9132	8.3611	-0.1556	0.1601	-0.1202	-0.1144	0.1328	-0.4686	-0.7011	1.091	-0.0274	0.2978	-0.1258	0.0043	0.3513	0.0206	0.2956	12.2077	59.2024	85.9202
8	8.0186	1.3771	-4.7348	2.7399	-5.0269	9.9141	0.1843	-0.0427	0.6589	0.2995	0.0904	0.7654	-0.5181	-0.7312	-0.3268	0.308	0.0344	-0.0179	0.2648	-0.0452	0.3579	-4.2091	59.3425	84.1651
9	3.6173	-1.1961	1.3914	4	1.1494	3.1001	-0.0166	0.0703	0.4496	0.284	0.3323	0.7532	-0.642	0.2842	-0.2961	0.5665	-0.0523	0.0065	0.2156	-0.0517	0.2774	-1.4822	64.5647	89.833
10	6.2884	1.9572	0.9288	5.7601	0.2653	3.6696	0.1038	-0.3364	0.1455	0.9279	-0.3043	-0.8515	-0.8744	0.733	0.1304	0.4662	-0.1086	-0.0725	0.2615	0.0133	0.2277	8.3346	64.0683	90.159
11	5.89	0.712	4.0707	3.839	1.3918	7.0836	0.1734	0.0492	-0.2182	-0.0372	-0.07	0.0812	-0.0317	-0.245	-0.1529	0.1353	0.0098	0.0374	0.1952	0.017	0.2139	-6.4806	45.6978	82.4477
12	4.408	1.5205	4.2238	5.5802	1.6321	4.4031	0.407	0.571	-0.9332	-0.5118	0.0908	0.2649	0.9909	0.1032	-0.372	0.2844	0.0256	-0.0264	0.3261	-0.0765	0.2785	-3.4542	38.6371	76.3248

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 20 through 43 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 44 through 122 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 123 through 149 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 150 through 214 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1 through 23 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 24 through 32 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 33 through 48 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 49 through 60 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 61 through 73 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 74 through 89 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 90 through 109 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 110 through 123 )

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