PDB-6dnz: Trypanosoma brucei PRMT1 enzyme-prozyme heterotetrameric complex ...

ID or keywords:

Entry

Database: PDB / ID: 6dnz

Title

Trypanosoma brucei PRMT1 enzyme-prozyme heterotetrameric complex with AdoHcy

Components

(Arginine N-methyltransferase, ...) x 2

Keywords

GENE REGULATION / protein arginine methyltransferase / prozyme / teterameric complex / PRMT1

Function / homology

Function and homology information

arginine N-methyltransferase activity / peptidyl-arginine methylation, to asymmetrical-dimethyl arginine / protein-arginine N-methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation / nucleus / cytoplasm
Similarity search - Function

Biological species

Trypanosoma brucei brucei TREU927 (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.384 Å

Authors

Hashimoto, H. / Kafkova, L. / Jordan, K. / Read, L.K. / Debler, E.W.

Funding support

United States, 1items

Citation

Journal: J.Mol.Biol. / Year: 2020
Title: Structural Basis of Protein Arginine Methyltransferase Activation by a Catalytically Dead Homolog (Prozyme).
Authors: Hashimoto, H. / Kafkova, L. / Raczkowski, A. / Jordan, K.D. / Read, L.K. / Debler, E.W.

History

Deposition	Jun 8, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 12, 2019	Provider: repository / Type: Initial release
Revision 1.1	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Dec 25, 2019	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3	Feb 12, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6dnz.cif.gz	725.7 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	6dnz.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6dnz_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	6dnz_full_validation.pdf.gz	1 MB	Display
Data in XML	6dnz_validation.xml.gz	45.6 KB	Display
Data in CIF	6dnz_validation.cif.gz	63.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dn/6dnz ftp://data.pdbj.org/pub/pdb/validation_reports/dn/6dnz	HTTPS FTP

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Related structure data

Similar structure data	1724 3saj-d 5hys-2 6qer-d 2wmc-d 4n0q-d 6uuh-d 3kl5-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

Deposited unit

A: Arginine N-methyltransferase, putative

B: Arginine N-methyltransferase, putative

C: Arginine N-methyltransferase, putative

D: Arginine N-methyltransferase, putative

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: SAXS, gel filtration, light scattering

Unit cell

Length a, b, c (Å)	196.582, 65.904, 141.028
Angle α, β, γ (deg.)	90.00, 106.90, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-535- HOH

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Arginine N-methyltransferase, ... , 2 types, 4 molecules ACBD

#1: Protein	Arginine N-methyltransferase, putative Mass: 39677.098 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei TREU927 (eukaryote) Gene: TB927.1.4690 / Plasmid: ED321 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-codonplus RIL / References: UniProt: Q4GYA9*PLUS
#2: Protein	Arginine N-methyltransferase, putative Mass: 42809.770 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei TREU927 (eukaryote) Strain: 927/4 GUTat10.1 / Gene: Tb10.70.3860 / Plasmid: ED321 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-codonplus RIL / References: UniProt: Q38BP3*PLUS

#1: Protein

Arginine N-methyltransferase, putative

Mass: 39677.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Trypanosoma brucei brucei TREU927 (eukaryote)
Gene: TB927.1.4690 / Plasmid: ED321 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-codonplus RIL / References: UniProt: Q4GYA9*PLUS

#2: Protein

Arginine N-methyltransferase, putative

Mass: 42809.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Trypanosoma brucei brucei TREU927 (eukaryote)
Strain: 927/4 GUTat10.1 / Gene: Tb10.70.3860 / Plasmid: ED321 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-codonplus RIL / References: UniProt: Q38BP3*PLUS

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Non-polymers , 4 types, 219 molecules

#3: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S
#4: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.68 Å³/Da / Density % sol: 54.13 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 7% (w/v) PEG 4000, 0.1 M Tris-HCl, pH 7.4

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 6, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.384→50 Å / Num. obs: 97551 / % possible obs: 88.7 % / Observed criterion σ(I): -3 / Redundancy: 10.5 % / CC_1/2: 0.997 / R_merge(I) obs: 0.103 / Net I/σ(I): 22.2
Reflection shell	Resolution: 2.384→2.49 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.773 / Num. unique obs: 3757 / CC_1/2: 0.651 / % possible all: 54

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Processing

Software

Name	Version	Classification
PHENIX	(dev_3071: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
AutoSol		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.384→50 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.57

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2217	3499	3.59 %	Random
R_work	0.1875	-	-	-
obs	0.1887	97551	72.17 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.384→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9986	0	80	213	10279

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	10274
X-RAY DIFFRACTION	f_angle_d	0.522	13958
X-RAY DIFFRACTION	f_dihedral_angle_d	12.08	6116
X-RAY DIFFRACTION	f_chiral_restr	0.044	1602
X-RAY DIFFRACTION	f_plane_restr	0.003	1792

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 (%)
2.384-2.4166	0.3936	24	0.3262	653	X-RAY DIFFRACTION	12
2.4166-2.4512	0.3539	42	0.2899	1094	X-RAY DIFFRACTION	21
2.4512-2.4877	0.4219	43	0.2784	1328	X-RAY DIFFRACTION	26
2.4877-2.5266	0.3447	63	0.2817	1627	X-RAY DIFFRACTION	31
2.5266-2.568	0.2662	66	0.2814	1865	X-RAY DIFFRACTION	37
2.568-2.6123	0.3026	86	0.2629	2195	X-RAY DIFFRACTION	42
2.6123-2.6598	0.2898	95	0.2588	2544	X-RAY DIFFRACTION	49
2.6598-2.711	0.3097	109	0.2579	2757	X-RAY DIFFRACTION	54
2.711-2.7663	0.3121	108	0.2705	3095	X-RAY DIFFRACTION	59
2.7663-2.8264	0.3262	128	0.2598	3442	X-RAY DIFFRACTION	66
2.8264-2.8922	0.2872	140	0.243	3850	X-RAY DIFFRACTION	73
2.8922-2.9645	0.2718	156	0.2382	4135	X-RAY DIFFRACTION	80
2.9645-3.0446	0.3123	171	0.2309	4456	X-RAY DIFFRACTION	86
3.0446-3.1342	0.2741	178	0.229	4695	X-RAY DIFFRACTION	90
3.1342-3.2354	0.233	182	0.217	4818	X-RAY DIFFRACTION	93
3.2354-3.351	0.2443	177	0.2127	4943	X-RAY DIFFRACTION	95
3.351-3.4851	0.2347	185	0.2071	5119	X-RAY DIFFRACTION	97
3.4851-3.6437	0.2178	196	0.1808	5154	X-RAY DIFFRACTION	99
3.6437-3.8357	0.235	194	0.1685	5204	X-RAY DIFFRACTION	100
3.8357-4.0759	0.1845	198	0.1553	5187	X-RAY DIFFRACTION	100
4.0759-4.3904	0.1652	197	0.1393	5195	X-RAY DIFFRACTION	99
4.3904-4.8319	0.1721	186	0.1284	5155	X-RAY DIFFRACTION	99
4.8319-5.5303	0.145	199	0.1396	5217	X-RAY DIFFRACTION	100
5.5303-6.9644	0.203	187	0.1871	5140	X-RAY DIFFRACTION	99
6.9644-49.056	0.2167	189	0.1827	5184	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	1.741	0.7417	0.2187	2.0151	-0.0011	3.0022	0.1157	0.1926	0.1362	-0.2097	-0.0839	-0.1873	-0.4789	0.0877	-0.0266	0.3071	0.0071	0.0161	0.2217	0.0958	0.2204	85.9547	29.2172	40.4639
2	0.6579	-0.4058	-0.3099	1.4278	0.4247	1.4528	-0.0264	-0.0591	-0.0477	-0.05	0.0432	-0.1596	0.0979	0.278	0.0018	0.2378	0.0012	0.0094	0.2727	0.1052	0.2488	92.9787	9.9551	51.3387
3	2.8418	-0.5708	1.0165	4.3163	-0.2314	2.6327	-0.129	-0.326	-0.3257	0.0452	0.2246	-0.6859	0.5678	0.3333	-0.0456	0.3992	0.1427	0.0477	0.3155	0.0598	0.3835	96.7727	0.1734	55.0953
4	2.3831	-0.911	0.1575	1.1373	-0.203	1.5611	-0.1508	0.0049	-0.3702	0.0821	-0.0075	-0.0894	0.207	0.5074	0.1694	0.2713	0.0744	-0.0016	0.402	0.0694	0.2781	108.3232	-3.0921	21.0649
5	1.1246	-0.925	-1.8575	4.3041	4.7316	5.9618	-0.0498	-0.0421	0.1624	-0.1344	0.0957	-0.0043	-0.4189	0.3858	-0.0489	0.3112	-0.0015	-0.0222	0.453	0.0594	0.2135	83.4037	19.7615	26.0783
6	3.6003	-0.8204	-0.3308	1.2376	-0.3123	1.92	-0.0291	0.0602	-0.1413	-0.0608	0.0267	0.0331	-0.0295	0.0121	0.001	0.2064	0.0072	0.0047	0.2902	-0.0177	0.0818	92.1673	7.8159	9.39
7	1.7928	-0.2687	0.8651	2.5343	0.1004	1.5962	0.0652	0.1393	0.2791	-0.1431	0.0341	0.1133	-0.6284	-0.0639	-0.0725	0.3996	0.1457	-0.008	0.3505	0.1099	0.2862	60.1793	28.4183	22.3304
8	2.8066	0.3239	-1.0158	0.5303	-0.0211	2.5962	0.0297	0.3238	-0.4528	0.0256	-0.176	0.2641	0.1959	-0.251	0.1238	0.2855	0.0901	-0.0358	0.3217	-0.0314	0.4279	44.6644	9.5627	25.9775
9	5.087	-0.023	0.5367	6.1404	-2.2539	7.1836	0.1043	0.7793	-0.5409	-0.1528	0.2142	0.6738	0.5971	-0.8153	-0.2706	0.2758	-0.026	0.0294	0.6253	-0.1041	0.6397	32.336	4.8308	25.2523
10	6.4884	-0.1286	-1.034	2.4977	0.8248	3.0198	-0.1154	-0.5575	-0.2793	0.2587	-0.0682	0.2244	0.4089	-0.5921	0.1355	0.3602	0.0094	0.0505	0.5347	0.0463	0.4555	26.9046	19.1043	56.614
11	6.7905	0.4612	0.7416	2.0307	1.7096	4.1406	0.4353	-0.0028	-0.153	-0.0798	-0.7042	0.3743	-0.1605	-0.7094	0.345	0.3573	0.0615	0.0201	0.5419	0.0092	0.4229	19.4195	22.1689	46.9951
12	6.3337	2.9628	-0.1285	1.504	0.2925	1.6237	0.208	-0.5719	0.4899	0.023	-0.0461	0.295	-0.0694	-0.3935	-0.1776	0.3821	0.1983	0.021	0.6551	0.0282	0.4479	28.9345	31.7782	56.4212
13	2.2655	0.6542	0.1756	1.1201	0.0009	1.0613	0.0605	-0.2761	0.357	0.0135	-0.1363	0.3511	-0.2165	-0.4252	0.068	0.3275	0.1473	-0.0648	0.4063	-0.0535	0.3065	40.503	31.8865	56.4041
14	1.5632	0.2807	-2.7616	1.6828	-1.2938	7.6264	0.1838	0.1695	0.267	-0.0941	-0.237	0.0041	-0.4779	-0.2408	0.0239	0.3881	0.1447	-0.0982	0.3213	0.0491	0.3316	60.8364	29.3378	39.7748
15	3.1568	-0.6392	-0.0009	1.4199	0.403	1.208	0.0569	-0.2014	0.2808	-0.0859	-0.2205	0.2526	-0.3481	-0.3635	0.0606	0.25	0.1147	0.0069	0.2843	-0.0707	0.2493	50.2179	34.0044	58.9467

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 20 through 113 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 114 through 276 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 277 through 345 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 71 through 221 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 222 through 250 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 251 through 389 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 20 through 113 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 114 through 303 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 304 through 345 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 71 through 128 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 129 through 159 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 160 through 180 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 181 through 221 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 222 through 250 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 251 through 389 )

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-Non-polymers , 4 types, 219 molecules

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Arginine N-methyltransferase, ... , 2 types, 4 molecules ACBD

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Non-polymers , 4 types, 219 molecules

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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