PDB-7ov9: Heterodimeric tRNA-Guanine Transglycosylase from mouse, apo-structure

ID or keywords:

Entry

Database: PDB / ID: 7ov9

Title

Heterodimeric tRNA-Guanine Transglycosylase from mouse, apo-structure

Components

(Queuine tRNA-ribosyltransferase ...) x 2

Keywords

TRANSFERASE / TRANSGLYCOSYLASE / TIM BARREL / DIMER / TGT

Function / homology

Function and homology information

tRNA-guanosine34 queuine transglycosylase / tRNA-guanine transglycosylase complex / cytoplasmic side of mitochondrial outer membrane / tRNA-guanosine(34) queuine transglycosylase activity / : / tRNA binding / protein heterodimerization activity / protein homodimerization activity / protein-containing complex / mitochondrion ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Sebastiani, M. / Heine, A. / Reuter, K.

Citation

Journal: Acs Chem.Biol. / Year: 2022
Title: Structural and Biochemical Investigation of the Heterodimeric Murine tRNA-Guanine Transglycosylase.
Authors: Sebastiani, M. / Behrens, C. / Dorr, S. / Gerber, H.D. / Benazza, R. / Hernandez-Alba, O. / Cianferani, S. / Klebe, G. / Heine, A. / Reuter, K.

History

Deposition	Jun 14, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 22, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jun 28, 2023	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Feb 7, 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	7ov9.cif.gz	375.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7ov9.ent.gz	253 KB	Display	PDB format
PDBx/mmJSON format	7ov9.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/ov/7ov9 ftp://data.pdbj.org/pub/pdb/validation_reports/ov/7ov9	HTTPS FTP

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Related structure data

Related structure data	6h62SC 7b2iC 7ovoC 7ovsC 7owzC 6fv5S 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

Deposited unit

A: Queuine tRNA-ribosyltransferase accessory subunit 2

C: Queuine tRNA-ribosyltransferase catalytic subunit 1

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: mass spectrometry

Unit cell

Length a, b, c (Å)	100.257, 100.257, 202.480
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	95
Space group name H-M	P4₃22
Space group name Hall	P4cw2c
Symmetry operation	#1: x,y,z #2: -y,x,z+3/4 #3: y,-x,z+1/4 #4: x,-y,-z+1/2 #5: -x,y,-z #6: -x,-y,z+1/2 #7: y,x,-z+1/4 #8: -y,-x,-z+3/4

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Queuine tRNA-ribosyltransferase ... , 2 types, 2 molecules AC

#1: Protein	Queuine tRNA-ribosyltransferase accessory subunit 2 / Queuine tRNA-ribosyltransferase domain-containing protein 1 Mass: 46710.465 Da / Num. of mol.: 1 / Mutation: M1del Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Qtrt2, Qtrtd1 / Production host: Vibrio natriegens (bacteria) / Variant (production host): Vmax References: UniProt: B8ZXI1, tRNA-guanosine34 preQ1 transglycosylase
#2: Protein	Queuine tRNA-ribosyltransferase catalytic subunit 1 / Guanine insertion enzyme / tRNA-guanine transglycosylase Mass: 43428.980 Da / Num. of mol.: 1 / Mutation: M1_L10del Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Qtrt1, Tgt, Tgut / Production host: Vibrio natriegens (bacteria) / Variant (production host): Vmax References: UniProt: Q9JMA2, tRNA-guanosine34 preQ1 transglycosylase

#1: Protein

Queuine tRNA-ribosyltransferase accessory subunit 2 / Queuine tRNA-ribosyltransferase domain-containing protein 1

Mass: 46710.465 Da / Num. of mol.: 1 / Mutation: M1del
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mus musculus (house mouse) / Gene: Qtrt2, Qtrtd1 / Production host:

Vibrio natriegens (bacteria) / Variant (production host): Vmax
References: UniProt: B8ZXI1, tRNA-guanosine34 preQ1 transglycosylase

#2: Protein

Queuine tRNA-ribosyltransferase catalytic subunit 1 / Guanine insertion enzyme / tRNA-guanine transglycosylase

Mass: 43428.980 Da / Num. of mol.: 1 / Mutation: M1_L10del
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mus musculus (house mouse) / Gene: Qtrt1, Tgt, Tgut / Production host:

Vibrio natriegens (bacteria) / Variant (production host): Vmax
References: UniProt: Q9JMA2, tRNA-guanosine34 preQ1 transglycosylase

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Non-polymers , 6 types, 381 molecules

#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#6: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#7: Chemical	ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₂H₂₆O₇ / Comment: precipitant*YM
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.83 Å³/Da / Density % sol: 56.52 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100 mM Citrate pH 6.5, 700 mM Ammonium sulfate, 1 M Lithium sulfate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 12, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.9→50 Å / Num. obs: 82034 / % possible obs: 99.9 % / Redundancy: 14.57 % / B_iso Wilson estimate: 31.56 Å² / R_sym value: 0.08 / Net I/σ(I): 24.55
Reflection shell	Resolution: 1.9→2.01 Å / Num. unique obs: 13000 / CC_1/2: 0.872

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Processing

Software

Name	Version	Classification
PHENIX	1.14_3260	refinement
Coot	0.8.9	model building
XDS	1.02	data reduction
XDS	1.02	data scaling
PHASER	7.0.047	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6H62, 6FV5

6h62

6fv5

Resolution: 1.9→48.66 Å / SU ML: 0.1974 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.0009 / Stereochemistry target values: CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1993	4102	5 %
R_work	0.1755	77914	-
obs	0.1767	82016	99.93 %

Solvent computation

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

Displacement parameters

B_iso mean: 38.41 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→48.66 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5633	0	97	368	6098

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0064	6026
X-RAY DIFFRACTION	f_angle_d	0.7807	8174
X-RAY DIFFRACTION	f_chiral_restr	0.0519	924
X-RAY DIFFRACTION	f_plane_restr	0.0057	1056
X-RAY DIFFRACTION	f_dihedral_angle_d	17.6585	3611

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 (%)
1.9-1.92	0.3106	136	0.2697	2585	X-RAY DIFFRACTION	98.8
1.92-1.94	0.2362	139	0.2362	2643	X-RAY DIFFRACTION	99.89
1.94-1.97	0.2833	141	0.2204	2672	X-RAY DIFFRACTION	99.89
1.97-2	0.248	139	0.1992	2635	X-RAY DIFFRACTION	99.96
2-2.02	0.2356	138	0.2017	2624	X-RAY DIFFRACTION	99.96
2.02-2.05	0.2631	141	0.1901	2678	X-RAY DIFFRACTION	100
2.05-2.08	0.2326	138	0.1955	2632	X-RAY DIFFRACTION	99.96
2.08-2.11	0.2101	140	0.184	2664	X-RAY DIFFRACTION	100
2.11-2.15	0.2256	140	0.1757	2646	X-RAY DIFFRACTION	100
2.15-2.19	0.2395	139	0.1744	2654	X-RAY DIFFRACTION	99.96
2.19-2.23	0.2044	142	0.1666	2680	X-RAY DIFFRACTION	100
2.23-2.27	0.187	138	0.167	2634	X-RAY DIFFRACTION	99.96
2.27-2.32	0.2351	139	0.1693	2645	X-RAY DIFFRACTION	100
2.32-2.37	0.1969	141	0.1662	2677	X-RAY DIFFRACTION	100
2.37-2.42	0.2855	140	0.1703	2661	X-RAY DIFFRACTION	99.96
2.42-2.48	0.1968	141	0.1717	2681	X-RAY DIFFRACTION	100
2.48-2.55	0.2378	141	0.1725	2675	X-RAY DIFFRACTION	99.96
2.55-2.62	0.2213	141	0.173	2680	X-RAY DIFFRACTION	99.96
2.62-2.71	0.2144	142	0.1758	2681	X-RAY DIFFRACTION	100
2.71-2.8	0.1994	140	0.1807	2673	X-RAY DIFFRACTION	99.96
2.8-2.92	0.2412	142	0.1842	2686	X-RAY DIFFRACTION	100
2.92-3.05	0.2157	142	0.1942	2706	X-RAY DIFFRACTION	100
3.05-3.21	0.2139	142	0.1953	2705	X-RAY DIFFRACTION	100
3.21-3.41	0.2055	143	0.1813	2699	X-RAY DIFFRACTION	100
3.41-3.67	0.1748	143	0.1656	2727	X-RAY DIFFRACTION	100
3.67-4.04	0.1549	145	0.1476	2746	X-RAY DIFFRACTION	100
4.04-4.63	0.1835	145	0.1407	2757	X-RAY DIFFRACTION	100
4.63-5.83	0.1551	147		2808	X-RAY DIFFRACTION	99.97
5.83-48.66	0.189	157		2960	X-RAY DIFFRACTION	99.68

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	4.17887027932	0.472129832557	0.157944384024	2.03759584863	-0.834939561164	3.18705081385	-0.0368493241171	-0.311403292562	0.341889914959	0.589214366478	-0.263398885209	-0.177406443827	-0.730215113448	0.668280387283	0.281420381686	0.451850089791	-0.071250286269	-0.0651921334532	0.238035730901	-0.0337769258635	0.315465744169	48.3030078704	27.2688021566	64.0410874449
2	2.69258278582	0.138793622652	-0.45698532411	2.16017058849	-1.64387730741	2.89957555046	-0.10203220562	-0.0990301161164	-0.300421076034	-0.0733063963009	-0.328092533527	-0.574124580077	0.136401533641	0.577526095605	0.337995710289	0.275489550032	-0.0114609998124	-0.0326179535972	0.431816085967	0.110835243486	0.477736422146	64.4453264988	24.7217476624	52.8726157265
3	2.83846076023	-0.245385316028	0.5866929197	2.29456268222	-1.06913706984	3.07826856505	-0.0427786160404	-0.257405170276	-0.337740457878	0.188469905332	-0.148396951272	-0.49424132538	0.154832048261	0.510861771371	0.01255688826	0.293740699519	0.050840900608	-0.0332430132623	0.285530202019	0.110221389945	0.347868028761	53.6397736135	13.8543925583	61.9690572465
4	5.84697271056	-0.212669688436	4.07342368092	3.78757952067	0.867529732539	5.98770035269	0.200974175278	-0.298260257601	-0.453374486185	0.165577431132	0.017747870393	-0.0809344546316	0.709056850518	-0.0891793073746	-0.341377955015	0.349969259174	-0.0187481609406	-0.030389880972	0.187547067892	0.0335469173216	0.221314199208	31.8515649194	12.8182400959	54.6235094617
5	2.48651235818	-0.939010890619	2.74326651333	0.93645250758	-1.79945323461	3.94912855118	-0.00525554026456	-0.197444795235	-0.0141468922045	0.143722076125	0.0172165448264	0.0386712047841	0.0487666788956	-0.234840032702	0.0117448515321	0.324141856382	-0.0105189707737	0.0102104482384	0.186823178234	0.0117146492053	0.201752328572	33.7266627857	18.5113679724	58.6328257174
6	1.87674815306	0.1601669569	-0.788385219814	1.35846181022	-0.290095453355	2.26855783292	0.079788485802	0.153614261307	0.600324899622	-0.0233705647653	0.0278321541426	0.357385572266	-0.44999761123	-0.43610195304	0.00560093070346	0.303434820995	0.0607748722496	-0.00770824767617	0.3641236916	-0.00650453428503	0.296327181996	9.42000821779	54.7685618147	41.0312530702
7	0.451133568194	-0.197085749775	-0.152638199498	0.750371689254	0.2633979761	0.661173845339	-0.0027266795558	0.0473790187408	-0.109146670577	0.0373090532434	-0.0304928677473	0.0153766153434	0.107961779598	-0.0885229571483	0.0233940703799	0.19241476652	-0.025240946571	0.00187822277433	0.25789592896	-0.00675682595538	0.208839421437	14.0949554106	31.7855810137	32.5875880834
8	1.58516355314	0.748292959899	0.571425416121	1.52921504947	0.32813560278	1.14043256179	-0.113482628553	0.209095329454	-0.00966429311964	-0.173011415194	0.0378686496998	0.0155097749775	-0.0750101697849	-0.152159092037	0.0999437725557	0.216341004364	0.0461100539799	-0.00185221265319	0.241072791799	-0.00127797427286	0.162320343242	11.1738717397	47.7583568359	27.0379864927
9	8.04274987316	-0.925504557532	2.98607591722	0.47459438251	-0.674097933821	1.54746058102	0.176057674749	0.533291189694	-0.313983610122	-0.0406163113121	-0.161919762136	-0.12163364194	0.0461004987964	0.221244912287	-0.0607221849414	0.272501478535	0.0263916848627	0.00836340547963	0.286639864156	-0.00467318679381	0.219122398613	26.9256901114	46.387101669	32.8626985298
10	4.44800684776	-1.61155493672	0.955250207325	1.6295478999	-0.834544557406	0.949286981705	0.00482837343438	-0.0137660407049	0.0232781723719	0.0128737666959	-0.0838816734966	-0.263923059468	0.0263626207269	0.174797194443	0.0492141760627	0.283836740161	-0.0226530640093	0.000780634652764	0.247909704345	0.0125436218286	0.248389728432	39.6809817035	45.4305523258	40.4023876627
11	3.09905874647	-1.2897834247	0.459536247704	2.25599532657	-0.0105687283139	2.88022355143	0.0455476796646	-0.0175968424812	0.234833475879	-0.143607604886	-0.0196386027415	-0.228868772257	-0.54621494076	0.370185094423	0.0716298272429	0.3364665714	-0.0424178950885	-0.010190728462	0.207693398242	0.0369983637799	0.2701023518	28.0335197252	63.0592232394	29.5166551142

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 59 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 60 through 229 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 230 through 282 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 283 through 340 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 341 through 414 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 12 through 35 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 36 through 188 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 189 through 272 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 273 through 294 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 295 through 365 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 366 through 402 )

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Queuine tRNA-ribosyltransferase ... , 2 types, 2 molecules AC

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Non-polymers , 6 types, 381 molecules

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-Queuine tRNA-ribosyltransferase ... , 2 types, 2 molecules AC

-Non-polymers , 6 types, 381 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

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Movie

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Structure viewers

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This web site

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Open data

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Basic information

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Structure visualization

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Queuine tRNA-ribosyltransferase ... , 2 types, 2 molecules AC

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Non-polymers , 6 types, 381 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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