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- PDB-7nq4: Human tRNA guanine transglycosylase (TGT), RNA-bound covalent int... -

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Basic information

Entry
Database: PDB / ID: 7nq4
TitleHuman tRNA guanine transglycosylase (TGT), RNA-bound covalent intermediate
Components
  • (Queuine tRNA-ribosyltransferase ...) x 2
  • RNA
KeywordsRNA BINDING PROTEIN / tRNA modification / queuine incorporation / RNA complex / heterodimer
Function / homology
Function and homology information


tRNA-guanosine34 queuine transglycosylase / transferase complex / tRNA modification in the nucleus and cytosol / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / tRNA modification / mitochondrial outer membrane / tRNA binding / protein heterodimerization activity / protein homodimerization activity ...tRNA-guanosine34 queuine transglycosylase / transferase complex / tRNA modification in the nucleus and cytosol / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / tRNA modification / mitochondrial outer membrane / tRNA binding / protein heterodimerization activity / protein homodimerization activity / protein-containing complex / mitochondrion / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Queuine tRNA-ribosyltransferase accessory subunit QTRTD1 / tRNA-guanine transglycosylase / tRNA-guanine(15) transglycosylase-like / Queuine tRNA-ribosyltransferase-like / Queuine tRNA-ribosyltransferase
Similarity search - Domain/homology
9-DEAZAGUANINE / RNA / RNA (> 10) / Queuine tRNA-ribosyltransferase catalytic subunit 1 / Queuine tRNA-ribosyltransferase accessory subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsSievers, K. / Ficner, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Rna Biol. / Year: 2021
Title: Structural and functional insights into human tRNA guanine transgylcosylase.
Authors: Sievers, K. / Welp, L. / Urlaub, H. / Ficner, R.
History
DepositionMar 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 29, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Queuine tRNA-ribosyltransferase catalytic subunit 1
B: Queuine tRNA-ribosyltransferase accessory subunit 2
C: RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,7306
Polymers97,4493
Non-polymers2813
Water724
1
A: Queuine tRNA-ribosyltransferase catalytic subunit 1
B: Queuine tRNA-ribosyltransferase accessory subunit 2
C: RNA
hetero molecules

A: Queuine tRNA-ribosyltransferase catalytic subunit 1
B: Queuine tRNA-ribosyltransferase accessory subunit 2
C: RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,46112
Polymers194,8996
Non-polymers5626
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area16660 Å2
ΔGint-90 kcal/mol
Surface area57510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.840, 56.960, 102.960
Angle α, β, γ (deg.)90.000, 124.935, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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

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


Mass: 44251.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: D279 is covalently bound to guanine 34 (chain C) / Source: (gene. exp.) Homo sapiens (human) / Gene: QTRT1, TGT, TGUT / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9BXR0, tRNA-guanosine34 preQ1 transglycosylase
#2: Protein Queuine tRNA-ribosyltransferase accessory subunit 2 / Queuine tRNA-ribosyltransferase domain-containing protein 1


Mass: 46775.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: QTRT2, QTRTD1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9H974

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RNA chain , 1 types, 1 molecules C

#3: RNA chain RNA /


Mass: 6421.895 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: guanine 34 is covalently linked to D279 (chain A) / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 7 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-9DG / 9-DEAZAGUANINE


Mass: 150.138 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N4O / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity % sol: 38.38 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: PEG 1500, MMT pH 6

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Data collection

DiffractionMean temperature: 93.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.88→42.2 Å / Num. obs: 17591 / % possible obs: 81.6 % / Redundancy: 6.788 % / Biso Wilson estimate: 67.811 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.116 / Net I/σ(I): 13.83
Reflection shellResolution: 2.88→2.98 Å / Redundancy: 6.985 % / Mean I/σ(I) obs: 1.81 / Num. unique obs: 1703 / CC1/2: 0.876 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMACv5.8.0267refinement
PHENIXv1.19.1_4122refinement
XDSdata reduction
XSCALEdata scaling
PHASERv2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H42, 6FV5

6h42

6fv5


Resolution: 2.88→42.2 Å / SU ML: 0.4209 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.5249
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2484 878 5 %
Rwork0.2117 16672 -
obs0.2135 17550 99.17 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.88→42.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5965 414 13 4 6396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00756564
X-RAY DIFFRACTIONf_angle_d1.41428983
X-RAY DIFFRACTIONf_chiral_restr0.09651034
X-RAY DIFFRACTIONf_plane_restr0.00441087
X-RAY DIFFRACTIONf_dihedral_angle_d15.46252487
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.88-3.060.41731450.38792755X-RAY DIFFRACTION99.62
3.06-3.30.38981460.33742752X-RAY DIFFRACTION98.84
3.3-3.630.30951440.26392748X-RAY DIFFRACTION99.48
3.63-4.150.22921460.2122775X-RAY DIFFRACTION99.08
4.15-5.230.21171460.16542784X-RAY DIFFRACTION99.36
5.23-42.20.19231510.16012858X-RAY DIFFRACTION98.66
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
11.938657001950.3969418074010.338294330631.162299389250.4163517985282.005310654990.106186070267-0.588327190462-0.07011259059360.137226213663-0.120990935459-0.0892480742230.04491769371710.29109864182-2.21976572171E-50.559561416697-0.0100290847625-0.004753834495050.7117426658140.09054122884280.61604128089728.5200911412-24.742810473833.5431203241
21.88886365361-0.1744832602860.715021648141.44167899921-0.3916475203191.61434647108-0.07313006031040.568883137639-0.110343398065-0.2131401010690.05004413141810.02589077926950.1576644883520.343281520575-5.32252579308E-100.639747483335-0.07904632126560.04967964329090.64806960845-0.09663592126120.60412484675718.1117081071-30.4747246117-9.56342941669
30.123471674523-0.01928273979520.0156712551894-0.0535225320674-0.009419162096240.140520981571-0.351645021288-0.1687522924310.172898572748-0.13951268062-0.280496363293-0.000293643735844-0.299965879331-0.578437345702-0.0004467699860720.7934035703990.0869796561179-0.1203970654270.94188370788-0.07045373939920.86541084825211.0809737074-14.739766204821.2471773763
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain AAA - C14 - 6011
22chain BBD - E1 - 5011
33chain CCF25 - 44

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