+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Human tRNA guanine transglycosylase (TGT) bound to tRNAAsp | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
![]() | RNA modification / transglycosylation / nucleid acid-protein complex / tRNA binding / RNA BINDING PROTEIN | |||||||||
Function / homology | ![]() tRNA-guanosine34 queuine transglycosylase / transferase complex / tRNA modification in the nucleus and cytosol / tRNA modification / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / 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 modification / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / mitochondrial outer membrane / tRNA binding / protein heterodimerization activity / protein homodimerization activity / protein-containing complex / mitochondrion / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
![]() | Sievers K / Neumann P / Susac L / Trowitzsch S / Tampe R / Ficner R | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Structural and functional insights into tRNA recognition by human tRNA guanine transglycosylase. Authors: Katharina Sievers / Piotr Neumann / Lukas Sušac / Stefano Da Vela / Melissa Graewert / Simon Trowitzsch / Dmitri Svergun / Robert Tampé / Ralf Ficner / ![]() Abstract: Eukaryotic tRNA guanine transglycosylase (TGT) is an RNA-modifying enzyme which catalyzes the base exchange of the genetically encoded guanine 34 of tRNAs for queuine, a hypermodified 7-deazaguanine ...Eukaryotic tRNA guanine transglycosylase (TGT) is an RNA-modifying enzyme which catalyzes the base exchange of the genetically encoded guanine 34 of tRNAs for queuine, a hypermodified 7-deazaguanine derivative. Eukaryotic TGT is a heterodimer comprised of a catalytic and a non-catalytic subunit. While binding of the tRNA anticodon loop to the active site is structurally well understood, the contribution of the non-catalytic subunit to tRNA binding remained enigmatic, as no complex structure with a complete tRNA was available. Here, we report a cryo-EM structure of eukaryotic TGT in complex with a complete tRNA, revealing the crucial role of the non-catalytic subunit in tRNA binding. We decipher the functional significance of these additional tRNA-binding sites, analyze solution state conformation, flexibility, and disorder of apo TGT, and examine conformational transitions upon tRNA binding. | |||||||||
History |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 35.7 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 17.3 KB 17.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.5 KB | Display | ![]() |
Images | ![]() | 100.1 KB | ||
Masks | ![]() | 71.8 MB | ![]() | |
Filedesc metadata | ![]() | 6.3 KB | ||
Others | ![]() ![]() | 66.8 MB 66.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8omrMC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 0.78 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_16976_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_16976_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : Ternary complex of human tRNA guanine transglycosylase and tRNAAsp
Entire | Name: Ternary complex of human tRNA guanine transglycosylase and tRNAAsp |
---|---|
Components |
|
-Supramolecule #1: Ternary complex of human tRNA guanine transglycosylase and tRNAAsp
Supramolecule | Name: Ternary complex of human tRNA guanine transglycosylase and tRNAAsp type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
---|---|
Source (natural) | Organism: ![]() |
-Macromolecule #1: Queuine tRNA-ribosyltransferase catalytic subunit 1
Macromolecule | Name: Queuine tRNA-ribosyltransferase catalytic subunit 1 / type: protein_or_peptide / ID: 1 / Details: Zn ion and 9DG are ligands / Number of copies: 1 / Enantiomer: LEVO / EC number: tRNA-guanosine34 preQ1 transglycosylase |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 44.25177 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GPMAGAATQA SLESAPRIMR LVAECSRSRA RAGELWLPHG TVATPVFMPV GTQATMKGIT TEQLDALGCR ICLGNTYHLG LRPGPELIQ KANGLHGFMN WPHNLLTDSG GFQMVSLVSL SEVTEEGVRF RSPYDGNETL LSPEKSVQIQ NALGSDIIMQ L DDVVSSTV ...String: GPMAGAATQA SLESAPRIMR LVAECSRSRA RAGELWLPHG TVATPVFMPV GTQATMKGIT TEQLDALGCR ICLGNTYHLG LRPGPELIQ KANGLHGFMN WPHNLLTDSG GFQMVSLVSL SEVTEEGVRF RSPYDGNETL LSPEKSVQIQ NALGSDIIMQ L DDVVSSTV TGPRVEEAMY RSIRWLDRCI AAHQRPDKQN LFAIIQGGLD ADLRATCLEE MTKRDVPGFA IGGLSGGESK SQ FWRMVAL STSRLPKDKP RYLMGVGYAT DLVVCVALGC DMFDCVFPTR TARFGSALVP TGNLQLRKKV FEKDFGPIDP ECT CPTCQK HSRAFLHALL HSDNTAALHH LTVHNIAYQL QLMSAVRTSI VEKRFPDFVR DFMGAMYGDP TLCPTWATDA LASV GITLG UniProtKB: Queuine tRNA-ribosyltransferase catalytic subunit 1 |
-Macromolecule #2: Queuine tRNA-ribosyltransferase accessory subunit 2
Macromolecule | Name: Queuine tRNA-ribosyltransferase accessory subunit 2 / type: protein_or_peptide / ID: 2 / Details: Zn is an ion / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 46.77568 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MKLSLTKVVN GCRLGKIKNL GKTGDHTMDI PGCLLYTKTG SAPHLTHHTL HNIHGVPAMA QLTLSSLAEH HEVLTEYKEG VGKFIGMPE SLLYCSLHDP VSPCPAGYVT NKSVSVWSVA GRVEMTVSKF MAIQKALQPD WFQCLSDGEV SCKEATSIKR V RKSVDRSL ...String: MKLSLTKVVN GCRLGKIKNL GKTGDHTMDI PGCLLYTKTG SAPHLTHHTL HNIHGVPAMA QLTLSSLAEH HEVLTEYKEG VGKFIGMPE SLLYCSLHDP VSPCPAGYVT NKSVSVWSVA GRVEMTVSKF MAIQKALQPD WFQCLSDGEV SCKEATSIKR V RKSVDRSL LFLDNCLRLQ EESEVLQKSV IIGVIEGGDV MEERLRSARE TAKRPVGGFL LDGFQGNPTT LEARLRLLSS VT AELPEDK PRLISGVSRP DEVLECIERG VDLFESFFPY QVTERGCALT FSFDYQPNPE ETLLQQNGTQ EEIKCMDQIK KIE TTGCNQ EITSFEINLK EKKYQEDFNP LVRGCSCYCC KNHTRAYIHH LLVTNELLAG VLLMMHNFEH YFGFFHYIRE ALKS DKLAQ LKELIHRQAS UniProtKB: Queuine tRNA-ribosyltransferase accessory subunit 2 |
-Macromolecule #3: tRNAAsp
Macromolecule | Name: tRNAAsp / type: rna / ID: 3 / Number of copies: 1 |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 24.148312 KDa |
Sequence | String: AGGUCGUUAG UAUAGUGGUG AGUAUCCCCG CCUGUCACGC GGGAGACCGG GGUUCGAUUC CCCGACGGCC UGCCA |
-Macromolecule #4: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ZN |
---|---|
Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #5: 9-DEAZAGUANINE
Macromolecule | Name: 9-DEAZAGUANINE / type: ligand / ID: 5 / Number of copies: 1 / Formula: 9DG |
---|---|
Molecular weight | Theoretical: 150.138 Da |
Chemical component information | ![]() ChemComp-9DG: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
Microscope | TFS GLACIOS |
---|---|
Image recording | Film or detector model: OTHER / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average exposure time: 44.46 sec. / Average electron dose: 62.1 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm |