+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19836 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Human pseudouridine synthase 3 (wild type) | ||||||||||||
Map data | |||||||||||||
Sample |
| ||||||||||||
Keywords | RNA modification / pseudouridylation / tRNA / homodimer / RNA BINDING PROTEIN | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.02 Å | ||||||||||||
Authors | Lin T-Y / Glatt S | ||||||||||||
Funding support | Poland, European Union, Switzerland, 3 items
| ||||||||||||
Citation | Journal: Mol.Cell / Year: 2024 Title: The molecular basis of tRNA selectivity by human pseudouridine synthase 3 (PUS3) Authors: Lin T-Y / Koziej L / Glatt S | ||||||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_19836.map.gz | 62.2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-19836-v30.xml emd-19836.xml | 16.2 KB 16.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19836_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_19836.png | 78.9 KB | ||
Filedesc metadata | emd-19836.cif.gz | 5.1 KB | ||
Others | emd_19836_half_map_1.map.gz emd_19836_half_map_2.map.gz | 115.9 MB 115.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19836 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19836 | HTTPS FTP |
-Validation report
Summary document | emd_19836_validation.pdf.gz | 785.7 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_19836_full_validation.pdf.gz | 785.3 KB | Display | |
Data in XML | emd_19836_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | emd_19836_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19836 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19836 | HTTPS FTP |
-Related structure data
Related structure data | 19830 19831 19832 19833 19834 19835 9enbC 9encC 9eneC 9enfC 9f9qC 16917 16926 C: citing same article (ref.) |
---|
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_19836.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Sample components
-Entire : Homodimer of human PUS3 (Wild type)
Entire | Name: Homodimer of human PUS3 (Wild type) |
---|---|
Components |
|
-Supramolecule #1: Homodimer of human PUS3 (Wild type)
Supramolecule | Name: Homodimer of human PUS3 (Wild type) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 110 KDa |
-Macromolecule #1: Pseudouridine synthase 3 homodimer
Macromolecule | Name: Pseudouridine synthase 3 homodimer / type: protein_or_peptide / ID: 1 / Details: wild type / Enantiomer: LEVO / EC number: tRNA pseudouridine38/39 synthase |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MAYNDTDRNQ TEKLLKRVRE LEQEVQRLKK EQAKNKEDSN IRENSAGAGK TKRAFDFSAH GRRHVALRIA YMGWGYQGFA SQENTNNTI EEKLFEALTK TRLVESRQTS NYHRCGRTDK GVSAFGQVIS LDLRSQFPRG RDSEDFNVKE EANAAAEEIR Y THILNRVL ...String: MAYNDTDRNQ TEKLLKRVRE LEQEVQRLKK EQAKNKEDSN IRENSAGAGK TKRAFDFSAH GRRHVALRIA YMGWGYQGFA SQENTNNTI EEKLFEALTK TRLVESRQTS NYHRCGRTDK GVSAFGQVIS LDLRSQFPRG RDSEDFNVKE EANAAAEEIR Y THILNRVL PPDIRILAWA PVEPSFSARF SCLERTYRYF FPRADLDIVT MDYAAQKYVG THDFRNLCKM DVANGVINFQ RT ILSAQVQ LVGQSPGEGR WQEPFQLCQF EVTGQAFLYH QVRCMMAILF LIGQGMEKPE IIDELLNIEK NPQKPQYSMA VEF PLVLYD CKFENVKWIY DQEAQEFNIT HLQQLWANHA VKTHMLYSML QGLDTVPVPC GIGPKMDGMT EWGNVKPSVI KQTS AFVEG VKMRTYKPLM DRPKCQGLES RIQHFVRRGR IEHPHLFHEE ETKAKRDCND TLEEENTNLE TPTKRVCVDT EIKSI I |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL |
---|---|
Buffer | pH: 7.5 |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 11944 / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |