+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4573 | |||||||||
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Title | Full Elongator catalytic subcomplex Elp123 | |||||||||
Map data | Postprocessed map of the full Elongator catalytic subcomplex Elp123 from yeast at 4.5 A resolution. | |||||||||
Sample |
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Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
Authors | Dauden MI / Weis F | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Sci Adv / Year: 2019 Title: Molecular basis of tRNA recognition by the Elongator complex. Authors: Maria I Dauden / Marcin Jaciuk / Felix Weis / Ting-Yu Lin / Carolin Kleindienst / Nour El Hana Abbassi / Heena Khatter / Rościsław Krutyhołowa / Karin D Breunig / Jan Kosinski / Christoph ...Authors: Maria I Dauden / Marcin Jaciuk / Felix Weis / Ting-Yu Lin / Carolin Kleindienst / Nour El Hana Abbassi / Heena Khatter / Rościsław Krutyhołowa / Karin D Breunig / Jan Kosinski / Christoph W Müller / Sebastian Glatt / Abstract: The highly conserved Elongator complex modifies transfer RNAs (tRNAs) in their wobble base position, thereby regulating protein synthesis and ensuring proteome stability. The precise mechanisms of ...The highly conserved Elongator complex modifies transfer RNAs (tRNAs) in their wobble base position, thereby regulating protein synthesis and ensuring proteome stability. The precise mechanisms of tRNA recognition and its modification reaction remain elusive. Here, we show cryo-electron microscopy structures of the catalytic subcomplex of Elongator and its tRNA-bound state at resolutions of 3.3 and 4.4 Å. The structures resolve details of the catalytic site, including the substrate tRNA, the iron-sulfur cluster, and a SAM molecule, which are all validated by mutational analyses in vitro and in vivo. tRNA binding induces conformational rearrangements, which precisely position the targeted anticodon base in the active site. Our results provide the molecular basis for substrate recognition of Elongator, essential to understand its cellular function and role in neurodegenerative diseases and cancer. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4573.map.gz | 9.8 MB | EMDB map data format | |
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Header (meta data) | emd-4573-v30.xml emd-4573.xml | 22.7 KB 22.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4573_fsc.xml | 13.1 KB | Display | FSC data file |
Images | emd_4573.png | 300.7 KB | ||
Others | emd_4573_half_map_1.map.gz emd_4573_half_map_2.map.gz | 148.8 MB 148.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4573 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4573 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4573.map.gz / Format: CCP4 / Size: 190.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Postprocessed map of the full Elongator catalytic subcomplex Elp123 from yeast at 4.5 A resolution. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Half map of the full Elongator catalytic subcomplex...
File | emd_4573_half_map_1.map | ||||||||||||
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Annotation | Half map of the full Elongator catalytic subcomplex Elp123 from yeast. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map of the full Elongator catalytic subcomplex...
File | emd_4573_half_map_2.map | ||||||||||||
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Annotation | Half map of the full Elongator catalytic subcomplex Elp123 from yeast. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Full Elongator catalytic subcomplex Elp123
Entire | Name: Full Elongator catalytic subcomplex Elp123 |
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Components |
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-Supramolecule #1: Full Elongator catalytic subcomplex Elp123
Supramolecule | Name: Full Elongator catalytic subcomplex Elp123 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: The EM map corresponds to the full Elp123 complex, composed by two copies of Elp1, Elp2 and Elp3 forming a C2 symmetric complex. |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 621 KDa |
-Macromolecule #1: Elongator complex protein 1, Elp1
Macromolecule | Name: Elongator complex protein 1, Elp1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: MVEHDKSGSK RQELRSNMRN LITLNKGKFK PTASTAEGDE DDLSFTLLDS VFDTLSDSIT CVLGSTDIG AIEVQQFMKD GSRNVLASFN IQTFDDKLLS FVHFADINQL VFVFEQGDII T ATYDPVSL DPAETLIEIM GTIDNGIAAA QWSYDEETLA MVTKDRNVVV ...String: MVEHDKSGSK RQELRSNMRN LITLNKGKFK PTASTAEGDE DDLSFTLLDS VFDTLSDSIT CVLGSTDIG AIEVQQFMKD GSRNVLASFN IQTFDDKLLS FVHFADINQL VFVFEQGDII T ATYDPVSL DPAETLIEIM GTIDNGIAAA QWSYDEETLA MVTKDRNVVV LSKLFEPISE YH LEVDDLK ISKHVTVGWG KKETQFRGKG ARAMEREALA SLKASGLVGN QLRDPTMPYM VDT GDVTAL DSHEITISWR GDCDYFAVSS VEEVPDEDDE TKSIKRRAFR VFSREGQLDS ASEP VTGME HQLSWKPQGS LIASIQRKTD LGEEDSVDVI FFERNGLRHG EFDTRLPLDE KVESV CWNS NSEALAVVLA NRIQLWTSKN YHWYLKQELY ASDISYVKWH PEKDFTLMFS DAGFIN IVD FAYKMAQGPT LEPFDNGTSL VVDGRTVNIT PLALANVPPP MYYRDFETPG NVLDVAC SF SNEIYAAINK DVLIFAAVPS IEEMKKGKHP SIVCEFPKSE FTSEVDSLRQ VAFINDSI V GVLLDTDNLS RIALLDIQDI TQPTLITIVE VYDKIVLLRS DFDYNHLVYE TRDGTVCQL DAEGQLMEIT KFPQLVRDFR VKRVHNTSAE DDDNWSAESS ELVAFGITNN GKLFANQVLL ASAVTSLEI TDSFLLFTTA QHNLQFVHLN STDFKPLPLV EEGVEDERVR AIERGSILVS V IPSKSSVV LQATRGNLET IYPRIMVLAE VRKNIMAKRY KEAFIVCRTH RINLDILHDY AP ELFIENL EVFINQIGRV DYLNLFISCL SEDDVTKTKY KETLYSGISK SFGMEPAPLT EMQ IYMKKK MFDPKTSKVN KICDAVLNVL LSNPEYKKKY LQTIITAYAS QNPQNLSAAL KLIS ELENS EEKDSCVTYL CFLQDVNVVY KSALSLYDVS LALLVAQKSQ MDPREYLPFL QELQD NEPL RRKFLIDDYL GNYEKALEHL SEIDKDGNVS EEVIDYVESH DLYKHGLALY RYDSEK QNV IYNIYAKHLS SNQMYTDAAV AYEMLGKLKE AMGAYQSAKR WREAMSIAVQ KFPEEVE SV AEELISSLTF EHRYVDAADI QLEYLDNVKE AVALYCKAYR YDIASLVAIK AKKDELLE E VVDPGLGEGF GIIAELLADC KGQINSQLRR LRELRAKKEE NPYAFYGQET EQADDVSVA PSETSTQESF FTRYTGKTGG TAKTGASRRT AKNKRREERK RARGKKGTIY EEEYLVQSVG RLIERLNQT KPDAVRVVEG LCRRNMREQA HQIQKNFVEV LDLLKANVKE IYSISEKDRE R VNENGEVY YIPEIPVPEI HDFPKSHIVD F |
-Macromolecule #2: Elongator complex protein 2, Elp2
Macromolecule | Name: Elongator complex protein 2, Elp2 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: MVECITPEAI FIGANKQTQV SDIHKVKKIV AFGAGKTIAL WDPIEPNNKG VYATLKGHEA EVTCVRFVP DSDFMVSASE DHHVKIWKFT DYSHLQCIQT IQHYSKTIVA LSALPSLISV G CADGTISI WRQNIQNDEF GLAHEFTIKK GFFYPLCLSL SKVEEKKYLL ...String: MVECITPEAI FIGANKQTQV SDIHKVKKIV AFGAGKTIAL WDPIEPNNKG VYATLKGHEA EVTCVRFVP DSDFMVSASE DHHVKIWKFT DYSHLQCIQT IQHYSKTIVA LSALPSLISV G CADGTISI WRQNIQNDEF GLAHEFTIKK GFFYPLCLSL SKVEEKKYLL AIGGTNVNVF IA SFILSDS GIEKCRVVAE LEGHEDWVKS LAFRHQETPG DYLLCSGSQD RYIRLWRIRI NDL IDDSEE DSKKLTLLSN KQYKFQIDDE LRVGINFEAL IMGHDDWISS LQWHESRLQL LAAT ADTSL MVWEPDETSG IWVCSLRLGE MSSKGASTAT GSSGGFWSCL WFTHERMDFF LTNGK TGSW RMWATKDNII CDQRLGISGA TKDVTDIAWS PSGEYLLATS LDQTTRLFAP WIYDAS GRK REIATWHEFS RPQIHGYDMI CVETVTDTRF VSGGDEKILR SFDLPKGVAG MLQKFVG IQ FEEKSEMPDS ATVPVLGLSN KAGEDDANED DEEEEGGNKE TPDITDPLSL LECPPMED Q LQRHLLWPEV EKLYGHGFEI TCLDISPDQK LIASACRSNN VQNAVIRIFS TENWLEIKP ALPFHSLTIT RLKFSKDGKF LLSVCRDRKW ALWERNMEDN TFELRFKNEK PHTRIIWDAD WAPLEFGNV FVTASRDKTV KVWRHQKEPA DDYVLEASIK HTKAVTAISI HDSMIREKIL I SVGLENGE IYLYSYTLGK FELITQLNED ITPADKITRL RWSHLKRNGK LFLGVGSSDL ST RIYSLAY E |
-Macromolecule #3: Elongator complex protein 3, Elp3
Macromolecule | Name: Elongator complex protein 3, Elp3 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: MARHGKGPKT NKKKLAPEKE RFIQCCADIT LELTDSLTSG TTREINLNGL ITKYSKKYKL KQQPRLTDI INSIPDQYKK YLLPKLKAKP VRTASGIAVV AVMCKPHRCP HIAYTGNICV Y CPGGPDSD FEYSTQSYTG YEPTSMRAIR ARYDPYEQAR GRVEQLKQLG ...String: MARHGKGPKT NKKKLAPEKE RFIQCCADIT LELTDSLTSG TTREINLNGL ITKYSKKYKL KQQPRLTDI INSIPDQYKK YLLPKLKAKP VRTASGIAVV AVMCKPHRCP HIAYTGNICV Y CPGGPDSD FEYSTQSYTG YEPTSMRAIR ARYDPYEQAR GRVEQLKQLG HSIDKVEYVL MG GTFMSLP KEYREDFIVK LHNALSGFNG NDIDEAILYS QQSLTKCVGI TIETRPDYCT QTH LDDMLK YGCTRLEIGV QSLYEDVARD TNRGHTVRSV CETFAVSKDA GYKVVSHMMP DLPN VGMER DIEQFKEYFE NPDFRTDGLK IYPTLVIRGT GLYELWKTGR YKSYSANALV DLVAR ILAL VPPWTRIYRV QRDIPMPLVT SGVDNGNLRE LALARMKDLG TTCRDVRTRE VGIQEV HHK VQPDQVELIR RDYYANGGWE TFLSYEDPKK DILIGLLRLR KASKKYTYRK EFTSQRT SI VRELHVYGSV VPLHSRDPRK FQHQGFGTLL MEEAERIAKE EHGSEKISVI SGVGVRNY Y GKLGYELDGP YMSKRI |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.4 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Details: Pelco EasyGlow glow discharger | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: 2.5 ul of sample, blotting parameters: wait time 15 s, blot force 5, blot time 5-8 s.. | ||||||||||||||||||
Details | The sample was cross-linked with 0.01% glutaraldehyde, quenched and then plunged. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Details | Gatan Quantum energy filter and a K2 Summit direct detector |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 4614 / Average electron dose: 43.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |