+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15623 | |||||||||
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Title | Cryo-EM structure of yeast Elp123 in complex with alanine tRNA | |||||||||
Map data | ||||||||||
Sample |
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Keywords | wobble uridine modification / TRANSLATION | |||||||||
Function / homology | Function and homology information tRNA carboxymethyluridine synthase / tRNA uridine(34) acetyltransferase activity / elongator holoenzyme complex / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / protein urmylation / tRNA wobble uridine modification / protein transport / regulation of translation / 4 iron, 4 sulfur cluster binding / microtubule binding ...tRNA carboxymethyluridine synthase / tRNA uridine(34) acetyltransferase activity / elongator holoenzyme complex / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / protein urmylation / tRNA wobble uridine modification / protein transport / regulation of translation / 4 iron, 4 sulfur cluster binding / microtubule binding / tRNA binding / regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.96 Å | |||||||||
Authors | Jaciuk M / Scherf D / Kaszuba K / Gaik M / Koscielniak A / Krutyholowa R / Rawski M / Indyka P / Biela A / Dobosz D ...Jaciuk M / Scherf D / Kaszuba K / Gaik M / Koscielniak A / Krutyholowa R / Rawski M / Indyka P / Biela A / Dobosz D / Lin T-Y / Abbassi N / Hammermeister A / Chramiec-Glabik A / Kosinski J / Schaffrath R / Glatt S | |||||||||
Funding support | Poland, European Union, 2 items
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Citation | Journal: Nucleic Acids Res / Year: 2023 Title: Cryo-EM structure of the fully assembled Elongator complex. Authors: Marcin Jaciuk / David Scherf / Karol Kaszuba / Monika Gaik / Alexander Rau / Anna Kościelniak / Rościsław Krutyhołowa / Michał Rawski / Paulina Indyka / Andrea Graziadei / Andrzej ...Authors: Marcin Jaciuk / David Scherf / Karol Kaszuba / Monika Gaik / Alexander Rau / Anna Kościelniak / Rościsław Krutyhołowa / Michał Rawski / Paulina Indyka / Andrea Graziadei / Andrzej Chramiec-Głąbik / Anna Biela / Dominika Dobosz / Ting-Yu Lin / Nour-El-Hana Abbassi / Alexander Hammermeister / Juri Rappsilber / Jan Kosinski / Raffael Schaffrath / Sebastian Glatt / Abstract: Transfer RNA (tRNA) molecules are essential to decode messenger RNA codons during protein synthesis. All known tRNAs are heavily modified at multiple positions through post-transcriptional addition ...Transfer RNA (tRNA) molecules are essential to decode messenger RNA codons during protein synthesis. All known tRNAs are heavily modified at multiple positions through post-transcriptional addition of chemical groups. Modifications in the tRNA anticodons are directly influencing ribosome decoding and dynamics during translation elongation and are crucial for maintaining proteome integrity. In eukaryotes, wobble uridines are modified by Elongator, a large and highly conserved macromolecular complex. Elongator consists of two subcomplexes, namely Elp123 containing the enzymatically active Elp3 subunit and the associated Elp456 hetero-hexamer. The structure of the fully assembled complex and the function of the Elp456 subcomplex have remained elusive. Here, we show the cryo-electron microscopy structure of yeast Elongator at an overall resolution of 4.3 Å. We validate the obtained structure by complementary mutational analyses in vitro and in vivo. In addition, we determined various structures of the murine Elongator complex, including the fully assembled mouse Elongator complex at 5.9 Å resolution. Our results confirm the structural conservation of Elongator and its intermediates among eukaryotes. Furthermore, we complement our analyses with the biochemical characterization of the assembled human Elongator. Our results provide the molecular basis for the assembly of Elongator and its tRNA modification activity in eukaryotes. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15623.map.gz | 18.2 MB | EMDB map data format | |
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Header (meta data) | emd-15623-v30.xml emd-15623.xml | 26.2 KB 26.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15623_fsc.xml | 15 KB | Display | FSC data file |
Images | emd_15623.png | 83.8 KB | ||
Filedesc metadata | emd-15623.cif.gz | 8.6 KB | ||
Others | emd_15623_half_map_1.map.gz emd_15623_half_map_2.map.gz | 225.5 MB 225.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15623 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15623 | HTTPS FTP |
-Validation report
Summary document | emd_15623_validation.pdf.gz | 941.3 KB | Display | EMDB validaton report |
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Full document | emd_15623_full_validation.pdf.gz | 940.8 KB | Display | |
Data in XML | emd_15623_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | emd_15623_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15623 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15623 | HTTPS FTP |
-Related structure data
Related structure data | 8aswMC 8asvC 8at6C 8avgC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_15623.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.81 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_15623_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_15623_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Yeast Elp123 in complex with alanine tRNA
Entire | Name: Yeast Elp123 in complex with alanine tRNA |
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Components |
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-Supramolecule #1: Yeast Elp123 in complex with alanine tRNA
Supramolecule | Name: Yeast Elp123 in complex with alanine tRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 636.1 KDa |
-Macromolecule #1: Elongator complex protein 1
Macromolecule | Name: Elongator complex protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 153.166266 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: MVEHDKSGSK RQELRSNMRN LITLNKGKFK PTASTAEGDE DDLSFTLLDS VFDTLSDSIT CVLGSTDIGA IEVQQFMKDG SRNVLASFN IQTFDDKLLS FVHFADINQL VFVFEQGDII TATYDPVSLD PAETLIEIMG TIDNGIAAAQ WSYDEETLAM V TKDRNVVV ...String: MVEHDKSGSK RQELRSNMRN LITLNKGKFK PTASTAEGDE DDLSFTLLDS VFDTLSDSIT CVLGSTDIGA IEVQQFMKDG SRNVLASFN IQTFDDKLLS FVHFADINQL VFVFEQGDII TATYDPVSLD PAETLIEIMG TIDNGIAAAQ WSYDEETLAM V TKDRNVVV LSKLFEPISE YHLEVDDLKI SKHVTVGWGK KETQFRGKGA RAMEREALAS LKASGLVGNQ LRDPTMPYMV DT GDVTALD SHEITISWRG DCDYFAVSSV EEVPDEDDET KSIKRRAFRV FSREGQLDSA SEPVTGMEHQ LSWKPQGSLI ASI QRKTDL GEEDSVDVIF FERNGLRHGE FDTRLPLDEK VESVCWNSNS EALAVVLANR IQLWTSKNYH WYLKQELYAS DISY VKWHP EKDFTLMFSD AGFINIVDFA YKMAQGPTLE PFDNGTSLVV DGRTVNITPL ALANVPPPMY YRDFETPGNV LDVAC SFSN EIYAAINKDV LIFAAVPSIE EMKKGKHPSI VCEFPKSEFT SEVDSLRQVA FINDSIVGVL LDTDNLSRIA LLDIQD ITQ PTLITIVEVY DKIVLLRSDF DYNHLVYETR DGTVCQLDAE GQLMEITKFP QLVRDFRVKR VHNTSAEDDD NWSAESS EL VAFGITNNGK LFANQVLLAS AVTSLEITDS FLLFTTAQHN LQFVHLNSTD FKPLPLVEEG VEDERVRAIE RGSILVSV I PSKSSVVLQA TRGNLETIYP RIMVLAEVRK NIMAKRYKEA FIVCRTHRIN LDILHDYAPE LFIENLEVFI NQIGRVDYL NLFISCLSED DVTKTKYKET LYSGISKSFG MEPAPLTEMQ IYMKKKMFDP KTSKVNKICD AVLNVLLSNP EYKKKYLQTI ITAYASQNP QNLSAALKLI SELENSEEKD SCVTYLCFLQ DVNVVYKSAL SLYDVSLALL VAQKSQMDPR EYLPFLQELQ D NEPLRRKF LIDDYLGNYE KALEHLSEID KDGNVSEEVI DYVESHDLYK HGLALYRYDS EKQNVIYNIY AKHLSSNQMY TD AAVAYEM LGKLKEAMGA YQSAKRWREA MSIAVQKFPE EVESVAEELI SSLTFEHRYV DAADIQLEYL DNVKEAVALY CKA YRYDIA SLVAIKAKKD ELLEEVVDPG LGEGFGIIAE LLADCKGQIN SQLRRLRELR AKKEENPYAF YGQETEQADD VSVA PSETS TQESFFTRYT GKTGGTAKTG ASRRTAKNKR REERKRARGK KGTIYEEEYL VQSVGRLIER LNQTKPDAVR VVEGL CRRN MREQAHQIQK NFVEVLDLLK ANVKEIYSIS EKDRERVNEN GEVYYIPEIP VPEIHDFPKS HIVDF UniProtKB: Elongator complex protein 1 |
-Macromolecule #2: Elongator complex protein 2
Macromolecule | Name: Elongator complex protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 89.51943 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: MVECITPEAI FIGANKQTQV SDIHKVKKIV AFGAGKTIAL WDPIEPNNKG VYATLKGHEA EVTCVRFVPD SDFMVSASED HHVKIWKFT DYSHLQCIQT IQHYSKTIVA LSALPSLISV GCADGTISIW RQNIQNDEFG LAHEFTIKKG FFYPLCLSLS K VEEKKYLL ...String: MVECITPEAI FIGANKQTQV SDIHKVKKIV AFGAGKTIAL WDPIEPNNKG VYATLKGHEA EVTCVRFVPD SDFMVSASED HHVKIWKFT DYSHLQCIQT IQHYSKTIVA LSALPSLISV GCADGTISIW RQNIQNDEFG LAHEFTIKKG FFYPLCLSLS K VEEKKYLL AIGGTNVNVF IASFILSDSG IEKCRVVAEL EGHEDWVKSL AFRHQETPGD YLLCSGSQDR YIRLWRIRIN DL IDDSEED SKKLTLLSNK QYKFQIDDEL RVGINFEALI MGHDDWISSL QWHESRLQLL AATADTSLMV WEPDETSGIW VCS LRLGEM SSKGASTATG SSGGFWSCLW FTHERMDFFL TNGKTGSWRM WATKDNIICD QRLGISGATK DVTDIAWSPS GEYL LATSL DQTTRLFAPW IYDASGRKRE IATWHEFSRP QIHGYDMICV ETVTDTRFVS GGDEKILRSF DLPKGVAGML QKFVG IQFE EKSEMPDSAT VPVLGLSNKA GEDDANEDDE EEEGGNKETP DITDPLSLLE CPPMEDQLQR HLLWPEVEKL YGHGFE ITC LDISPDQKLI ASACRSNNVQ NAVIRIFSTE NWLEIKPALP FHSLTITRLK FSKDGKFLLS VCRDRKWALW ERNMEDN TF ELRFKNEKPH TRIIWDADWA PLEFGNVFVT ASRDKTVKVW RHQKEPADDY VLEASIKHTK AVTAISIHDS MIREKILI S VGLENGEIYL YSYTLGKFEL ITQLNEDITP ADKITRLRWS HLKRNGKLFL GVGSSDLSTR IYSLAYE UniProtKB: Elongator complex protein 2 |
-Macromolecule #3: Elongator complex protein 3
Macromolecule | Name: Elongator complex protein 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO EC number: Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 63.755059 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: MARHGKGPKT NKKKLAPEKE RFIQCCADIT LELTDSLTSG TTREINLNGL ITKYSKKYKL KQQPRLTDII NSIPDQYKKY LLPKLKAKP VRTASGIAVV AVMCKPHRCP HIAYTGNICV YCPGGPDSDF EYSTQSYTGY EPTSMRAIRA RYDPYEQARG R VEQLKQLG ...String: MARHGKGPKT NKKKLAPEKE RFIQCCADIT LELTDSLTSG TTREINLNGL ITKYSKKYKL KQQPRLTDII NSIPDQYKKY LLPKLKAKP VRTASGIAVV AVMCKPHRCP HIAYTGNICV YCPGGPDSDF EYSTQSYTGY EPTSMRAIRA RYDPYEQARG R VEQLKQLG HSIDKVEYVL MGGTFMSLPK EYREDFIVKL HNALSGFNGN DIDEAILYSQ QSLTKCVGIT IETRPDYCTQ TH LDDMLKY GCTRLEIGVQ SLYEDVARDT NRGHTVRSVC ETFAVSKDAG YKVVSHMMPD LPNVGMERDI EQFKEYFENP DFR TDGLKI YPTLVIRGTG LYELWKTGRY KSYSANALVD LVARILALVP PWTRIYRVQR DIPMPLVTSG VDNGNLRELA LARM KDLGT TCRDVRTREV GIQEVHHKVQ PDQVELIRRD YYANGGWETF LSYEDPKKDI LIGLLRLRKA SKKYTYRKEF TSQRT SIVR ELHVYGSVVP LHSRDPRKFQ HQGFGTLLME EAERIAKEEH GSEKISVISG VGVRNYYGKL GYELDGPYMS KRI UniProtKB: Elongator complex protein 3 |
-Macromolecule #4: Alanine tRNA
Macromolecule | Name: Alanine tRNA / type: rna / ID: 4 / Number of copies: 1 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 23.538932 KDa |
Sequence | String: GGGCACAUGG CGCAGUUGGU AGCGCGCUUC CCUUGCAAGG AAGAGGUCAU CGGUUCGAUU CCGGUUGCGU CCA |
-Macromolecule #5: IRON/SULFUR CLUSTER
Macromolecule | Name: IRON/SULFUR CLUSTER / type: ligand / ID: 5 / Number of copies: 1 / Formula: SF4 |
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Molecular weight | Theoretical: 351.64 Da |
Chemical component information | ChemComp-FS1: |
-Macromolecule #6: 5'-DEOXYADENOSINE
Macromolecule | Name: 5'-DEOXYADENOSINE / type: ligand / ID: 6 / Number of copies: 1 / Formula: 5AD |
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Molecular weight | Theoretical: 251.242 Da |
Chemical component information | ChemComp-5AD: |
-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 / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 15 s wait time, blot force 5, 5 s blot time. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number real images: 11080 / Average electron dose: 42.45 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Details | After initial rigid body fit, further fitting was done using MDFF and NAMDINATOR | ||||||
Refinement | Protocol: RIGID BODY FIT | ||||||
Output model | PDB-8asw: |