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- EMDB-15626: Cryo-EM structure of mouse Elongator complex -

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Basic information

Entry
Database: EMDB / ID: EMD-15626
TitleCryo-EM structure of mouse Elongator complex
Map data
Sample
  • Complex: Mouse Elongator complex
    • Protein or peptide: Elongator complex protein 1
    • Protein or peptide: Elongator complex protein 2
    • Protein or peptide: Elongator complex protein 3
    • Protein or peptide: Elongator complex protein 4
    • Protein or peptide: Elongator complex protein 5
    • Protein or peptide: Elongator complex protein 6
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.92 Å
AuthorsJaciuk 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
OrganizationGrant numberCountry
Polish National Science Centre2018/31/B/NZ1/03559 Poland
European Research Council (ERC)101001394European Union
CitationJournal: 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
DepositionAug 22, 2022-
Header (metadata) releaseDec 7, 2022-
Map releaseDec 7, 2022-
UpdateMar 29, 2023-
Current statusMar 29, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15626.png

Downloads & links

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Map

FileDownload / File: emd_15626.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 420 pix.
= 361.2 Å		0.86 Å/pix.
x 420 pix.
= 361.2 Å		0.86 Å/pix.
x 420 pix.
= 361.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00332
Minimum - Maximum-0.0045286147 - 0.015202945
Average (Standard dev.)9.210786e-05 (±0.00065676955)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 361.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_15626_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_15626_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mouse Elongator complex

EntireName: Mouse Elongator complex
Components
  • Complex: Mouse Elongator complex
    • Protein or peptide: Elongator complex protein 1
    • Protein or peptide: Elongator complex protein 2
    • Protein or peptide: Elongator complex protein 3
    • Protein or peptide: Elongator complex protein 4
    • Protein or peptide: Elongator complex protein 5
    • Protein or peptide: Elongator complex protein 6

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Supramolecule #1: Mouse Elongator complex

SupramoleculeName: Mouse Elongator complex / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 828.2 KDa

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Macromolecule #1: Elongator complex protein 1

MacromoleculeName: Elongator complex protein 1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MRNLKLHRTL EFRDIQAPGK PQCFCLRAEQ GTVLIGSERG LTEVDPVRRE VKTEISLVAE GFLPEDGSG CIVGIQDLLD QESVCVATAS GDVIVCNLST QQLECVGSVA SGISVMSWSP D QELLLLAT AQQTLIMMTK DFEVIAEEQI HQDDFGEGKF VTVGWGSKQT ...String:
MRNLKLHRTL EFRDIQAPGK PQCFCLRAEQ GTVLIGSERG LTEVDPVRRE VKTEISLVAE GFLPEDGSG CIVGIQDLLD QESVCVATAS GDVIVCNLST QQLECVGSVA SGISVMSWSP D QELLLLAT AQQTLIMMTK DFEVIAEEQI HQDDFGEGKF VTVGWGSKQT QFHGSEGRPT AF PVQLPEN ALPWDDRRPH ITWRGDGQYF AVSVVCRQTE ARKIRVWNRE FALQSTSESV PGL GPALAW KPSGSLIAST QDKPNQQDVV FFEKNGLLHG HFTLPFLKDE VKVNDLLWNA DSSV LAIWL EDLPKEDSST LKSYVQLWTV GNYHWYLKQS LPFSTTGKNQ IVSLLWDPVT PCRLH VLCT GWRYLCCDWH WTTDRSSGNS ANDLANVAVI DGNRVLVTVF RQTVVPPPMC TYRLLI PHP VNQVIFSAHL GNDLAVLDAS NQISVYKCGD KPNMDSTVKL GAVGGNGFKV PLTTPHL EK RYSIQFGNNE EEEEEEVNAL QLSFLTWVED DTFLAISYSH SSSQSIIHHL TVTHSEVD E EQGQLDVSSS VTVDGVVIGL CCCSKTKSLA VQLADGQVLK YLWESPSLAV EPWKNSEGI PVRFVHPCTQ MEVATIGGEE CVLGLTDRCR FFINDTEVAS NITSFAVCDD FLLVTTHSHT CQVFSLSGA SLKMLQAALS GSHEASGEIL RKVERGSRIV TVVPQDTKLI LQMPRGNLEV V HHRALVLA QIRKWLDKLM FKEAFECMRK LRINLNLIHD HNPKVFLENV ETFVKQIDSV NH INLFFTE LREEDVTKTM YPPPITKSVQ VSTHPDGKKL DLICDAMRAA MEAINPRKFC LSI LTSHVK KTTPELEIVL QKVQELQGNL PFDPESVSVE EALKYLLLLV DVNELFNHSL GTYD FNLVL MVAEKSQKDP KEYLPFLNTL KKMETNYQRF TIDKYLKRYE KALGHLSKCG PEYFT ECLN LIKDKNLYKE ALKLYRPDSP QYQAVSMAYG EHLMQEHLYE PAGLVFARCG AQEKAL EAF LACGSWQQAL CVAAQLQMSK DKVAGLARTL AGKLVEQRKH SEAATVLEQY AQDYEEA VL LLLEGSAWEE ALRLVYKYDR VDIIETSVKP SILEAQKNYM DFLDSETATF IRHKNRLQ V VRALRRQAPQ VHVDHEVAHG PESDLFSETS SIMSGSEMSG RYSHSNSRIS ARSSKNRRK AERKKHSLKE GSPLEGLALL EALSEVVQSV EKLKDEVRAI LKVLFLFEFE EQAKELQRAF ESTLQLMER AVPEIWTPAG QQSSTTPVLG PSSTANSITA SYQQQKTCVP ALDAGVYMPP K MDPRSQWK LSLLE

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Macromolecule #2: Elongator complex protein 2

MacromoleculeName: Elongator complex protein 2 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MVSSVLEVSH VFCCPNRVRG ALSWNTGPGG LLAFGTSCSV VLYDPQKKVV ITNLNGHTAR VNCLQWIRT EDGSPSNELV SGGSDNRVIH WELENNQVLK SVRLQGHEGP VCAVHAIYQS G PSEGEQHA LIASAASDST VRIWSKKGSE VKYLQTLSFR DGFVLSVCLA ...String:
MVSSVLEVSH VFCCPNRVRG ALSWNTGPGG LLAFGTSCSV VLYDPQKKVV ITNLNGHTAR VNCLQWIRT EDGSPSNELV SGGSDNRVIH WELENNQVLK SVRLQGHEGP VCAVHAIYQS G PSEGEQHA LIASAASDST VRIWSKKGSE VKYLQTLSFR DGFVLSVCLA ILPGTNVPVL AC GDDDCRI HLYIQQDDQF QKALSLCGHE DWIRGVEWAT FGRDLFLASC SQDCLIRIWR LYM KPASFE TKDGSLRLKE NTFTIKDGGV RTTVAVTLET VLAGHENWVN AVHWQPSFYK DGVL QQPVR LLSASMDKTM ILWAPDEESG VWLEQVRVGE VGGNTLGFYD CQFGENGTMI IAHAF HGAL HLWKQSTVNP RQWAPEIVIS GHFDGVQDLM WDPEGEFIIT TSTDQTTRLF APWKKK DQK DRSQVTWHEI ARPQIHGYNI KCLAMIDRFQ FVSGADEKVL RVFSAPRNFV ENFSVIS RQ SLSHMLCDDQ DLPEGATVPA LGLSNKALFQ GDIASQPFEE DELISPAFGS PQVTFQPA V LNEPPTEDHL LQNTLWPEIQ KLYGHGYEIV CVACNNSKTL LASACKASQK EHAAIILWS TASWKQVQSL AFHTLTVTQM TFSPDDKFLL AVSRDRTWSL WKRQDATSSE FDPFFSLFAF TNKITSVHS RIIWSCDWSP DNKYFFTGSR DKKVVVWGEC KSSHNPMEHP IRPCSSILDV G SSVTAVSV CPVLNPAQRY IVAIGLESGK ICIYSWNKTN QEINDWTSCV ETNPSQSHSL GI RRLCWKS CSDDDDDDDD DDTEQSEEGP EWLHFASCGE DHTVKIYRVN RRAL

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Macromolecule #3: Elongator complex protein 3

MacromoleculeName: Elongator complex protein 3 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
EC number: Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MRQKRKGDLS PAELMMLTIG DVIKQLVEAH EQGKDVDLNK MKTKTAAKYG LASQPRLVDI IAAVPPHYR KILIPKLKAK PVRTASGIAV VAVMCKPHRC PHISFTGNIC IYCPGGPDSD F EYSTQSYT GYEPTSMRAI RARYDPFLQT RHRIEQLKQL GHSVDKVEFI ...String:
MRQKRKGDLS PAELMMLTIG DVIKQLVEAH EQGKDVDLNK MKTKTAAKYG LASQPRLVDI IAAVPPHYR KILIPKLKAK PVRTASGIAV VAVMCKPHRC PHISFTGNIC IYCPGGPDSD F EYSTQSYT GYEPTSMRAI RARYDPFLQT RHRIEQLKQL GHSVDKVEFI VMGGTFMALP EE YRDYFIR SLHDALSGHT SNNIHEAIKY SERSFTKCVG ITIETRPDYC MKRHLSDMLT YGC TRLEIG VQSVYEDVAR DTNRGHTVKA ACESFHLAKD SGFKVVTHMM PDLPNVGLER DIEQ FIEFF ENPAFRPDGL KLYPTLVIRG TGLYELWKSG RYRSYSPSDL IELVARILAL VPPWT RVYR VQRDIPMPLV SSGVEHGNLR ELAFARMKDL GIQCRDVRTR EVGIQEIHHR VRPYQV ELV RRDYVANGGW ETFLSYEDPD QDILIGLLRL RKCSEETFRF ELGGGVSIVR ELHVYGS VV PVSSRDPTKF QHQGFGMLLM EEAERIAREE HGSGKMAVIS GVGTRNYYRK IGYRLQGP Y MVKMLK

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Macromolecule #4: Elongator complex protein 4

MacromoleculeName: Elongator complex protein 4 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAAADTCGAG TLSSRSVASE AGQGGTSSFQ RKGKASGGPG GGPRLLSIAG TRPSVRNGQL LVSTGLPAL DQLLGGGLAV GTLLLIEEDK YNIYSPLLFK YFMAEGIING HTLLVASAKE N PAKILQEL PAPLLDDNSK KELEDVHSAK TPEPNVNMKI AWRYQLQPKM ...String:
MAAADTCGAG TLSSRSVASE AGQGGTSSFQ RKGKASGGPG GGPRLLSIAG TRPSVRNGQL LVSTGLPAL DQLLGGGLAV GTLLLIEEDK YNIYSPLLFK YFMAEGIING HTLLVASAKE N PAKILQEL PAPLLDDNSK KELEDVHSAK TPEPNVNMKI AWRYQLQPKM EVGPVSSSRF GH YYDLSKR IPWELLQSSK WHGFFLPEHI SPDLKGESCF LSCGYMRLLE FIQKSVYAEG FDG ANPQKK QKNILRIGIQ NLGSPLWGDD ICCKENCDNN HRLTKFLYIL RGLLRSSLSA CIIT MPAHL VQNKSITTRV RNLSDTVVGL ESFIGSERET NPLYKDYHGL IHIRKIPRLN NLTCD ESDV KDLAFKLKRK LFTIERLHLP PDLSDTVGRS SKQDLAASTA RLGAGCSSMA EGKKHL DF

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Macromolecule #5: Elongator complex protein 5

MacromoleculeName: Elongator complex protein 5 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MLDSLLAIGG LVLLRDSVEW EGRSLLKALI KKSALRGEQV HVLGCEVSEE EFREGFDSDV NSRLVYHDL FRDPLNWSKP GEAVPEGPLK ALRSMCKRTD HGSVTIALDS LSWLLCHIPC V TLCQALHA LSQQNGDPGD NSLVEQVRVL GLLHEELHGP GSMGALNTLA ...String:
MLDSLLAIGG LVLLRDSVEW EGRSLLKALI KKSALRGEQV HVLGCEVSEE EFREGFDSDV NSRLVYHDL FRDPLNWSKP GEAVPEGPLK ALRSMCKRTD HGSVTIALDS LSWLLCHIPC V TLCQALHA LSQQNGDPGD NSLVEQVRVL GLLHEELHGP GSMGALNTLA HTEVTLSGKV DQ TSASILC RRPQQRATYQ TWWFSVLPDF SLTLHEGLPL RSELHPDHHT TQVDPTAHLT FNL HLSKKE REARDSLTLP FQFSSEKQKA LLHPVPSRTT GHIFYEPDAF DDVDPEDPDD DLDI

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Macromolecule #6: Elongator complex protein 6

MacromoleculeName: Elongator complex protein 6 / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MFPELNNLLS TTPDKTEQGT LTLLCDAKTD GSFLVHHFLS FYLKANCKVC FVALVQSFSH YNIVGQKLG VSLTAARDRG QLVFLEGLKS SVEVLFHSQD EPHPLQFLRE AGTGNLQSLY T FIQDTLKP ADSEESPWKY PVLLVDNLSV LLSLGVGAVA VLDFMQYCRA ...String:
MFPELNNLLS TTPDKTEQGT LTLLCDAKTD GSFLVHHFLS FYLKANCKVC FVALVQSFSH YNIVGQKLG VSLTAARDRG QLVFLEGLKS SVEVLFHSQD EPHPLQFLRE AGTGNLQSLY T FIQDTLKP ADSEESPWKY PVLLVDNLSV LLSLGVGAVA VLDFMQYCRA TVCCELKGNV VA LVHDTEG ATDEGNDTLL NGLSHQSHLI LRAEGLATGF CKDVHGQLSI LWRRPSRSTA QRA QSLTYQ YKIQDKNVSF FAKGMSPAVL

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.4 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
100.0 mMNaClsodium chloride
20.0 mMHEPESHEPES
5.0 mMDithiothreitolDithiothreitol
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen 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.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 5232 / Average exposure time: 1.82 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Details20 eV slit, fully tuned before the experiment
Particle selectionNumber selected: 607086
Details: given number of particles is after TOPAZ picking and 2D classification curation, without removal of duplicate picks
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.92 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1)
Details: Overal resolution estimation given for a post-process sharpened map
Number images used: 27128
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.2.0) / Software - details: Ab-Initio Reconstruction / Details: Ab-Initio Reconstruction
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) / Software - details: 3D auto-refine / Details: 3D auto-refine
Final 3D classificationNumber classes: 2 / Avg.num./class: 28800 / Software - Name: RELION (ver. 3.1) / Software - details: Masked 3D classification
Details: Final masked 3D classification to improve Elp456 density
FSC plot (resolution estimation)

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