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- EMDB-17924: Cryo-EM structure of human Elp123 in complex with tRNA, acetyl-Co... -

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Basic information

Entry
Database: EMDB / ID: EMD-17924
TitleCryo-EM structure of human Elp123 in complex with tRNA, acetyl-CoA, 5'-deoxyadenosine and methionine
Map datadeepEMhancer sharpened map
Sample
  • Complex: Human Elp123 in complex with glutamine tRNA, acetyl-CoA, 5'-deoxyadenosine and methionine
    • Protein or peptide: Elongator complex protein 1
    • Protein or peptide: Elongator complex protein 2
    • Protein or peptide: Elongator complex protein 3
    • RNA: tRNA Gln
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: 5'-DEOXYADENOSINE
  • Ligand: ACETYL COENZYME *A
  • Ligand: METHIONINE
  • Ligand: MAGNESIUM ION
KeywordsElongator / tRNA modification / acetyl-CoA hydrolysis / TRANSLATION
Function / homology
Function and homology information


phosphorylase kinase regulator activity / tRNA uridine(34) acetyltransferase activity / tRNA carboxymethyluridine synthase / elongator holoenzyme complex / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / tRNA wobble uridine modification / regulation of receptor signaling pathway via JAK-STAT / acetyltransferase activity / transcription elongation factor complex / central nervous system development ...phosphorylase kinase regulator activity / tRNA uridine(34) acetyltransferase activity / tRNA carboxymethyluridine synthase / elongator holoenzyme complex / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / tRNA wobble uridine modification / regulation of receptor signaling pathway via JAK-STAT / acetyltransferase activity / transcription elongation factor complex / central nervous system development / transcription elongation by RNA polymerase II / neuron migration / regulation of translation / HATs acetylate histones / 4 iron, 4 sulfur cluster binding / tRNA binding / positive regulation of cell migration / regulation of transcription by RNA polymerase II / protein kinase binding / nucleolus / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / : / : / : / : / ELP1 N-terminal second beta-propeller / ELP1 TPR domain / ELP1 alpha-solenoid / ELP1 three-helix bundle / ELP3 N-terminal domain ...: / : / : / : / : / ELP1 N-terminal second beta-propeller / ELP1 TPR domain / ELP1 alpha-solenoid / ELP1 three-helix bundle / ELP3 N-terminal domain / Elongator complex protein 1 / Elongator complex protein 2 / ELP1 first N-terminal beta-propeller / Radical SAM, C-terminal extension / Elongator complex protein 3-like / ELP3/YhcC / Radical_SAM C-terminal domain / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Elongator complex protein 1 / Elongator complex protein 2 / Elongator complex protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsAbbassi N / Jaciuk M / Lin T-Y / Glatt S
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)101001394European Union
CitationJournal: Nat Commun / Year: 2024
Title: Cryo-EM structures of the human Elongator complex at work.
Authors: Nour-El-Hana Abbassi / Marcin Jaciuk / David Scherf / Pauline Böhnert / Alexander Rau / Alexander Hammermeister / Michał Rawski / Paulina Indyka / Grzegorz Wazny / Andrzej Chramiec- ...Authors: Nour-El-Hana Abbassi / Marcin Jaciuk / David Scherf / Pauline Böhnert / Alexander Rau / Alexander Hammermeister / Michał Rawski / Paulina Indyka / Grzegorz Wazny / Andrzej Chramiec-Głąbik / Dominika Dobosz / Bozena Skupien-Rabian / Urszula Jankowska / Juri Rappsilber / Raffael Schaffrath / Ting-Yu Lin / Sebastian Glatt /
Abstract: tRNA modifications affect ribosomal elongation speed and co-translational folding dynamics. The Elongator complex is responsible for introducing 5-carboxymethyl at wobble uridine bases (cmU) in ...tRNA modifications affect ribosomal elongation speed and co-translational folding dynamics. The Elongator complex is responsible for introducing 5-carboxymethyl at wobble uridine bases (cmU) in eukaryotic tRNAs. However, the structure and function of human Elongator remain poorly understood. In this study, we present a series of cryo-EM structures of human ELP123 in complex with tRNA and cofactors at four different stages of the reaction. The structures at resolutions of up to 2.9 Å together with complementary functional analyses reveal the molecular mechanism of the modification reaction. Our results show that tRNA binding exposes a universally conserved uridine at position 33 (U), which triggers acetyl-CoA hydrolysis. We identify a series of conserved residues that are crucial for the radical-based acetylation of U and profile the molecular effects of patient-derived mutations. Together, we provide the high-resolution view of human Elongator and reveal its detailed mechanism of action.
History
DepositionJul 16, 2023-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17924.png

Downloads & links

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Map

FileDownload / File: emd_17924.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationdeepEMhancer sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 480 pix.
= 412.8 Å		0.86 Å/pix.
x 480 pix.
= 412.8 Å		0.86 Å/pix.
x 480 pix.
= 412.8 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: 0.156
Minimum - Maximum-0.016732717 - 1.9152904
Average (Standard dev.)0.0008482741 (±0.019432118)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 412.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17924_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_17924_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_17924_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 : Human Elp123 in complex with glutamine tRNA, acetyl-CoA, 5'-deoxy...

EntireName: Human Elp123 in complex with glutamine tRNA, acetyl-CoA, 5'-deoxyadenosine and methionine
Components
  • Complex: Human Elp123 in complex with glutamine tRNA, acetyl-CoA, 5'-deoxyadenosine and methionine
    • Protein or peptide: Elongator complex protein 1
    • Protein or peptide: Elongator complex protein 2
    • Protein or peptide: Elongator complex protein 3
    • RNA: tRNA Gln
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: 5'-DEOXYADENOSINE
  • Ligand: ACETYL COENZYME *A
  • Ligand: METHIONINE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Human Elp123 in complex with glutamine tRNA, acetyl-CoA, 5'-deoxy...

SupramoleculeName: Human Elp123 in complex with glutamine tRNA, acetyl-CoA, 5'-deoxyadenosine and methionine
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 635 KDa

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Macromolecule #1: Elongator complex protein 1

MacromoleculeName: Elongator complex protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 150.427484 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MRNLKLFRTL EFRDIQGPGN PQCFSLRTEQ GTVLIGSEHG LIEVDPVSRE VKNEVSLVAE GFLPEDGSGR IVGVQDLLDQ ESVCVATAS GDVILCSLST QQLECVGSVA SGISVMSWSP DQELVLLATG QQTLIMMTKD FEPILEQQIH QDDFGESKFI T VGWGRKET ...String:
MRNLKLFRTL EFRDIQGPGN PQCFSLRTEQ GTVLIGSEHG LIEVDPVSRE VKNEVSLVAE GFLPEDGSGR IVGVQDLLDQ ESVCVATAS GDVILCSLST QQLECVGSVA SGISVMSWSP DQELVLLATG QQTLIMMTKD FEPILEQQIH QDDFGESKFI T VGWGRKET QFHGSEGRQA AFQMQMHESA LPWDDHRPQV TWRGDGQFFA VSVVCPETGA RKVRVWNREF ALQSTSEPVA GL GPALAWK PSGSLIASTQ DKPNQQDIVF FEKNGLLHGH FTLPFLKDEV KVNDLLWNAD SSVLAVWLED LQREESSIPK TCV QLWTVG NYHWYLKQSL SFSTCGKSKI VSLMWDPVTP YRLHVLCQGW HYLAYDWHWT TDRSVGDNSS DLSNVAVIDG NRVL VTVFR QTVVPPPMCT YQLLFPHPVN QVTFLAHPQK SNDLAVLDAS NQISVYKCGD CPSADPTVKL GAVGGSGFKV CLRTP HLEK RYKIQFENNE DQDVNPLKLG LLTWIEEDVF LAVSHSEFSP RSVIHHLTAA SSEMDEEHGQ LNVSSSAAVD GVIISL CCN SKTKSVVLQL ADGQIFKYLW ESPSLAIKPW KNSGGFPVRF PYPCTQTELA MIGEEECVLG LTDRCRFFIN DIEVASN IT SFAVYDEFLL LTTHSHTCQC FCLRDASFKT LQAGLSSNHV SHGEVLRKVE RGSRIVTVVP QDTKLVLQMP RGNLEVVH H RALVLAQIRK WLDKLMFKEA FECMRKLRIN LNLIYDHNPK VFLGNVETFI KQIDSVNHIN LFFTELKEED VTKTMYPAP VTSSVYLSRD PDGNKIDLVC DAMRAVMESI NPHKYCLSIL TSHVKKTTPE LEIVLQKVHE LQGNAPSDPD AVSAEEALKY LLHLVDVNE LYDHSLGTYD FDLVLMVAEK SQKDPKEYLP FLNTLKKMET NYQRFTIDKY LKRYEKAIGH LSKCGPEYFP E CLNLIKDK NLYNEALKLY SPSSQQYQDI SIAYGEHLMQ EHMYEPAGLM FARCGAHEKA LSAFLTCGNW KQALCVAAQL NF TKDQLVG LGRTLAGKLV EQRKHIDAAM VLEECAQDYE EAVLLLLEGA AWEEALRLVY KYNRLDIIET NVKPSILEAQ KNY MAFLDS QTATFSRHKK RLLVVRELKE QAQQAGLDDE VPHGQESDLF SETSSVVSGS EMSGKYSHSN SRISARSSKN RRKA ERKKH SLKEGSPLED LALLEALSEV VQNTENLKDE VYHILKVLFL FEFDEQGREL QKAFEDTLQL MERSLPEIWT LTYQQ NSAT PVLGPNSTAN SIMASYQQQK TSVPVLDAEL FIPPKINRRT QWKLSLLD

UniProtKB: Elongator complex protein 1

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Macromolecule #2: Elongator complex protein 2

MacromoleculeName: Elongator complex protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 92.597766 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MVAPVLETSH VFCCPNRVRG VLNWSSGPRG LLAFGTSCSV VLYDPLKRVV VTNLNGHTAR VNCIQWICKQ DGSPSTELVS GGSDNQVIH WEIEDNQLLK AVHLQGHEGP VYAVHAVYQR RTSDPALCTL IVSAAADSAV RLWSKKGPEV MCLQTLNFGN G FALALCLS ...String:
MVAPVLETSH VFCCPNRVRG VLNWSSGPRG LLAFGTSCSV VLYDPLKRVV VTNLNGHTAR VNCIQWICKQ DGSPSTELVS GGSDNQVIH WEIEDNQLLK AVHLQGHEGP VYAVHAVYQR RTSDPALCTL IVSAAADSAV RLWSKKGPEV MCLQTLNFGN G FALALCLS FLPNTDVPIL ACGNDDCRIH IFAQQNDQFQ KVLSLCGHED WIRGVEWAAF GRDLFLASCS QDCLIRIWKL YI KSTSLET QDDDNIRLKE NTFTIENESV KIAFAVTLET VLAGHENWVN AVHWQPVFYK DGVLQQPVRL LSASMDKTMI LWA PDEESG VWLEQVRVGE VGGNTLGFYD CQFNEDGSMI IAHAFHGALH LWKQNTVNPR EWTPEIVISG HFDGVQDLVW DPEG EFIIT VGTDQTTRLF APWKRKDQSQ VTWHEIARPQ IHGYDLKCLA MINRFQFVSG ADEKVLRVFS APRNFVENFC AITGQ SLNH VLCNQDSDLP EGATVPALGL SNKAVFQGDI ASQPSDEEEL LTSTGFEYQQ VAFQPSILTE PPTEDHLLQN TLWPEV QKL YGHGYEIFCV TCNSSKTLLA SACKAAKKEH AAIILWNTTS WKQVQNLVFH SLTVTQMAFS PNEKFLLAVS RDRTWSL WK KQDTISPEFE PVFSLFAFTN KITSVHSRII WSCDWSPDSK YFFTGSRDKK VVVWGECDST DDCIEHNIGP CSSVLDVG G AVTAVSVCPV LHPSQRYVVA VGLECGKICL YTWKKTDQVP EINDWTHCVE TSQSQSHTLA IRKLCWKNCS GKTEQKEAE GAEWLHFASC GEDHTVKIHR VNKCAL

UniProtKB: Elongator complex protein 2

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Macromolecule #3: Elongator complex protein 3

MacromoleculeName: 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
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 65.740539 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MRQKRKGDLS PAELMMLTIG DVIKQLIEAH EQGKDIDLNK VKTKTAAKYG LSAQPRLVDI IAAVPPQYRK VLMPKLKAKP IRTASGIAV VAVMCKPHRC PHISFTGNIC VYCPGGPDSD FEYSTQSYTG YEPTSMRAIR ARYDPFLQTR HRIEQLKQLG H SVDKVEFI ...String:
MRQKRKGDLS PAELMMLTIG DVIKQLIEAH EQGKDIDLNK VKTKTAAKYG LSAQPRLVDI IAAVPPQYRK VLMPKLKAKP IRTASGIAV VAVMCKPHRC PHISFTGNIC VYCPGGPDSD FEYSTQSYTG YEPTSMRAIR ARYDPFLQTR HRIEQLKQLG H SVDKVEFI VMGGTFMALP EEYRDYFIRN LHDALSGHTS NNIYEAVKYS ERSLTKCIGI TIETRPDYCM KRHLSDMLTY GC TRLEIGV QSVYEDVARD TNRGHTVKAV CESFHLAKDS GFKVVAHMMP DLPNVGLERD IEQFTEFFEN PAFRPDGLKL YPT LVIRGT GLYELWKSGR YKSYSPSDLV ELVARILALV PPWTRVYRVQ RDIPMPLVSS GVEHGNLREL ALARMKDLGI QCRD VRTRE VGIQEIHHKV RPYQVELVRR DYVANGGWET FLSYEDPDQD ILIGLLRLRK CSEETFRFEL GGGVSIVREL HVYGS VVPV SSRDPTKFQH QGFGMLLMEE AERIAREEHG SGKIAVISGV GTRNYYRKIG YRLQGPYMVK MLKGLEGSAW SHPQFE KGG GSGGGSGGSA WSHPQFEK

UniProtKB: Elongator complex protein 3

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Macromolecule #4: tRNA Gln

MacromoleculeName: tRNA Gln / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.047236 KDa
SequenceString:
GGCCCCAUGG UGUAAUGGUU AGCACUCUGG ACUUUGAAUC CAGCGAUCCG AGUUCAAAUC UCGGUGGGAC CUCCA

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Macromolecule #5: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 5 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #6: 5'-DEOXYADENOSINE

MacromoleculeName: 5'-DEOXYADENOSINE / type: ligand / ID: 6 / Number of copies: 1 / Formula: 5AD
Molecular weightTheoretical: 251.242 Da
Chemical component information

ChemComp-5AD:
5'-DEOXYADENOSINE

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Macromolecule #7: ACETYL COENZYME *A

MacromoleculeName: ACETYL COENZYME *A / type: ligand / ID: 7 / Number of copies: 1 / Formula: ACO
Molecular weightTheoretical: 809.571 Da
Chemical component information

ChemComp-ACO:
ACETYL COENZYME *A

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Macromolecule #8: METHIONINE

MacromoleculeName: METHIONINE / type: ligand / ID: 8 / Number of copies: 1 / Formula: MET
Molecular weightTheoretical: 149.211 Da
Chemical component information

ChemComp-MET:
METHIONINE

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Macromolecule #9: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 9 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

Concentration0.6 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
100.0 mMNaClsodium chloride
20.0 mMHEPESHEPES
2.0 mMDithiothreitolDithiothreitol
2.0 mMMgCl2magnesium chloride
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Details: 8 mA
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: 4214 / Average electron dose: 40.09 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: 2.1 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: 1250013
Details: given number of particles is the sum of blob and 3x TOPAZ pickings, each firstly curated in 2D classification
Startup modelType of model: INSILICO MODEL / In silico model: Ab-Initio Reconstruction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 215353
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Details: Ab-Initio Reconstruction
Final angle assignmentType: MAXIMUM LIKELIHOOD / Details: local refinement
Final 3D classificationNumber classes: 3
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

3-f1

source_name: AlphaFold, initial_model_type: in silico model

6-f1

source_name: AlphaFold, initial_model_type: in silico model

3-f1

source_name: AlphaFold, initial_model_type: in silico model
Output model

PDB-8ptx:
Cryo-EM structure of human Elp123 in complex with tRNA, acetyl-CoA, 5'-deoxyadenosine and methionine

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