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- EMDB-17711: Cryo-EM structure of MLE in complex with SL7UUC RNA and ADP -

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Basic information

Entry
Database: EMDB / ID: EMD-17711
TitleCryo-EM structure of MLE in complex with SL7UUC RNA and ADP
Map data
Sample
  • Complex: Complex of MLE, SL7UUC and ADP
    • Complex: Dosage compensation regulator
      • Protein or peptide: Dosage compensation regulator
    • Complex: SL7UUC RNA
      • RNA: SL7UUC RNA
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsRNA helicase / RNA BINDING PROTEIN
Function / homology
Function and homology information


RIP-mediated NFkB activation via ZBP1 / X chromosome located dosage compensation complex, transcription activating / dosage compensation complex assembly / 3'-5' DNA/RNA helicase activity / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / male courtship behavior, veined wing generated song production / regulatory region RNA binding / regulation of cytoplasmic translation / PKR-mediated signaling / MSL complex ...RIP-mediated NFkB activation via ZBP1 / X chromosome located dosage compensation complex, transcription activating / dosage compensation complex assembly / 3'-5' DNA/RNA helicase activity / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / male courtship behavior, veined wing generated song production / regulatory region RNA binding / regulation of cytoplasmic translation / PKR-mediated signaling / MSL complex / dosage compensation by hyperactivation of X chromosome / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / sex-chromosome dosage compensation / 3'-5' RNA helicase activity / regulation of mRNA processing / axon extension / DNA duplex unwinding / lncRNA binding / 3'-5' DNA helicase activity / nuclear chromosome / positive regulation of heterochromatin formation / X chromosome / DNA helicase activity / determination of adult lifespan / helicase activity / double-stranded RNA binding / chromosome / double-stranded DNA binding / RNA helicase activity / RNA helicase / ribonucleoprotein complex / chromatin binding / chromatin / nucleolus / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / RNA binding / ATP binding / nucleus / cytosol
Similarity search - Function
DHX9, first double-stranded RNA binding domain / DHX9, second double-stranded RNA binding domain / DHX9, DEXH-box helicase domain / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase associated domain (HA2), winged-helix / Helicase-associated domain / Helicase associated domain (HA2) Add an annotation ...DHX9, first double-stranded RNA binding domain / DHX9, second double-stranded RNA binding domain / DHX9, DEXH-box helicase domain / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase associated domain (HA2), winged-helix / Helicase-associated domain / Helicase associated domain (HA2) Add an annotation / Double-stranded RNA binding motif / Double-stranded RNA binding motif / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Dosage compensation regulator mle
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.24 Å
AuthorsJagtap PKA / Hennig J
Funding support Germany, 1 items
OrganizationGrant numberCountry
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND Germany
CitationJournal: Mol Cell / Year: 2023
Title: Structural basis of RNA-induced autoregulation of the DExH-type RNA helicase maleless.
Authors: Pravin Kumar Ankush Jagtap / Marisa Müller / Anna E Kiss / Andreas W Thomae / Karine Lapouge / Martin Beck / Peter B Becker / Janosch Hennig /
Abstract: RNA unwinding by DExH-type helicases underlies most RNA metabolism and function. It remains unresolved if and how the basic unwinding reaction of helicases is regulated by auxiliary domains. We ...RNA unwinding by DExH-type helicases underlies most RNA metabolism and function. It remains unresolved if and how the basic unwinding reaction of helicases is regulated by auxiliary domains. We explored the interplay between the RecA and auxiliary domains of the RNA helicase maleless (MLE) from Drosophila using structural and functional studies. We discovered that MLE exists in a dsRNA-bound open conformation and that the auxiliary dsRBD2 domain aligns the substrate RNA with the accessible helicase tunnel. In an ATP-dependent manner, dsRBD2 associates with the helicase module, leading to tunnel closure around ssRNA. Furthermore, our structures provide a rationale for blunt-ended dsRNA unwinding and 3'-5' translocation by MLE. Structure-based MLE mutations confirm the functional relevance of our model for RNA unwinding. Our findings contribute to our understanding of the fundamental mechanics of auxiliary domains in DExH helicase MLE, which serves as a model for its human ortholog and potential therapeutic target, DHX9/RHA.
History
DepositionJun 23, 2023-
Header (metadata) releaseNov 22, 2023-
Map releaseNov 22, 2023-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17711.png

Downloads & links

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Map

FileDownload / File: emd_17711.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 256 pix.
= 238.592 Å		0.93 Å/pix.
x 256 pix.
= 238.592 Å		0.93 Å/pix.
x 256 pix.
= 238.592 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.029
Minimum - Maximum-0.07277685 - 0.24990912
Average (Standard dev.)0.000088354514 (±0.010072702)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 238.592 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_17711_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_17711_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of MLE, SL7UUC and ADP

EntireName: Complex of MLE, SL7UUC and ADP
Components
  • Complex: Complex of MLE, SL7UUC and ADP
    • Complex: Dosage compensation regulator
      • Protein or peptide: Dosage compensation regulator
    • Complex: SL7UUC RNA
      • RNA: SL7UUC RNA
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Complex of MLE, SL7UUC and ADP

SupramoleculeName: Complex of MLE, SL7UUC and ADP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Molecular weightTheoretical: 150 KDa

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Supramolecule #2: Dosage compensation regulator

SupramoleculeName: Dosage compensation regulator / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Supramolecule #3: SL7UUC RNA

SupramoleculeName: SL7UUC RNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Macromolecule #1: Dosage compensation regulator

MacromoleculeName: Dosage compensation regulator / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 130.335961 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDIKSFLYQF CAKSQIEPKF DIRQTGPKNR QRFLCEVRVE PNTYIGVGNS TNKKDAEKNA CRDFVNYLVR VGKLNTNDVP ADAGASGGG PRTGLEGAGM AGGSGQQKRV FDGQSGPQDL GEAYRPLNHD GGDGGNRYSV IDRIQEQRDM NEAEAFDVNA A IHGNWTIE ...String:
MDIKSFLYQF CAKSQIEPKF DIRQTGPKNR QRFLCEVRVE PNTYIGVGNS TNKKDAEKNA CRDFVNYLVR VGKLNTNDVP ADAGASGGG PRTGLEGAGM AGGSGQQKRV FDGQSGPQDL GEAYRPLNHD GGDGGNRYSV IDRIQEQRDM NEAEAFDVNA A IHGNWTIE NAKERLNIYK QTNNIRDDYK YTPVGPEHAR SFLAELSIYV PALNRTVTAR ESGSNKKSAS KSCALSLVRQ LF HLNVIEP FSGTLKKKKD EQLKPYPVKL SPNLINKIDE VIKGLDLPVV NPRNIKIELD GPPIPLIVNL SRIDSSQQDG EKR QESSVI PWAPPQANWN TWHACNIDEG ELATTSIDDL SMDYERSLRD RRQNDNEYRQ FLEFREKLPI AAMRSEILTA INDN PVVII RGNTGCGKTT QIAQYILDDY ICSGQGGYAN IYVTQPRRIS AISVAERVAR ERCEQLGDTV GYSVRFESVF PRPYG AILF CTVGVLLRKL EAGLRGVSHI IVDEIHERDV NSDFLLVILR DMVDTYPDLH VILMSATIDT TKFSKYFGIC PVLEVP GRA FPVQQFFLED IIQMTDFVPS AESRRKRKEV EDEEQLLSED KDEAEINYNK VCEDKYSQKT RNAMAMLSES DVSFELL EA LLMHIKSKNI PGAILVFLPG WNLIFALMKF LQNTNIFGDT SQYQILPCHS QIPRDEQRKV FEPVPEGVTK IILSTNIA E TSITIDDIVF VIDICKARMK LFTSHNNLTS YATVWASKTN LEQRKGRAGR VRPGFCFTLC SRARFQALED NLTPEMFRT PLHEMALTIK LLRLGSIHHF LSKALEPPPV DAVIEAEVLL REMRCLDAND ELTPLGRLLA RLPIEPRLGK MMVLGAVFGC ADLMAIMAS YSSTFSEVFS LDIGQRRLAN HQKALSGTKC SDHVAMIVAS QMWRREKQRG EHMEARFCDW KGLQMSTMNV I WDAKQQLL DLLQQAGFPE ECMISHEVDE RIDGDDPVLD VSLALLCLGL YPNICVHKEK RKVLTTESKA ALLHKTSVNC SN LAVTFPY PFFVFGEKIR TRAVSCKQLS MVSPLQVILF GSRKIDLAAN NIVRVDNWLN FDIEPELAAK IGALKPALED LIT VACDNP SDILRLEEPY AQLVKVVKDL CVKSAGDFGL QR

UniProtKB: Dosage compensation regulator mle

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Macromolecule #2: SL7UUC RNA

MacromoleculeName: SL7UUC RNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 19.011131 KDa
SequenceString:
GUGUAAAAUG UUGCUAGCAA AUAUAUAUGC UAGUAACGUU UUACGCCCUC UUUCUUUCUU

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 52.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.24 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 61690
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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