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- EMDB-14511: Human NEXT dimer - focused reconstruction of the dimerization module -

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Basic information

Entry
Database: EMDB / ID: EMD-14511
TitleHuman NEXT dimer - focused reconstruction of the dimerization module
Map dataNEXT_S_dimerization_module_postprocess
Sample
  • Complex: Human NEXT dimer - focused reconstruction of the dimerization module
    • Protein or peptide: Zinc finger CCHC domain-containing protein 8
    • Protein or peptide: Exosome RNA helicase MTR4
KeywordsHELICASE / ATPASE / RNA DEGRADATION / EXOSOME / RNA BINDING PROTEIN
Function / homology
Function and homology information


snRNA catabolic process / TRAMP complex / mRNA 3'-end processing / RNA catabolic process / maturation of 5.8S rRNA / Major pathway of rRNA processing in the nucleolus and cytosol / RNA processing / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex ...snRNA catabolic process / TRAMP complex / mRNA 3'-end processing / RNA catabolic process / maturation of 5.8S rRNA / Major pathway of rRNA processing in the nucleolus and cytosol / RNA processing / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / mRNA splicing, via spliceosome / rRNA processing / RNA helicase activity / nuclear body / RNA helicase / nuclear speck / DNA damage response / nucleolus / ATP hydrolysis activity / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
: / rRNA-processing arch domain / Mtr4-like, beta-barrel domain / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / : / DSHCT (NUC185) domain / Exosome RNA helicase MTR4-like, stalk / DSHCT / : ...: / rRNA-processing arch domain / Mtr4-like, beta-barrel domain / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / : / DSHCT (NUC185) domain / Exosome RNA helicase MTR4-like, stalk / DSHCT / : / PSP, proline-rich / PSP / proline-rich domain in spliceosome associated proteins / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / zinc finger / Zinc knuckle / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / 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
Exosome RNA helicase MTR4 / Zinc finger CCHC domain-containing protein 8
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsGerlach P / Lingaraju M / Salerno-Kochan A / Bonneau F / Basquin J / Conti E
Funding support Germany, European Union, 4 items
OrganizationGrant numberCountry
Max Planck Society Germany
European CommissionERC-2016-ADG 740329 EXORICOEuropean Union
German Research Foundation (DFG)SFB/TRR 237 Germany
German Research Foundation (DFG)SFB 1035 Germany
CitationJournal: Mol Cell / Year: 2022
Title: Structure and regulation of the nuclear exosome targeting complex guides RNA substrates to the exosome.
Authors: Piotr Gerlach / William Garland / Mahesh Lingaraju / Anna Salerno-Kochan / Fabien Bonneau / Jérôme Basquin / Torben Heick Jensen / Elena Conti /
Abstract: In mammalian cells, spurious transcription results in a vast repertoire of unproductive non-coding RNAs, whose deleterious accumulation is prevented by rapid decay. The nuclear exosome targeting ...In mammalian cells, spurious transcription results in a vast repertoire of unproductive non-coding RNAs, whose deleterious accumulation is prevented by rapid decay. The nuclear exosome targeting (NEXT) complex plays a central role in directing non-functional transcripts to exosome-mediated degradation, but the structural and molecular mechanisms remain enigmatic. Here, we elucidated the architecture of the human NEXT complex, showing that it exists as a dimer of MTR4-ZCCHC8-RBM7 heterotrimers. Dimerization preconfigures the major MTR4-binding region of ZCCHC8 and arranges the two MTR4 helicases opposite to each other, with each protomer able to function on many types of RNAs. In the inactive state of the complex, the 3' end of an RNA substrate is enclosed in the MTR4 helicase channel by a ZCCHC8 C-terminal gatekeeping domain. The architecture of a NEXT-exosome assembly points to the molecular and regulatory mechanisms with which the NEXT complex guides RNA substrates to the exosome.
History
DepositionMar 6, 2022-
Header (metadata) releaseJun 22, 2022-
Map releaseJun 22, 2022-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14511.png

Downloads & links

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Map

FileDownload / File: emd_14511.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNEXT_S_dimerization_module_postprocess
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 200 pix.
= 218.8 Å		1.09 Å/pix.
x 200 pix.
= 218.8 Å		1.09 Å/pix.
x 200 pix.
= 218.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.094 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.031485483 - 0.04316537
Average (Standard dev.)0.0000093778735 (±0.0014424308)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 218.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14511_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: NEXT S dimerization module refine 238 denmod map

Fileemd_14511_additional_1.map
AnnotationNEXT_S_dimerization_module_refine_238_denmod_map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: NEXT S dimerization module half map 2

Fileemd_14511_half_map_1.map
AnnotationNEXT_S_dimerization_module_half_map_2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: NEXT S dimerization module half map 1

Fileemd_14511_half_map_2.map
AnnotationNEXT_S_dimerization_module_half_map_1
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 NEXT dimer - focused reconstruction of the dimerization module

EntireName: Human NEXT dimer - focused reconstruction of the dimerization module
Components
  • Complex: Human NEXT dimer - focused reconstruction of the dimerization module
    • Protein or peptide: Zinc finger CCHC domain-containing protein 8
    • Protein or peptide: Exosome RNA helicase MTR4

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Supramolecule #1: Human NEXT dimer - focused reconstruction of the dimerization module

SupramoleculeName: Human NEXT dimer - focused reconstruction of the dimerization module
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Zinc finger CCHC domain-containing protein 8

MacromoleculeName: Zinc finger CCHC domain-containing protein 8 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.668961 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GPDSENGVGD AELRERLRQC EETIEQLRAE NQELKRKLNI LTRPSGILVN DTKLDGPILQ ILFMNNAISK QYHQEIEEFV SNLVKRFEE QQKNDVEKTS FNLLPQPSSI VLEEDHKVEE SCAIKNNKEA FSVVGSVLYF TNFCLDKLGQ PLLNENPQLS E GWEIPKYH ...String:
GPDSENGVGD AELRERLRQC EETIEQLRAE NQELKRKLNI LTRPSGILVN DTKLDGPILQ ILFMNNAISK QYHQEIEEFV SNLVKRFEE QQKNDVEKTS FNLLPQPSSI VLEEDHKVEE SCAIKNNKEA FSVVGSVLYF TNFCLDKLGQ PLLNENPQLS E GWEIPKYH QVFSHIVSLE GQEIQVKAKR PKPHCFNCGS EEHQMKDCPM PRNAARISEK RKEYMDACGE ANNQNFQQRY HA EEVEERF GRFKPGVISE ELQDALGVTD KSLPPFIYRM RQLGYPPGWL KEAELENSGL ALYD

UniProtKB: Zinc finger CCHC domain-containing protein 8

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Macromolecule #2: Exosome RNA helicase MTR4

MacromoleculeName: Exosome RNA helicase MTR4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 118.32207 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GPDSMADAFG DELFSVFEGD STTAAGTKKD KEKDKGKWKG PPGSADKAGK RFDGKLQSES TNNGKNKRDV DFEGTDEPIF GKKPRIEES ITEDLSLADL MPRVKVQSVE TVEGCTHEVA LPAEEDYLPL KPRVGKAAKE YPFILDAFQR EAIQCVDNNQ S VLVSAHTS ...String:
GPDSMADAFG DELFSVFEGD STTAAGTKKD KEKDKGKWKG PPGSADKAGK RFDGKLQSES TNNGKNKRDV DFEGTDEPIF GKKPRIEES ITEDLSLADL MPRVKVQSVE TVEGCTHEVA LPAEEDYLPL KPRVGKAAKE YPFILDAFQR EAIQCVDNNQ S VLVSAHTS AGKTVCAEYA IALALREKQR VIFTSPIKAL SNQKYREMYE EFQDVGLMTG DVTINPTASC LVMTTEILRS ML YRGSEVM REVAWVIFDE IHYMRDSERG VVWEETIILL PDNVHYVFLS ATIPNARQFA EWICHLHKQP CHVIYTDYRP TPL QHYIFP AGGDGLHLVV DENGDFREDN FNTAMQVLRD AGDLAKGDQK GRKGGTKGPS NVFKIVKMIM ERNFQPVIIF SFSK KDCEA YALQMTKLDF NTDEEKKMVE EVFSNAIDCL SDEDKKLPQV EHVLPLLKRG IGIHHGGLLP ILKETIEILF SEGLI KALF ATETFAMGIN MPARTVLFTN ARKFDGKDFR WISSGEYIQM SGRAGRRGMD DRGIVILMVD EKMSPTIGKQ LLKGSA DPL NSAFHLTYNM VLNLLRVEEI NPEYMLEKSF YQFQHYRAIP GVVEKVKNSE EQYNKIVIPN EESVVIYYKI RQQLAKL GK EIEEYIHKPK YCLPFLQPGR LVKVKNEGDD FGWGVVVNFS KKSNVKPNSG ELDPLYVVEV LLRCSKESLK NSATEAAK P AKPDEKGEMQ VVPVLVHLLS AISSVRLYIP KDLRPVDNRQ SVLKSIQEVQ KRFPDGIPLL DPIDDMGIQD QGLKKVIQK VEAFEHRMYS HPLHNDPNLE TVYTLCEKKA QIAIDIKSAK RELKKARTVL QMDELKCRKR VLRRLGFATS SDVIEMKGRV ACEISSADE LLLTEMMFNG LFNDLSAEQA TALLSCFVFQ ENSSEMPKLT EQLAGPLRQM QECAKRIAKV SAEAKLEIDE E TYLSSFKP HLMDVVYTWA TGATFAHICK MTDVFEGSII RCMRRLEELL RQMCQAAKAI GNTELENKFA EGITKIKRDI VF AASLYL

UniProtKB: Exosome RNA helicase MTR4

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 2.09 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 55022
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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