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- EMDB-24883: Human Nuclear Exosome Targeting (NEXT) complex bound to RNA (subs... -

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Basic information

Entry
Database: EMDB / ID: EMD-24883
TitleHuman Nuclear Exosome Targeting (NEXT) complex bound to RNA (substrate 2)
Map dataNEXT-RNA subtrate 2 complex - composite reconstruction
Sample
  • Complex: human Nuclear Exosome Targeting (NEXT) complex bound to RNA (substrate 2)
    • Protein or peptide: Exosome RNA helicase MTR4
    • Protein or peptide: Zinc finger CCHC domain-containing protein 8
    • Protein or peptide: RNA-binding protein 7
    • RNA: RNA (30-MER)
  • Ligand: ZINC ION
Function / homology
Function and homology information


: / snRNA catabolic process / TRAMP complex / snRNA binding / RNA catabolic process / regulation of alternative mRNA splicing, via spliceosome / maturation of 5.8S rRNA / Major pathway of rRNA processing in the nucleolus and cytosol / pre-mRNA intronic binding / catalytic step 2 spliceosome ...: / snRNA catabolic process / TRAMP complex / snRNA binding / RNA catabolic process / regulation of alternative mRNA splicing, via spliceosome / maturation of 5.8S rRNA / Major pathway of rRNA processing in the nucleolus and cytosol / pre-mRNA intronic binding / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / 14-3-3 protein binding / meiotic cell cycle / mRNA splicing, via spliceosome / rRNA processing / RNA helicase activity / single-stranded RNA binding / 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
RBM7, RNA recognition motif / rRNA-processing arch domain / Mtr4-like, beta-barrel domain / : / Exosome RNA helicase MTR4-like, stalk / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / DSHCT (NUC185) domain / DSHCT / PSP, proline-rich ...RBM7, RNA recognition motif / rRNA-processing arch domain / Mtr4-like, beta-barrel domain / : / Exosome RNA helicase MTR4-like, stalk / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / DSHCT (NUC185) domain / DSHCT / PSP, proline-rich / PSP / proline-rich domain in spliceosome associated proteins / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Helicase conserved C-terminal domain / RNA-binding domain superfamily / 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 / Nucleotide-binding alpha-beta plait domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Exosome RNA helicase MTR4 / Zinc finger CCHC domain-containing protein 8 / RNA-binding protein 7
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.62 Å
AuthorsPuno MR / Lima CD
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118080 United States
CitationJournal: Cell / Year: 2022
Title: Structural basis for RNA surveillance by the human nuclear exosome targeting (NEXT) complex.
Authors: M Rhyan Puno / Christopher D Lima /
Abstract: RNA quality control relies on co-factors and adaptors to identify and prepare substrates for degradation by ribonucleases such as the 3' to 5' ribonucleolytic RNA exosome. Here, we determined ...RNA quality control relies on co-factors and adaptors to identify and prepare substrates for degradation by ribonucleases such as the 3' to 5' ribonucleolytic RNA exosome. Here, we determined cryogenic electron microscopy structures of human nuclear exosome targeting (NEXT) complexes bound to RNA that reveal mechanistic insights to substrate recognition and early steps that precede RNA handover to the exosome. The structures illuminate ZCCHC8 as a scaffold, mediating homodimerization while embracing the MTR4 helicase and flexibly anchoring RBM7 to the helicase core. All three subunits collaborate to bind the RNA, with RBM7 and ZCCHC8 surveying sequences upstream of the 3' end to facilitate RNA capture by MTR4. ZCCHC8 obscures MTR4 surfaces important for RNA binding and extrusion as well as MPP6-dependent recruitment and docking onto the RNA exosome core, interactions that contribute to RNA surveillance by coordinating RNA capture, translocation, and extrusion from the helicase to the exosome for decay.
History
DepositionSep 15, 2021-
Header (metadata) releaseJun 15, 2022-
Map releaseJun 15, 2022-
UpdateJun 22, 2022-
Current statusJun 22, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24883.png

Downloads & links

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Map

FileDownload / File: emd_24883.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNEXT-RNA subtrate 2 complex - composite reconstruction
Projections & slices

Image control

Size
Brightness
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Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.1 Å/pix.
x 280 pix.
= 308. Å		1.1 Å/pix.
x 280 pix.
= 308. Å		1.1 Å/pix.
x 280 pix.
= 308. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 8.0
Minimum - Maximum-43.078094 - 72.18847
Average (Standard dev.)0.001339072 (±1.0651523)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 308.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: overall map

Fileemd_24883_additional_1.map
Annotationoverall map
Projections & Slices
AxesZYX

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Additional map: focused refinement map of RBM7-ZCCHC8 middle region-RNA - half map 2

Fileemd_24883_additional_10.map
Annotationfocused refinement map of RBM7-ZCCHC8 middle region-RNA - half map 2
Projections & Slices
AxesZYX

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Additional map: overall reconstruction half map

Fileemd_24883_additional_11.map
Annotationoverall reconstruction half map
Projections & Slices
AxesZYX

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Additional map: focused refinement map of MTR4 core - half map 2

Fileemd_24883_additional_12.map
Annotationfocused refinement map of MTR4 core - half map 2
Projections & Slices
AxesZYX

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Density Histograms

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Additional map: focused refinement map of RBM7-ZCCHC8 middle region-RNA - half map 1

Fileemd_24883_additional_13.map
Annotationfocused refinement map of RBM7-ZCCHC8 middle region-RNA - half map 1
Projections & Slices
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Additional map: focused refinement map of MTR4 core - half map 1

Fileemd_24883_additional_14.map
Annotationfocused refinement map of MTR4 core - half map 1
Projections & Slices
AxesZYX

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Additional map: focused refinement map of MTR4-ZCCHC8 HD/KID - half map 1

Fileemd_24883_additional_15.map
Annotationfocused refinement map of MTR4-ZCCHC8 HD/KID - half map 1
Projections & Slices
AxesZYX

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Histogram

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Additional map: focused refinement map of MTR4-ZCCHC8 HD/KID - half map 2

Fileemd_24883_additional_16.map
Annotationfocused refinement map of MTR4-ZCCHC8 HD/KID - half map 2
Projections & Slices
AxesZYX

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Additional map: focused refinement map of MTR4 KOW-ZCCHC8 HD/KID region - half map 1

Fileemd_24883_additional_17.map
Annotationfocused refinement map of MTR4 KOW-ZCCHC8 HD/KID region - half map 1
Projections & Slices
AxesZYX

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Histogram

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Additional map: focused refinement map of MTR4 core-ZCCHC8 middle region-RBM7-RNA...

Fileemd_24883_additional_18.map
Annotationfocused refinement map of MTR4 core-ZCCHC8 middle region-RBM7-RNA - half map 2
Projections & Slices
AxesZYX

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Histogram

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Additional map: focused refinement map of MTR4 core - component...

Fileemd_24883_additional_2.map
Annotationfocused refinement map of MTR4 core - component of composite reconstruction
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: focused refinement map of MTR4 core-ZCCHC8 middle region-RBM7-RNA...

Fileemd_24883_additional_3.map
Annotationfocused refinement map of MTR4 core-ZCCHC8 middle region-RBM7-RNA - component of composite reconstruction
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: focused refinement map of RBM7-ZCCHC8 middle region-RNA -...

Fileemd_24883_additional_4.map
Annotationfocused refinement map of RBM7-ZCCHC8 middle region-RNA - component of composite reconstruction
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: focused refinement map of MTR4-ZCCHC8 HD/KID - component...

Fileemd_24883_additional_5.map
Annotationfocused refinement map of MTR4-ZCCHC8 HD/KID - component of composite reconstruction
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: focused refinement map of MTR4 KOW-ZCCHC8 HD/KID -...

Fileemd_24883_additional_6.map
Annotationfocused refinement map of MTR4 KOW-ZCCHC8 HD/KID - component of composite reconstruction
Projections & Slices
AxesZYX

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Histogram

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Additional map: overall reconstruction half map 1

Fileemd_24883_additional_7.map
Annotationoverall reconstruction half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: focused refinement map of MTR4 core-ZCCHC8 middle region-RBM7-RNA...

Fileemd_24883_additional_8.map
Annotationfocused refinement map of MTR4 core-ZCCHC8 middle region-RBM7-RNA - half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: focused refinement map of MTR4 KOW-ZCCHC8 HD/KID - half map 2

Fileemd_24883_additional_9.map
Annotationfocused refinement map of MTR4 KOW-ZCCHC8 HD/KID - half map 2
Projections & Slices
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Sample components

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Entire : human Nuclear Exosome Targeting (NEXT) complex bound to RNA (subs...

EntireName: human Nuclear Exosome Targeting (NEXT) complex bound to RNA (substrate 2)
Components
  • Complex: human Nuclear Exosome Targeting (NEXT) complex bound to RNA (substrate 2)
    • Protein or peptide: Exosome RNA helicase MTR4
    • Protein or peptide: Zinc finger CCHC domain-containing protein 8
    • Protein or peptide: RNA-binding protein 7
    • RNA: RNA (30-MER)
  • Ligand: ZINC ION

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Supramolecule #1: human Nuclear Exosome Targeting (NEXT) complex bound to RNA (subs...

SupramoleculeName: human Nuclear Exosome Targeting (NEXT) complex bound to RNA (substrate 2)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Exosome RNA helicase MTR4

MacromoleculeName: Exosome RNA helicase MTR4 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 118.224961 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SGDMADAFGD ELFSVFEGDS TTAAGTKKDK EKDKGKWKGP PGSADKAGKR FDGKLQSEST NNGKNKRDVD FEGTDEPIFG KKPRIEESI TEDLSLADLM PRVKVQSVET VEGCTHEVAL PAEEDYLPLK PRVGKAAKEY PFILDAFQRE AIQCVDNNQS V LVSAHTSA ...String:
SGDMADAFGD ELFSVFEGDS TTAAGTKKDK EKDKGKWKGP PGSADKAGKR FDGKLQSEST NNGKNKRDVD FEGTDEPIFG KKPRIEESI TEDLSLADLM PRVKVQSVET VEGCTHEVAL PAEEDYLPLK PRVGKAAKEY PFILDAFQRE AIQCVDNNQS V LVSAHTSA GKTVCAEYAI ALALREKQRV IFTSPIKALS NQKYREMYEE FQDVGLMTGD VTINPTASCL VMTTEILRSM LY RGSEVMR EVAWVIFDEI HYMRDSERGV VWEETIILLP DNVHYVFLSA TIPNARQFAE WICHLHKQPC HVIYTDYRPT PLQ HYIFPA GGDGLHLVVD ENGDFREDNF NTAMQVLRDA GDLAKGDQKG RKGGTKGPSN VFKIVKMIME RNFQPVIIFS FSKK DCEAY ALQMTKLDFN TDEEKKMVEE VFSNAIDCLS DEDKKLPQVE HVLPLLKRGI GIHHGGLLPI LKETIEILFS EGLIK ALFA TETFAMGINM PARTVLFTNA RKFDGKDFRW ISSGEYIQMS GRAGRRGMDD RGIVILMVDE KMSPTIGKQL LKGSAD PLN SAFHLTYNMV LNLLRVEEIN PEYMLEKSFY QFQHYRAIPG VVEKVKNSEE QYNKIVIPNE ESVVIYYKIR QQLAKLG KE IEEYIHKPKY CLPFLQPGRL VKVKNEGDDF GWGVVVNFSK KSNVKPNSGE LDPLYVVEVL LRCSKESLKN SATEAAKP A KPDEKGEMQV VPVLVHLLSA ISSVRLYIPK DLRPVDNRQS VLKSIQEVQK RFPDGIPLLD PIDDMGIQDQ GLKKVIQKV EAFEHRMYSH PLHNDPNLET VYTLCEKKAQ IAIDIKSAKR ELKKARTVLQ MDELKCRKRV LRRLGFATSS DVIEMKGRVA CEISSADEL LLTEMMFNGL FNDLSAEQAT ALLSCFVFQE NSSEMPKLTE QLAGPLRQMQ ECAKRIAKVS AEAKLEIDEE T YLSSFKPH LMDVVYTWAT GATFAHICKM TDVFEGSIIR CMRRLEELLR QMCQAAKAIG NTELENKFAE GITKIKRDIV FA ASLYL

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Macromolecule #2: Zinc finger CCHC domain-containing protein 8

MacromoleculeName: Zinc finger CCHC domain-containing protein 8 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 69.259805 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SGDMAAEVYF GDLELFEPFD HPEESIPKPV HTRFKDDDGD EEDENGVGDA ELRERLRQCE ETIEQLRAEN QELKRKLNIL TRPSGILVN DTKLDGPILQ ILFMNNAISK QYHQEIEEFV SNLVKRFEEQ QKNDVEKTSF NLLPQPSSIV LEEDHKVEES C AIKNNKEA ...String:
SGDMAAEVYF GDLELFEPFD HPEESIPKPV HTRFKDDDGD EEDENGVGDA ELRERLRQCE ETIEQLRAEN QELKRKLNIL TRPSGILVN DTKLDGPILQ ILFMNNAISK QYHQEIEEFV SNLVKRFEEQ QKNDVEKTSF NLLPQPSSIV LEEDHKVEES C AIKNNKEA FSVVGSVLYF TNFCLDKLGQ PLLNENPQLS EGWEIPKYHQ VFSHIVSLEG QEIQVKAKRP KPHCFNCGSE EH QMKDCPM PRNAARISEK RKEYMDACGE ANNQNFQQRY HAEEVEERFG RFKPGVISEE LQDALGVTDK SLPPFIYRMR QLG YPPGWL KEAELENSGL ALYDGKDGTD GETEVGEIQQ NKSVTYDLSK LVNYPGFNIS TPRGIPDEWR IFGSIPMQAC QQKD VFANY LTSNFQAPGV KSGGAVDEDA LTLEELEEQQ RRIWAALEQA ESVNSDSDVP VDTPLTGNSV ASSPCPNELD LPVPE GKTS EKQTLDEPEV PEIFTKKSEA GHASSPDSEV TSLCQKEKAE LAPVNTEGAL LDNGSVVPNC DISNGGSQKL FPADTS PST ATKIHSPIPD MSKFATGITP FEFENMAEST GMYLRIRSLL KNSPRNQQKN KKASE

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Macromolecule #3: RNA-binding protein 7

MacromoleculeName: RNA-binding protein 7 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.462986 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGDEADRTLF VGNLETKVTE ELLFELFHQA GPVIKVKIPK DKDGKPKQFA FVNFKHEVSV PYAMNLLNGI KLYGRPIKIQ FRS

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Macromolecule #4: RNA (30-MER)

MacromoleculeName: RNA (30-MER) / type: rna / ID: 4 / Number of copies: 2
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.017486 KDa
SequenceString:
GGCGCGCGCC AAAAAUUUUU AAAAAAAA

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 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

BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV / Details: 30 s wait time, blot for 2.5 s before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Detector mode: SUPER-RESOLUTION / #0 - Average electron dose: 77.5 e/Å2 / #0 - Details: Dataset 1 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 (6k x 4k) / #1 - Average electron dose: 66.0 e/Å2 / #1 - Details: Datasets 2 and 3
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf
Startup modelType of model: OTHER / Details: Ab initio model from cryosparc
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION
Details: A total of 252,638 gave rise to an overall map at 3.62 Angstrom resolution (FSC 0.143 cut off). A composite reconstruction (deposited main map) was generated by combining the overall map ...Details: A total of 252,638 gave rise to an overall map at 3.62 Angstrom resolution (FSC 0.143 cut off). A composite reconstruction (deposited main map) was generated by combining the overall map with focused refinement maps of MTR4 core (3.5 Angstrom FSC=0.143), MTR4 core-ZCCHC8 PSP-RBM7-RNA (3.42 Angstrom, FSC=0.143), RBM7-RNA (3.94 Angstrom, FSC=0.143), MTR4-ZCCHC8 HD/KID (3.62 Angstrom, FSC=0.143), and MTR4 KOW-ZCCHC8 HD/KID (3.34 Angstrom, FSC=0.143) regions.
Number images used: 252638
Details3 datasets collected using Gatan K2 Summit and Gatan K3 image detectors were used for the reconstructions.
Image recording ID2

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