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- EMDB-7819: Human nuclear exosome-MTR4 RNA complex - overall reconstruction -... -

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Basic information

Entry
Database: EMDB / ID: EMD-7819
TitleHuman nuclear exosome-MTR4 RNA complex - overall reconstruction - small class KOW domain closed
Map dataOverall reconstruction of a small class for human nuclear exosome-MTR4 complex with the MTR4 KOW domain in a closed conformation
Sample
  • Complex: Human nuclear exosome-MTR4 helicase captured after unwinding a DNA/RNA substrate
    • Protein or peptide: x 14 types
    • RNA: x 1 types
    • Other: x 1 types
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.22 Å
AuthorsWeick E-M / Lima CD
CitationJournal: Cell / Year: 2018
Title: Helicase-Dependent RNA Decay Illuminated by a Cryo-EM Structure of a Human Nuclear RNA Exosome-MTR4 Complex.
Authors: Eva-Maria Weick / M Rhyan Puno / Kurt Januszyk / John C Zinder / Michael A DiMattia / Christopher D Lima /
Abstract: The ribonucleolytic RNA exosome interacts with RNA helicases to degrade RNA. To understand how the 3' to 5' Mtr4 helicase engages RNA and the nuclear exosome, we reconstituted 14-subunit Mtr4- ...The ribonucleolytic RNA exosome interacts with RNA helicases to degrade RNA. To understand how the 3' to 5' Mtr4 helicase engages RNA and the nuclear exosome, we reconstituted 14-subunit Mtr4-containing RNA exosomes from Saccharomyces cerevisiae, Schizosaccharomyces pombe, and human and show that they unwind structured substrates to promote degradation. We loaded a human exosome with an optimized DNA-RNA chimera that stalls MTR4 during unwinding and determined its structure to an overall resolution of 3.45 Å by cryoelectron microscopy (cryo-EM). The structure reveals an RNA-engaged helicase atop the non-catalytic core, with RNA captured within the central channel and DIS3 exoribonuclease active site. MPP6 tethers MTR4 to the exosome through contacts to the RecA domains of MTR4. EXOSC10 remains bound to the core, but its catalytic module and cofactor C1D are displaced by RNA-engaged MTR4. Competition for the exosome core may ensure that RNA is committed to degradation by DIS3 when engaged by MTR4.
History
DepositionApr 22, 2018-
Header (metadata) releaseMay 9, 2018-
Map releaseJun 20, 2018-
UpdateJun 27, 2018-
Current statusJun 27, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7819.png

Downloads & links

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Map

FileDownload / File: emd_7819.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOverall reconstruction of a small class for human nuclear exosome-MTR4 complex with the MTR4 KOW domain in a closed conformation
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.012 / Movie #1: 0.012
Minimum - Maximum-0.012411459 - 0.034145005
Average (Standard dev.)0.00013792339 (±0.0015943364)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 410.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z410.880410.880410.880
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ384384384
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0120.0340.000

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Supplemental data

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Sample components

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Entire : Human nuclear exosome-MTR4 helicase captured after unwinding a DN...

EntireName: Human nuclear exosome-MTR4 helicase captured after unwinding a DNA/RNA substrate
Components
  • Complex: Human nuclear exosome-MTR4 helicase captured after unwinding a DNA/RNA substrate
    • Protein or peptide: EXOSC9
    • Protein or peptide: EXOSC4
    • Protein or peptide: EXOSC8
    • Protein or peptide: EXOSC5
    • Protein or peptide: EXOSC7
    • Protein or peptide: EXOSC6
    • Protein or peptide: EXOSC3
    • Protein or peptide: EXOSC2
    • Protein or peptide: EXOSC1
    • Protein or peptide: EXOSC10
    • Protein or peptide: DIS3
    • Protein or peptide: MPP6, MPHOSPH6
    • Protein or peptide: MTR4, MTREX
    • Protein or peptide: C1D, Rrp47
    • RNA: synthetic RNA
    • Other: DNA-RNA chimera

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Supramolecule #1: Human nuclear exosome-MTR4 helicase captured after unwinding a DN...

SupramoleculeName: Human nuclear exosome-MTR4 helicase captured after unwinding a DNA/RNA substrate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Human C1D/Rrp47 also in the sample, but was not observed in density
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 690 KDa

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Macromolecule #1: EXOSC9

MacromoleculeName: EXOSC9 / type: protein_or_peptide / ID: 1 / Details: MGSSHHHHHHSQDPNSH cloning artifact / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SQDPNSHMKE TPLSNCERRF LLRAIEEKKR LDGRQTYDYR NIRISFGTDY GCCIVELGK TRVLGQVSCE LVSPKLNRAT EGILFFNLEL SQMAAPAFEP GRQSDLLVKL N RLMERCLR NSKCIDTESL CVVAGEKVWQ IRVDLHLLNH DGNIIDAASI ...String:
MGSSHHHHHH SQDPNSHMKE TPLSNCERRF LLRAIEEKKR LDGRQTYDYR NIRISFGTDY GCCIVELGK TRVLGQVSCE LVSPKLNRAT EGILFFNLEL SQMAAPAFEP GRQSDLLVKL N RLMERCLR NSKCIDTESL CVVAGEKVWQ IRVDLHLLNH DGNIIDAASI AAIVALCHFR RP DVSVQGD EVTLYTPEER DPVPLSIHHM PICVSFAFFQ QGTYLLVDPN EREERVMDGL LVI AMNKHR EICTIQSSGG IMLLKDQVLR CSKIAGVKVA EITELILKAL ENDQKVRKEG GKFG FAESI ANQRITAFKM EKAPIDTSDV EEKAEEIIAE AEPPSEVVST PVLWTPGTAQ IGEGV ENSW GDLEDSEKED DEGGGDQAII LDGIKMDTGV EVSDIGSQEL GFHHVGQTGL EFLTSD API ILSDSEEEEM IILEPDKNPK KIRTQTTSAK QEKAPSKKPV KRRKKKRAAN

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Macromolecule #2: EXOSC4

MacromoleculeName: EXOSC4 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MADPMAGLEL LSDQGYRVDG RRAGELRKIQ ARMGVFAQAD GSAYIEQGNT KALAVVYGPH EIRGSRARA LPDRALVNCQ YSSATFSTGE RKRRPHGDRK SCEMGLQLRQ TFEAAILTQL H PRSQIDIY VQVLQADGGT YAACVNAATL AVLDAGIPMR DFVCACSAGF ...String:
MADPMAGLEL LSDQGYRVDG RRAGELRKIQ ARMGVFAQAD GSAYIEQGNT KALAVVYGPH EIRGSRARA LPDRALVNCQ YSSATFSTGE RKRRPHGDRK SCEMGLQLRQ TFEAAILTQL H PRSQIDIY VQVLQADGGT YAACVNAATL AVLDAGIPMR DFVCACSAGF VDGTALADLS HV EEAAGGP QLALALLPAS GQIALLEMDA RLHEDHLERV LEAAAQAARD VHTLLDRVVR QHV REASIL LGD

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Macromolecule #3: EXOSC8

MacromoleculeName: EXOSC8 / type: protein_or_peptide / ID: 3 / Details: N-terminal DP cloning artifact / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DPMAAGFKTV EPLEYYRRFL KENCRPDGRE LGEFRTTTVN IGSISTADGS ALVKLGNTTV ICGVKAEFA APSTDAPDKG YVVPNVDLPP LCSSRFRSGP PGEEAQVASQ FIADVIENSQ I IQKEDLCI SPGKLVWVLY CDLICLDYDG NILDACTFAL LAALKNVQLP ...String:
DPMAAGFKTV EPLEYYRRFL KENCRPDGRE LGEFRTTTVN IGSISTADGS ALVKLGNTTV ICGVKAEFA APSTDAPDKG YVVPNVDLPP LCSSRFRSGP PGEEAQVASQ FIADVIENSQ I IQKEDLCI SPGKLVWVLY CDLICLDYDG NILDACTFAL LAALKNVQLP EVTINEETAL AE VNLKKKS YLNIRTHPVA TSFAVFDDTL LIVDPTGEEE HLATGTLTIV MDEEGKLCCL HKP GGSGLT GAKLQDCMSR AVTRHKEVKK LMDEVIKSMK PK

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Macromolecule #4: EXOSC5

MacromoleculeName: EXOSC5 / type: protein_or_peptide / ID: 4 / Details: N-terminal SL cloning artifact / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SLMEEETHTD AKIRAENGTG SSPRGPGCSL RHFACEQNLL SRPDGSASFL QGDTSVLAGV YGPAEVKVS KEIFNKATLE VILRPKIGLP GVAEKSRERL IRNTCEAVVL GTLHPRTSIT V VLQVVSDA GSLLACCLNA ACMALVDAGV PMRALFCGVA CALDSDGTLV ...String:
SLMEEETHTD AKIRAENGTG SSPRGPGCSL RHFACEQNLL SRPDGSASFL QGDTSVLAGV YGPAEVKVS KEIFNKATLE VILRPKIGLP GVAEKSRERL IRNTCEAVVL GTLHPRTSIT V VLQVVSDA GSLLACCLNA ACMALVDAGV PMRALFCGVA CALDSDGTLV LDPTSKQEKE AR AVLTFAL DSVERKLLMS STKGLYSDTE LQQCLAAAQA ASQHVFRFYR ESLQRRYSKS

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Macromolecule #5: EXOSC7

MacromoleculeName: EXOSC7 / type: protein_or_peptide / ID: 5 / Details: N-terminal DP cloning artifact / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DPMASVTLSE AEKVYIVHGV QEDLRVDGRG CEDYRCVEVE TDVVSNTSGS ARVKLGHTDI LVGVKAEMG TPKLEKPNEG YLEFFVDCSA SATPEFEGRG GDDLGTEIAN TLYRIFNNKS S VDLKTLCI SPREHCWVLY VDVLLLECGG NLFDAISIAV KAALFNTRIP ...String:
DPMASVTLSE AEKVYIVHGV QEDLRVDGRG CEDYRCVEVE TDVVSNTSGS ARVKLGHTDI LVGVKAEMG TPKLEKPNEG YLEFFVDCSA SATPEFEGRG GDDLGTEIAN TLYRIFNNKS S VDLKTLCI SPREHCWVLY VDVLLLECGG NLFDAISIAV KAALFNTRIP RVRVLEDEEG SK DIELSDD PYDCIRLSVE NVPCIVTLCK IGYRHVVDAT LQEEACSLAS LLVSVTSKGV VTC MRKVGK GSLDPESIFE MMETGKRVGK VLHASLQSVV HKEESLGPKR QKVGFLG

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Macromolecule #6: EXOSC6

MacromoleculeName: EXOSC6 / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPGDHRRIRG PEESQPPQLY AADEEEAPGT RDPTRLRPVY ARAGLLSQAK GSAYLEAGGT KVLCAVSGP RQAEGGERGG GPAGAGGEAP AALRGRLLCD FRRAPFAGRR RRAPPGGCEE R ELALALQE ALEPAVRLGR YPRAQLEVSA LLLEDGGSAL AAALTAAALA ...String:
MPGDHRRIRG PEESQPPQLY AADEEEAPGT RDPTRLRPVY ARAGLLSQAK GSAYLEAGGT KVLCAVSGP RQAEGGERGG GPAGAGGEAP AALRGRLLCD FRRAPFAGRR RRAPPGGCEE R ELALALQE ALEPAVRLGR YPRAQLEVSA LLLEDGGSAL AAALTAAALA LADAGVEMYD LV VGCGLSL APGPAPTWLL DPTRLEEERA AAGLTVALMP VLNQVAGLLG SGEGGLTESW AEA VRLGLE GCQRLYPVLQ QSLVRAARRR GAAAQP

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Macromolecule #7: EXOSC3

MacromoleculeName: EXOSC3 / type: protein_or_peptide / ID: 7
Details: N-terminal DP cloning artifact Y to H at position 225, Natural variant (VAR_054098, dbSNP:rs3208406)
Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DPMAEPASVA AESLAGSRAR AARTVLGQVV LPGEELLLPE QEDAEGPGGA VERPLSLNAR ACSRVRVVC GPGLRRCGDR LLVTKCGRLR HKEPGSGSGG GVYWVDSQQK RYVPVKGDHV I GIVTAKSG DIFKVDVGGS EPASLSYLSF EGATKRNRPN VQVGDLIYGQ ...String:
DPMAEPASVA AESLAGSRAR AARTVLGQVV LPGEELLLPE QEDAEGPGGA VERPLSLNAR ACSRVRVVC GPGLRRCGDR LLVTKCGRLR HKEPGSGSGG GVYWVDSQQK RYVPVKGDHV I GIVTAKSG DIFKVDVGGS EPASLSYLSF EGATKRNRPN VQVGDLIYGQ FVVANKDMEP EM VCIDSCG RANGMGVIGQ DGLLFKVTLG LIRKLLAPDC EIIQEVGKLH PLEIVFGMNG RIW VKAKTI QQTLILANIL EACEHMTSDQ RKQIFSRLAE S

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Macromolecule #8: EXOSC2

MacromoleculeName: EXOSC2 / type: protein_or_peptide / ID: 8 / Details: N-terminal DP cloning artifact / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DPHMAMEMRL PVARKPLSER LGRDTKKHLV VPGDTITTDT GFMRGHGTYM GEEKLIASVA GSVERVNKL ICVKALKTRY IGEVGDIVVG RITEVQQKRW KVETNSRLDS VLLLSSMNLP G GELRRRSA EDELAMRGFL QEGDLISAEV QAVFSDGAVS LHTRSLKYGK ...String:
DPHMAMEMRL PVARKPLSER LGRDTKKHLV VPGDTITTDT GFMRGHGTYM GEEKLIASVA GSVERVNKL ICVKALKTRY IGEVGDIVVG RITEVQQKRW KVETNSRLDS VLLLSSMNLP G GELRRRSA EDELAMRGFL QEGDLISAEV QAVFSDGAVS LHTRSLKYGK LGQGVLVQVS PS LVKRQKT HFHDLPCGAS VILGNNGFIW IYPTPEHKEE EAGGFIANLE PVSLADREVI SRL RNCIIS LVTQRMMLYD TSILYCYEAS LPHQIKDILK PEIMEEIVME TRQRLLEQEG

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Macromolecule #9: EXOSC1

MacromoleculeName: EXOSC1 / type: protein_or_peptide / ID: 9 / Details: N-terminal DP cloning artifact / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DPMAPPVRYC IPGERLCNLE EGSPGSGTYT RHGYIFSSLA GCLMKSSENG ALPVVSVVRE TESQLLPDV GAIVTCKVSS INSRFAKVHI LYVGSMPLKN SFRGTIRKED VRATEKDKVE I YKSFRPGD IVLAKVISLG DAQSNYLLTT AENELGVVVA HSESGIQMVP ...String:
DPMAPPVRYC IPGERLCNLE EGSPGSGTYT RHGYIFSSLA GCLMKSSENG ALPVVSVVRE TESQLLPDV GAIVTCKVSS INSRFAKVHI LYVGSMPLKN SFRGTIRKED VRATEKDKVE I YKSFRPGD IVLAKVISLG DAQSNYLLTT AENELGVVVA HSESGIQMVP ISWCEMQCPK TH TKEFRKV ARVQPEFLQT

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Macromolecule #10: EXOSC10

MacromoleculeName: EXOSC10 / type: protein_or_peptide / ID: 10
Details: N-terminal S cloning artifact D313N mutation Residues 1-804 with internal deletion of 649-704
Enantiomer: LEVO
EC number: Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SMAPPSTREP RVLSATSATK SDGEMVLPGF PDADSFVKFA LGSVVAVTKA SGGLPQFGDE YDFYRSFPG FQAFCETQGD RLLQCMSRVM QYHGCRSNIK DRSKVTELED KFDLLVDAND V ILERVGIL LDEASGVNKN QQPVLPAGLQ VPKTVVSSWN RKAAEYGKKA ...String:
SMAPPSTREP RVLSATSATK SDGEMVLPGF PDADSFVKFA LGSVVAVTKA SGGLPQFGDE YDFYRSFPG FQAFCETQGD RLLQCMSRVM QYHGCRSNIK DRSKVTELED KFDLLVDAND V ILERVGIL LDEASGVNKN QQPVLPAGLQ VPKTVVSSWN RKAAEYGKKA KSETFRLLHA KN IIRPQLK FREKIDNSNT PFLPKIFIKP NAQKPLPQAL SKERRERPQD RPEDLDVPPA LAD FIHQQR TQQVEQDMFA HPYQYELNHF TPADAVLQKP QPQLYRPIEE TPCHFISSLD ELVE LNEKL LNCQEFAVNL EHHSYRSFLG LTCLMQISTR TEDFIIDTLE LRSDMYILNE SLTDP AIVK VFHGADSDIE WLQKDFGLYV VNMFDTHQAA RLLNLGRHSL DHLLKLYCNV DSNKQY QLA DWRIRPLPEE MLSYARDDTH YLLYIYDKMR LEMWERGNGQ PVQLQVVWQR SRDICLK KF IKPIFTDESY LELYRKQKKH LNTQQLTAFQ LLFAWRDKTA RREDESYGYV LPNHMMLK I AEELPKEPQG IIACCNPVPP LVRQQINEMH LLIQQAREMP LLKSEVAAGV KKSGPLPSA ERLENVLFGP HDCSHAPPDG YPIIPTSGSV PVQKQASLFP DEKEDNLLGS RGSGSGSGSG SVSQAAKFD PSTKIYEISN RWKLAQVQVQ KDSKEAVKKK AAEQTAAREQ AKEACKAAAE Q AISVRQQV VLENAAKKRE RATSDPRTTE QKQEKKRLKI SKK

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Macromolecule #11: DIS3

MacromoleculeName: DIS3 / type: protein_or_peptide / ID: 11
Details: N-terminal GS cloning artifact D146N, D487N mutations 269 N-S natural variant (VAR_023099 - dbSNP:rs4883918)
Enantiomer: LEVO
EC number: Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSMLKSKTFL KKTRAGGVMK IVREHYLRDD IGCGAPGCAA CGGAHEGPAL EPQPQDPASS VCPQPHYLL PDTNVLLHQI DVLEDPAIRN VIVLQTVLQE VRNRSAPVYK RIRDVTNNQE K HFYTFTNE HHRETYVEQE QGENANDRNN RAIRVAAKWY NEHLKKMSAD ...String:
GSMLKSKTFL KKTRAGGVMK IVREHYLRDD IGCGAPGCAA CGGAHEGPAL EPQPQDPASS VCPQPHYLL PDTNVLLHQI DVLEDPAIRN VIVLQTVLQE VRNRSAPVYK RIRDVTNNQE K HFYTFTNE HHRETYVEQE QGENANDRNN RAIRVAAKWY NEHLKKMSAD NQLQVIFITN DR RNKEKAI EEGIPAFTCE EYVKSLTANP ELIDRLACLS EEGNEIESGK IIFSEHLPLS KLQ QGIKSG TYLQGTFRAS RENYLEATVW IHGDSEENKE IILQGLKHLN RAVHEDIVAV ELLP KSQWV APSSVVLHDE GQNEEDVEKE EETERMLKTA VSEKMLKPTG RVVGIIKRNW RPYCG MLSK SDIKESRRHL FTPADKRIPR IRIETRQAST LEGRRIIVAI DGWPRNSRYP NGHFVR NLG DVGEKETETE VLLLEHDVPH QPFSQAVLSF LPKMPWSITE KDMKNREDLR HLCICSV DP PGCTDINDAL HCRELENGNL EVGVHIADVS HFIRPGNALD QESARRGTTV YLCEKRID M VPELLSSNLC SLKCDVDRLA FSCIWEMNHN AEILKTKFTK SVINSKASLT YAEAQLRID SANMNDDITT SLRGLNKLAK ILKKRRIEKG ALTLSSPEVR FHMDSETHDP IDLQTKELRE TNSMVEEFM LLANISVAKK IHEEFSEHAL LRKHPAPPPS NYEILVKAAR SRNLEIKTDT A KSLAESLD QAESPTFPYL NTLLRILATR CMMQAVYFCS GMDNDFHHYG LASPIYTHFT SP IRRYADV IVHRLLAVAI GADCTYPELT DKHKLADICK NLNFRHKMAQ YAQRASVAFH TQL FFKSNG IVSEEAYILF VRKNAIVVLI PKYGLEGTVF FEEKDKPNPQ LIYDDEIPSL KIED TVFHV FDKVKVKIML DSSNLQHQKI RMSLVEPQIP GISIPTDTSN MDLNGPKKKK MKLGK

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Macromolecule #12: MPP6, MPHOSPH6

MacromoleculeName: MPP6, MPHOSPH6 / type: protein_or_peptide / ID: 12 / Details: N-terminal DP cloning artifact / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
DPMAAERKTR LSKNLLRMKF MQRGLDSETK KQLEEEEKKI ISEEHWYLDL PELKEKESFI IEEQSFLLC EDLLYGRMSF RGFNPEVEKL MLQMNAKHKA EEVEDETVEL DVSDEEMARR Y ETLVGTIG KKFARKRDHA NYEEDENGDI TPIKAKKMFL KPQD

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Macromolecule #13: MTR4, MTREX

MacromoleculeName: MTR4, MTREX / type: protein_or_peptide / ID: 13 / Details: N-terminal SGD cloning artifact / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SGDMADAFGD ELFSVFEGDS TTAAGTKKDK EKDKGKWKGP PGSADKAGKR FDGKLQSEST NNGKNKRDV DFEGTDEPIF GKKPRIEESI TEDLSLADLM PRVKVQSVET VEGCTHEVAL P AEEDYLPL KPRVGKAAKE YPFILDAFQR EAIQCVDNNQ SVLVSAHTSA ...String:
SGDMADAFGD ELFSVFEGDS TTAAGTKKDK EKDKGKWKGP PGSADKAGKR FDGKLQSEST NNGKNKRDV DFEGTDEPIF GKKPRIEESI TEDLSLADLM PRVKVQSVET VEGCTHEVAL P AEEDYLPL KPRVGKAAKE YPFILDAFQR EAIQCVDNNQ SVLVSAHTSA GKTVCAEYAI AL ALREKQR VIFTSPIKAL SNQKYREMYE EFQDVGLMTG DVTINPTASC LVMTTEILRS MLY RGSEVM REVAWVIFDE IHYMRDSERG VVWEETIILL PDNVHYVFLS ATIPNARQFA EWIC HLHKQ PCHVIYTDYR PTPLQHYIFP AGGDGLHLVV DENGDFREDN FNTAMQVLRD AGDLA KGDQ KGRKGGTKGP SNVFKIVKMI MERNFQPVII FSFSKKDCEA YALQMTKLDF NTDEEK KMV EEVFSNAIDC LSDEDKKLPQ VEHVLPLLKR GIGIHHGGLL PILKETIEIL FSEGLIK AL FATETFAMGI NMPARTVLFT NARKFDGKDF RWISSGEYIQ MSGRAGRRGM DDRGIVIL M VDEKMSPTIG KQLLKGSADP LNSAFHLTYN MVLNLLRVEE INPEYMLEKS FYQFQHYRA IPGVVEKVKN SEEQYNKIVI PNEESVVIYY KIRQQLAKLG KEIEEYIHKP KYCLPFLQPG RLVKVKNEG DDFGWGVVVN FSKKSNVKPN SGELDPLYVV EVLLRCSKES LKNSATEAAK P AKPDEKGE MQVVPVLVHL LSAISSVRLY IPKDLRPVDN RQSVLKSIQE VQKRFPDGIP LL DPIDDMG IQDQGLKKVI QKVEAFEHRM YSHPLHNDPN LETVYTLCEK KAQIAIDIKS AKR ELKKAR TVLQMDELKC RKRVLRRLGF ATSSDVIEMK GRVACEISSA DELLLTEMMF NGLF NDLSA EQATALLSCF VFQENSSEMP KLTEQLAGPL RQMQECAKRI AKVSAEAKLE IDEET YLSS FKPHLMDVVY TWATGATFAH ICKMTDVFEG SIIRCMRRLE ELLRQMCQAA KAIGNT ELE NKFAEGITKI KRDIVFAASL YL

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Macromolecule #14: C1D, Rrp47

MacromoleculeName: C1D, Rrp47 / type: protein_or_peptide / ID: 14 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAGEEINEDY PVEIHEYLSA FENSIGAVDE MLKTMMSVSR NELLQKLDPL EQAKVDLVSA YTLNSMFWV YLATQGVNPK EHPVKQELER IRVYMNRVKE ITDKKKAGKL DRGAASRFVK N ALWEPKSK NASKVANKGK SKS

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Macromolecule #15: synthetic RNA

MacromoleculeName: synthetic RNA / type: rna / ID: 15
Source (natural)Organism: synthetic construct (others)
SequenceString:
AGCACCGUAA AGACGC

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Macromolecule #16: DNA-RNA chimera

MacromoleculeName: DNA-RNA chimera / type: other / ID: 16
Classification: polydeoxyribonucleotide/polyribonucleotide hybrid
Source (natural)Organism: synthetic construct (others)
SequenceString:
(DG)(DC)(DG)(DT)(DC)(DT)(DT)(DT)(DA)(DC) (DG)(DG)(DT)(DG)(DC)(DT)CACC ACACCACACC ACACCACACC ACACCACACC ACACAAAAAA AA

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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

Concentration1.0 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
20.0 mMTris-HClTris
100.0 mMsodium chlorideNaClSodium chloride
0.5 mMmagnesium chlorideMgCl2
2.0 mMAMPPNP
1.0 mMBME
0.05 %CHAPSOCHAPS detergent
GridModel: Quantifoil R2/2 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.037 kPa
VitrificationCryogen name: ETHANE / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: 30 sec wait time, 2.5 sec blot time.
DetailsSample was monodisperse upon elution from gel filtration prior to vitrification.

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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 recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 1439 / Average electron dose: 85.23 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 278185
CTF correctionSoftware:
Namedetails
Gctf (ver. 1.06)determine
RELION (ver. 2.1.b1)apply
Startup modelType of model: NONE / Details: Ab initio model determination
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 0.6.1) / Software - details: from 0.6.1 to 0.6.5
Final 3D classificationNumber classes: 8 / Avg.num./class: 122284 / Software - Name: RELION (ver. 2.1b1)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1b1)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.22 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1b1)
Details: Overall reconstruction for a small class that shows the MTR4 KOW domain in an open conformation
Number images used: 2973
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsModels can be manually docked into this map.

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