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- EMDB-0128: Human nuclear RNA exosome EXO-10-MPP6 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-0128
TitleHuman nuclear RNA exosome EXO-10-MPP6 complex
Map dataCryo-EM reconstruction of the human nuclear RNA exosome EXO-10-MPP6 complex
Sample
  • Complex: Human nuclear RNA exosome EXO-14 complex
    • Complex: exosome complex
      • Protein or peptide: x 11 types
    • Complex: U44 ssRNA
      • RNA: x 1 types
Keywordsnuclear exosome / RNA decay / cryoEM / hEXO-10 / hDIS3 / hMPP6 / RNA BINDING PROTEIN
Function / homology
Function and homology information


DNA deamination / nucleolar exosome (RNase complex) / nuclear mRNA surveillance of mRNA 3'-end processing / CUT catabolic process / cytoplasmic exosome (RNase complex) / U1 snRNA 3'-end processing / U5 snRNA 3'-end processing / mRNA decay by 3' to 5' exoribonuclease / TRAMP-dependent tRNA surveillance pathway / exosome (RNase complex) ...DNA deamination / nucleolar exosome (RNase complex) / nuclear mRNA surveillance of mRNA 3'-end processing / CUT catabolic process / cytoplasmic exosome (RNase complex) / U1 snRNA 3'-end processing / U5 snRNA 3'-end processing / mRNA decay by 3' to 5' exoribonuclease / TRAMP-dependent tRNA surveillance pathway / exosome (RNase complex) / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / nuclear exosome (RNase complex) / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / ATF4 activates genes in response to endoplasmic reticulum stress / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / positive regulation of isotype switching / histone mRNA catabolic process / nuclear mRNA surveillance / rRNA catabolic process / 7S RNA binding / mRNA 3'-UTR AU-rich region binding / isotype switching / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA catabolic process / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / KSRP (KHSRP) binds and destabilizes mRNA / maturation of 5.8S rRNA / nuclear chromosome / mRNA catabolic process / nuclear-transcribed mRNA catabolic process / Major pathway of rRNA processing in the nucleolus and cytosol / RNA processing / guanyl-nucleotide exchange factor activity / euchromatin / fibrillar center / rRNA processing / chromosome / positive regulation of cell growth / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / endonuclease activity / defense response to virus / RNA polymerase II-specific DNA-binding transcription factor binding / immune response / intracellular membrane-bounded organelle / nucleolus / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
M-phase phosphoprotein 6 / Exosome complex component Rrp43 / M-phase phosphoprotein 6 / : / Mammalian exosome complex component RRP40, N-terminal / Exosome complex exonuclease RRP44, S1 domain / S1 domain / PIN domain / Exosome complex component RRP45 / Rrp40, S1 domain ...M-phase phosphoprotein 6 / Exosome complex component Rrp43 / M-phase phosphoprotein 6 / : / Mammalian exosome complex component RRP40, N-terminal / Exosome complex exonuclease RRP44, S1 domain / S1 domain / PIN domain / Exosome complex component RRP45 / Rrp40, S1 domain / : / Exosome complex component RRP40, S1 domain / Exosome complex component CSL4, C-terminal / Exosome complex component, N-terminal domain / Exosome complex component Csl4 / Exosome component EXOSC1/CSL4 / Exosome complex exonuclease RRP4 N-terminal region / RRP4, S1 domain / Rrp44-like cold shock domain / Rrp44-like cold shock domain / : / KH domain / Exosome complex RNA-binding protein 1/RRP40/RRP4 / Dis3-like cold-shock domain 2 / Dis3-like cold-shock domain 2 (CSD2) / : / Ribonuclease II/R, conserved site / Ribonuclease II family signature. / : / Ribonuclease II/R / RNB domain / RNB / : / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily / 3' exoribonuclease family, domain 1 / Large family of predicted nucleotide-binding domains / PIN domain / K Homology domain, type 1 / K Homology domain, type 1 superfamily / PIN-like domain superfamily / Ribosomal protein S1-like RNA-binding domain / S1 domain / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Exosome complex component RRP45 / Exosome complex component RRP4 / Exosome complex component RRP42 / Exosome complex component MTR3 / Exosome complex component RRP43 / M-phase phosphoprotein 6 / Exosome complex component RRP41 / Exosome complex component RRP46 / Exosome complex component RRP40 / Exosome complex exonuclease RRP44 / Exosome complex component CSL4
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsGerlach P / Schuller JM / Falk S / Basquin J / Conti E
Funding support5 items
OrganizationGrant numberCountry
European Molecular Biology OrganizationALTF 1008-2015
European CommissionERC-2016-ADG 740329 EXORICO
German Research FoundationSFB646, SFB1035, GRK1721
Louis-Jeantet Foundation
Max Planck Society
CitationJournal: Elife / Year: 2018
Title: Distinct and evolutionary conserved structural features of the human nuclear exosome complex.
Authors: Piotr Gerlach / Jan M Schuller / Fabien Bonneau / Jérôme Basquin / Peter Reichelt / Sebastian Falk / Elena Conti /
Abstract: The nuclear RNA exosome complex mediates the processing of structured RNAs and the decay of aberrant non-coding RNAs, an important function particularly in human cells. Most mechanistic studies to ...The nuclear RNA exosome complex mediates the processing of structured RNAs and the decay of aberrant non-coding RNAs, an important function particularly in human cells. Most mechanistic studies to date have focused on the yeast system. Here, we reconstituted and studied the properties of a recombinant 14-subunit human nuclear exosome complex. In biochemical assays, the human exosome embeds a longer RNA channel than its yeast counterpart. The 3.8 Å resolution cryo-EM structure of the core complex bound to a single-stranded RNA reveals that the RNA channel path is formed by two distinct features of the hDIS3 exoribonuclease: an open conformation and a domain organization more similar to bacterial RNase II than to yeast Rrp44. The cryo-EM structure of the holo-complex shows how obligate nuclear cofactors position the hMTR4 helicase at the entrance of the core complex, suggesting a striking structural conservation from lower to higher eukaryotes.
History
DepositionJul 13, 2018-
Header (metadata) releaseAug 1, 2018-
Map releaseAug 15, 2018-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6h25
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0128.png

Downloads & links

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Map

FileDownload / File: emd_0128.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM reconstruction of the human nuclear RNA exosome EXO-10-MPP6 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 250 pix.
= 337.5 Å		1.35 Å/pix.
x 250 pix.
= 337.5 Å		1.35 Å/pix.
x 250 pix.
= 337.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.24137774 - 0.3664702
Average (Standard dev.)0.00017617023 (±0.00808426)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 337.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z337.500337.500337.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean-0.2410.3660.000

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Supplemental data

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Sample components

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Entire : Human nuclear RNA exosome EXO-14 complex

EntireName: Human nuclear RNA exosome EXO-14 complex
Components
  • Complex: Human nuclear RNA exosome EXO-14 complex
    • Complex: exosome complex
      • Protein or peptide: Exosome complex component RRP45
      • Protein or peptide: Exosome complex component RRP41
      • Protein or peptide: Exosome complex component RRP43
      • Protein or peptide: Exosome complex component RRP46
      • Protein or peptide: Exosome complex component RRP42
      • Protein or peptide: Exosome complex component MTR3
      • Protein or peptide: Exosome complex component RRP40
      • Protein or peptide: Exosome complex component RRP4
      • Protein or peptide: Exosome complex component CSL4
      • Protein or peptide: Exosome complex exonuclease RRP44
      • Protein or peptide: M-phase phosphoprotein 6
    • Complex: U44 ssRNA
      • RNA: U44 ssRNA

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Supramolecule #1: Human nuclear RNA exosome EXO-14 complex

SupramoleculeName: Human nuclear RNA exosome EXO-14 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: exosome complex

SupramoleculeName: exosome complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#11
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: U44 ssRNA

SupramoleculeName: U44 ssRNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #12
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: Exosome complex component RRP45

MacromoleculeName: Exosome complex component RRP45 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.370312 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPDSMKETPL SNCERRFLLR AIEEKKRLDG RQTYDYRNIR ISFGTDYGCC IVELGKTRVL GQVSCELVSP KLNRATEGIL FFNLELSQM AAPAFEPGRQ SDLLVKLNRL MERCLRNSKC IDTESLCVVA GEKVWQIRVD LHLLNHDGNI IDAASIAAIV A LCHFRRPD ...String:
GPDSMKETPL SNCERRFLLR AIEEKKRLDG RQTYDYRNIR ISFGTDYGCC IVELGKTRVL GQVSCELVSP KLNRATEGIL FFNLELSQM AAPAFEPGRQ SDLLVKLNRL MERCLRNSKC IDTESLCVVA GEKVWQIRVD LHLLNHDGNI IDAASIAAIV A LCHFRRPD VSVQGDEVTL YTPEERDPVP LSIHHMPICV SFAFFQQGTY LLVDPNEREE RVMDGLLVIA MNKHREICTI QS SGGIMLL KDQVLRCSKI AGVKVAEITE LILKALENDQ KVRKEGGKFG FAESIANQRI TAFKMEKAPI DTSDVEEKAE EII AEAEPP SEVVSTPVLW TPGTAQIGEG VENSWGDLED SEKEDDEGGG DQAIILDGIK MDTGVEVSDI GSQDAPIILS DSEE EEMII LEPDKNPKKI RTQTTSAKQE KAPSKKPVKR RKKKRAAN

UniProtKB: Exosome complex component RRP45

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Macromolecule #2: Exosome complex component RRP41

MacromoleculeName: Exosome complex component RRP41 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.773328 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPDSMAGLEL LSDQGYRVDG RRAGELRKIQ ARMGVFAQAD GSAYIEQGNT KALAVVYGPH EIRGSRARAL PDRALVNCQY SSATFSTGE RKRRPHGDRK SCEMGLQLRQ TFEAAILTQL HPRSQIDIYV QVLQADGGTY AACVNAATLA VLDAGIPMRD F VCACSAGF ...String:
GPDSMAGLEL LSDQGYRVDG RRAGELRKIQ ARMGVFAQAD GSAYIEQGNT KALAVVYGPH EIRGSRARAL PDRALVNCQY SSATFSTGE RKRRPHGDRK SCEMGLQLRQ TFEAAILTQL HPRSQIDIYV QVLQADGGTY AACVNAATLA VLDAGIPMRD F VCACSAGF VDGTALADLS HVEEAAGGPQ LALALLPASG QIALLEMDAR LHEDHLERVL EAAAQAARDV HTLLDRVVRQ HV REASILL GD

UniProtKB: Exosome complex component RRP41

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Macromolecule #3: Exosome complex component RRP43

MacromoleculeName: Exosome complex component RRP43 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.317828 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: RSMAAGFKTV EPLEYYRRFL KENCRPDGRE LGEFRTTTVN IGSISTADGS ALVKLGNTTV ICGVKAEFAA PSTDAPDKGY VVPNVDLPP LCSSRFRSGP PGEEAQVASQ FIADVIENSQ IIQKEDLCIS PGKLVWVLYC DLICLDYDGN ILDACTFALL A ALKNVQLP ...String:
RSMAAGFKTV EPLEYYRRFL KENCRPDGRE LGEFRTTTVN IGSISTADGS ALVKLGNTTV ICGVKAEFAA PSTDAPDKGY VVPNVDLPP LCSSRFRSGP PGEEAQVASQ FIADVIENSQ IIQKEDLCIS PGKLVWVLYC DLICLDYDGN ILDACTFALL A ALKNVQLP EVTINEETAL AEVNLKKKSY LNIRTHPVAT SFAVFDDTLL IVDPTGEEEH LATGTLTIVM DEEGKLCCLH KP GGSGLTG AKLQDCMSRA VTRHKEVKKL MDEVIKSMKP K

UniProtKB: Exosome complex component RRP43

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Macromolecule #4: Exosome complex component RRP46

MacromoleculeName: Exosome complex component RRP46 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.52425 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: RSMEEETHTD AKIRAENGTG SSPRGPGCSL RHFACEQNLL SRPDGSASFL QGDTSVLAGV YGPAEVKVSK EIFNKATLEV ILRPKIGLP GVAEKSRERL IRNTCEAVVL GTLHPRTSIT VVLQVVSDAG SLLACCLNAA CMALVDAGVP MRALFCGVAC A LDSDGTLV ...String:
RSMEEETHTD AKIRAENGTG SSPRGPGCSL RHFACEQNLL SRPDGSASFL QGDTSVLAGV YGPAEVKVSK EIFNKATLEV ILRPKIGLP GVAEKSRERL IRNTCEAVVL GTLHPRTSIT VVLQVVSDAG SLLACCLNAA CMALVDAGVP MRALFCGVAC A LDSDGTLV LDPTSKQEKE ARAVLTFALD SVERKLLMSS TKGLYSDTEL QQCLAAAQAA SQHVFRFYRE SLQRRYSKS

UniProtKB: Exosome complex component RRP46

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Macromolecule #5: Exosome complex component RRP42

MacromoleculeName: Exosome complex component RRP42 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.216762 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPDSMASVTL SEAEKVYIVH GVQEDLRVDG RGCEDYRCVE VETDVVSNTS GSARVKLGHT DILVGVKAEM GTPKLEKPNE GYLEFFVDC SASATPEFEG RGGDDLGTEI ANTLYRIFNN KSSVDLKTLC ISPREHCWVL YVDVLLLECG GNLFDAISIA V KAALFNTR ...String:
GPDSMASVTL SEAEKVYIVH GVQEDLRVDG RGCEDYRCVE VETDVVSNTS GSARVKLGHT DILVGVKAEM GTPKLEKPNE GYLEFFVDC SASATPEFEG RGGDDLGTEI ANTLYRIFNN KSSVDLKTLC ISPREHCWVL YVDVLLLECG GNLFDAISIA V KAALFNTR IPRVRVLEDE EGSKDIELSD DPYDCIRLSV ENVPCIVTLC KIGYRHVVDA TLQEEACSLA SLLVSVTSKG VV TCMRKVG KGSLDPESIF EMMETGKRVG KVLHASLQSV VHKEESLGPK RQKVGFLG

UniProtKB: Exosome complex component RRP42

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Macromolecule #6: Exosome complex component MTR3

MacromoleculeName: Exosome complex component MTR3 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.623469 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPDSMPGDHR RIRGPEESQP PQLYAADEEE APGTRDPTRL RPVYARAGLL SQAKGSAYLE AGGTKVLCAV SGPRQAEGGE RGGGPAGAG GEAPAALRGR LLCDFRRAPF AGRRRRAPPG GCEERELALA LQEALEPAVR LGRYPRAQLE VSALLLEDGG S ALAAALTA ...String:
GPDSMPGDHR RIRGPEESQP PQLYAADEEE APGTRDPTRL RPVYARAGLL SQAKGSAYLE AGGTKVLCAV SGPRQAEGGE RGGGPAGAG GEAPAALRGR LLCDFRRAPF AGRRRRAPPG GCEERELALA LQEALEPAVR LGRYPRAQLE VSALLLEDGG S ALAAALTA AALALADAGV EMYDLVVGCG LSLAPGPAPT WLLDPTRLEE ERAAAGLTVA LMPVLNQVAG LLGSGEGGLT ES WAEAVRL GLEGCQRLYP VLQQSLVRAA RRRGAAAQP

UniProtKB: Exosome complex component MTR3

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Macromolecule #7: Exosome complex component RRP40

MacromoleculeName: Exosome complex component RRP40 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.906359 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSGSGSGSGS GSGSGSGSMA EPASVAAESL AGSRARAART VLGQVVLPGE ELLLPEQEDA EGPGGAVERP LSLNARACSR VRVVCGPGL RRCGDRLLVT KCGRLRHKEP GSGSGGGVYW VDSQQKRYVP VKGDHVIGIV TAKSGDIFKV DVGGSEPASL S YLSFEGAT ...String:
GSGSGSGSGS GSGSGSGSMA EPASVAAESL AGSRARAART VLGQVVLPGE ELLLPEQEDA EGPGGAVERP LSLNARACSR VRVVCGPGL RRCGDRLLVT KCGRLRHKEP GSGSGGGVYW VDSQQKRYVP VKGDHVIGIV TAKSGDIFKV DVGGSEPASL S YLSFEGAT KRNRPNVQVG DLIYGQFVVA NKDMEPEMVC IDSCGRANGM GVIGQDGLLF KVTLGLIRKL LAPDCEIIQE VG KLYPLEI VFGMNGRIWV KAKTIQQTLI LANILEACEH MTSDQRKQIF SRLAES

UniProtKB: Exosome complex component RRP40

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Macromolecule #8: Exosome complex component RRP4

MacromoleculeName: Exosome complex component RRP4 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.190355 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPDSMAMEMR LPVARKPLSE RLGRDTKKHL VVPGDTITTD TGFMRGHGTY MGEEKLIASV AGSVERVNKL ICVKALKTRY IGEVGDIVV GRITEVQQKR WKVETNSRLD SVLLLSSMNL PGGELRRRSA EDELAMRGFL QEGDLISAEV QAVFSDGAVS L HTRSLKYG ...String:
GPDSMAMEMR LPVARKPLSE RLGRDTKKHL VVPGDTITTD TGFMRGHGTY MGEEKLIASV AGSVERVNKL ICVKALKTRY IGEVGDIVV GRITEVQQKR WKVETNSRLD SVLLLSSMNL PGGELRRRSA EDELAMRGFL QEGDLISAEV QAVFSDGAVS L HTRSLKYG KLGQGVLVQV SPSLVKRQKT HFHDLPCGAS VILGNNGFIW IYPTPEHKEE EAGGFIANLE PVSLADREVI SR LRNCIIS LVTQRMMLYD TSILYCYEAS LPHQIKDILK PEIMEEIVME TRQRLLEQEG

UniProtKB: Exosome complex component RRP4

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Macromolecule #9: Exosome complex component CSL4

MacromoleculeName: Exosome complex component CSL4 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.8351 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPDSMAPPVR YCIPGERLCN LEEGSPGSGT YTRHGYIFSS LAGCLMKSSE NGALPVVSVV RETESQLLPD VGAIVTCKVS SINSRFAKV HILYVGSMPL KNSFRGTIRK EDVRATEKDK VEIYKSFRPG DIVLAKVISL GDAQSNYLLT TAENELGVVV A HSESGIQM ...String:
GPDSMAPPVR YCIPGERLCN LEEGSPGSGT YTRHGYIFSS LAGCLMKSSE NGALPVVSVV RETESQLLPD VGAIVTCKVS SINSRFAKV HILYVGSMPL KNSFRGTIRK EDVRATEKDK VEIYKSFRPG DIVLAKVISL GDAQSNYLLT TAENELGVVV A HSESGIQM VPISWCEMQC PKTHTKEFRK VARVQPEFLQ T

UniProtKB: Exosome complex component CSL4

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Macromolecule #10: Exosome complex exonuclease RRP44

MacromoleculeName: Exosome complex exonuclease RRP44 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 109.522227 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPDSMLKSKT FLKKTRAGGV MKIVREHYLR DDIGCGAPGC AACGGAHEGP ALEPQPQDPA SSVCPQPHYL LPDTNVLLHQ IDVLEDPAI RNVIVLQTVL QEVRNRSAPV YKRIRDVTNN QEKHFYTFTN EHHRETYVEQ EQGENANDRN NRAIRVAAKW Y NEHLKKMS ...String:
GPDSMLKSKT FLKKTRAGGV MKIVREHYLR DDIGCGAPGC AACGGAHEGP ALEPQPQDPA SSVCPQPHYL LPDTNVLLHQ IDVLEDPAI RNVIVLQTVL QEVRNRSAPV YKRIRDVTNN QEKHFYTFTN EHHRETYVEQ EQGENANDRN NRAIRVAAKW Y NEHLKKMS ADNQLQVIFI TNDRRNKEKA IEEGIPAFTC EEYVKSLTAN PELIDRLACL SEEGNEIESG KIIFSEHLPL SK LQQGIKS GTYLQGTFRA SRENYLEATV WIHGDNEENK EIILQGLKHL NRAVHEDIVA VELLPKSQWV APSSVVLHDE GQN EEDVEK EEETERMLKT AVSEKMLKPT GRVVGIIKRN WRPYCGMLSK SDIKESRRHL FTPADKRIPR IRIETRQAST LEGR RIIVA IDGWPRNSRY PNGHFVRNLG DVGEKETETE VLLLEHDVPH QPFSQAVLSF LPKMPWSITE KDMKNREDLR HLCIC SVDP PGCTDINDAL HCRELENGNL EVGVHIADVS HFIRPGNALD QESARRGTTV YLCEKRIDMV PELLSSNLCS LKCDVD RLA FSCIWEMNHN AEILKTKFTK SVINSKASLT YAEAQLRIDS ANMNDDITTS LRGLNKLAKI LKKRRIEKGA LTLSSPE VR FHMDSETHDP IDLQTKELRE TNSMVEEFML LANISVAKKI HEEFSEHALL RKHPAPPPSN YEILVKAARS RNLEIKTD T AKSLAESLDQ AESPTFPYLN TLLRILATRC MMQAVYFCSG MDNDFHHYGL ASPIYTHFTS PIRRYADVIV HRLLAVAIG ADCTYPELTD KHKLADICKN LNFRHKMAQY AQRASVAFHT QLFFKSKGIV SEEAYILFVR KNAIVVLIPK YGLEGTVFFE EKDKPNPQL IYDDEIPSLK IEDTVFHVFD KVKVKIMLDS SNLQHQKIRM SLVEPQIPGI SIPTDTSNMD LNGPKKKKMK L GK

UniProtKB: Exosome complex exonuclease RRP44

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Macromolecule #11: M-phase phosphoprotein 6

MacromoleculeName: M-phase phosphoprotein 6 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.542234 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPDSASMAAE RKTKLSKNLL RMKFMQRGLD SETKKQLEEE EKKIISEEHW YLDLPELKEK ESFIIEEQSF LLCEDLLYGR MSFRGFNPE VEKLMLQMNA KHKAEEVEDE TVELDVSDEE MARRYETLVG TIGKKFARKR DHANYEEDEN GDITPIKAKK M FLKPQD

UniProtKB: M-phase phosphoprotein 6

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Macromolecule #12: U44 ssRNA

MacromoleculeName: U44 ssRNA / type: rna / ID: 12 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 13.426333 KDa
SequenceString:
UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUU

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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

Concentration0.3 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
20.0 mMHepes
150.0 mMNaCl
2.0 mMDTT
VitrificationCryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 8047 / Average electron dose: 47.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2396236
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 110958
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

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