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- EMDB-13928: 80S-bound human SKI complex in the closed state -

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Basic information

Entry
Database: EMDB / ID: EMD-13928
Title80S-bound human SKI complex in the closed state
Map dataporstprocessed_map_hSKI_ribosome-bound_closed
Sample
  • Complex: H.s. SKI complex bound to the ribosome in closed state
    • Protein or peptide: Helicase SKI2W
    • Protein or peptide: Tetratricopeptide repeat protein 37
    • Protein or peptide: WD repeat-containing protein 61
    • RNA: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
Keywordsmultiprotein complex / RNA helicase / DExH-box helicase / ATPase / RNA binding / RNA BINDING PROTEIN
Function / homology
Function and homology information


Ski complex / mRNA decay by 3' to 5' exoribonuclease / Cdc73/Paf1 complex / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / negative regulation of myeloid cell differentiation / 3'-5' RNA helicase activity / Association of TriC/CCT with target proteins during biosynthesis / nuclear-transcribed mRNA catabolic process / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex ...Ski complex / mRNA decay by 3' to 5' exoribonuclease / Cdc73/Paf1 complex / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / negative regulation of myeloid cell differentiation / 3'-5' RNA helicase activity / Association of TriC/CCT with target proteins during biosynthesis / nuclear-transcribed mRNA catabolic process / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / rescue of stalled ribosome / transcription elongation by RNA polymerase II / euchromatin / Wnt signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / RNA helicase activity / RNA helicase / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ski3/TTC37 / Ski2, N-terminal domain / Ski2 N-terminal region / : / 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 ...Ski3/TTC37 / Ski2, N-terminal domain / Ski2 N-terminal region / : / 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 / : / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Tetratricopeptide repeat / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Tetratricopeptide-like helical domain superfamily / 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 / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Superkiller complex protein 2 / Superkiller complex protein 3 / Superkiller complex protein 8
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsKoegel A / Keidel A
Funding support Germany, 5 items
OrganizationGrant numberCountry
European Research Council (ERC)EXORICO Germany
German Research Foundation (DFG)DFG SFB1035 Germany
German Research Foundation (DFG)GRK1721 Germany
German Research Foundation (DFG)SFB/TRR 237 Germany
Max Planck Society Germany
CitationJournal: Mol Cell / Year: 2022
Title: The human SKI complex regulates channeling of ribosome-bound RNA to the exosome via an intrinsic gatekeeping mechanism.
Authors: Alexander Kögel / Achim Keidel / Fabien Bonneau / Ingmar B Schäfer / Elena Conti /
Abstract: The superkiller (SKI) complex is the cytoplasmic co-factor and regulator of the RNA-degrading exosome. In human cells, the SKI complex functions mainly in co-translational surveillance-decay ...The superkiller (SKI) complex is the cytoplasmic co-factor and regulator of the RNA-degrading exosome. In human cells, the SKI complex functions mainly in co-translational surveillance-decay pathways, and its malfunction is linked to a severe congenital disorder, the trichohepatoenteric syndrome. To obtain insights into the molecular mechanisms regulating the human SKI (hSKI) complex, we structurally characterized several of its functional states in the context of 80S ribosomes and substrate RNA. In a prehydrolytic ATP form, the hSKI complex exhibits a closed conformation with an inherent gating system that effectively traps the 80S-bound RNA into the hSKI2 helicase subunit. When active, hSKI switches to an open conformation in which the gating is released and the RNA 3' end exits the helicase. The emerging picture is that the gatekeeping mechanism and architectural remodeling of hSKI underpin a regulated RNA channeling system that is mechanistically conserved among the cytoplasmic and nuclear helicase-exosome complexes.
History
DepositionDec 1, 2021-
Header (metadata) releaseFeb 9, 2022-
Map releaseFeb 9, 2022-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.01
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  • Surface view with fitted model
  • Atomic models: PDB-7qdz
  • Surface level: 0.01
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13928.png

Downloads & links

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Map

FileDownload / File: emd_13928.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationporstprocessed_map_hSKI_ribosome-bound_closed
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 272.384 Å		0.85 Å/pix.
x 320 pix.
= 272.384 Å		0.85 Å/pix.
x 320 pix.
= 272.384 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8512 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.022124728 - 0.048355173
Average (Standard dev.)0.00020662199 (±0.0017794176)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.384 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.85120.85120.8512
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z272.384272.384272.384
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0220.0480.000

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Supplemental data

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Mask #1

Fileemd_13928_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: postprocessed map hSKI-40S closed

Fileemd_13928_additional_1.map
Annotationpostprocessed_map_hSKI-40S_closed
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_13928_half_map_1.map
Annotationhalf_map_1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_13928_half_map_2.map
Annotationhalf_map_2
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Histogram (log scale)

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Sample components

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Entire : H.s. SKI complex bound to the ribosome in closed state

EntireName: H.s. SKI complex bound to the ribosome in closed state
Components
  • Complex: H.s. SKI complex bound to the ribosome in closed state
    • Protein or peptide: Helicase SKI2W
    • Protein or peptide: Tetratricopeptide repeat protein 37
    • Protein or peptide: WD repeat-containing protein 61
    • RNA: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')

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Supramolecule #1: H.s. SKI complex bound to the ribosome in closed state

SupramoleculeName: H.s. SKI complex bound to the ribosome in closed state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 380 KDa

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Macromolecule #1: Helicase SKI2W

MacromoleculeName: Helicase SKI2W / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 137.913688 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MMETERLVLP PPDPLDLPLR AVELGCTGHW ELLNLPGAPE SSLPHGLPPC APDLQQEAEQ LFLSSPAWLP LHGVEHSARK WQRKTDPWS LLAVLGAPVP SDLQAQRHPT TGQILGYKEV LLENTNLSAT TSLSLRRPPG PASQSLWGNP TQYPFWPGGM D EPTITDLN ...String:
MMETERLVLP PPDPLDLPLR AVELGCTGHW ELLNLPGAPE SSLPHGLPPC APDLQQEAEQ LFLSSPAWLP LHGVEHSARK WQRKTDPWS LLAVLGAPVP SDLQAQRHPT TGQILGYKEV LLENTNLSAT TSLSLRRPPG PASQSLWGNP TQYPFWPGGM D EPTITDLN TREEAEEEID FEKDLLTIPP GFKKGMDFAP KDCPTPAPGL LSLSCMLEPL DLGGGDEDEN EAVGQPGGPR GD TVSASPC SAPLARASSL EDLVLKEAST AVSTPEAPEP PSQEQWAIPV DATSPVGDFY RLIPQPAFQW AFEPDVFQKQ AIL HLERHD SVFVAAHTSA GKTVVAEYAI ALAQKHMTRT IYTSPIKALS NQKFRDFRNT FGDVGLLTGD VQLHPEASCL IMTT EILRS MLYSGSDVIR DLEWVIFDEV HYINDVERGV VWEEVLIMLP DHVSIILLSA TVPNALEFAD WIGRLKRRQI YVIST VTRP VPLEHYLFTG NSSKTQGELF LLLDSRGAFH TKGYYAAVEA KKERMSKHAQ TFGAKQPTHQ GGPAQDRGVY LSLLAS LRT RAQLPVVVFT FSRGRCDEQA SGLTSLDLTT SSEKSEIHLF LQRCLARLRG SDRQLPQVLH MSELLNRGLG VHHSGIL PI LKEIVEMLFS RGLVKVLFAT ETFAMGVNMP ARTVVFDSMR KHDGSTFRDL LPGEYVQMAG RAGRRGLDPT GTVILLCK G RVPEMADLHR MMMGKPSQLQ SQFRLTYTMI LNLLRVDALR VEDMMKRSFS EFPSRKDSKA HEQALAELTK RLGALEEPD MTGQLVDLPE YYSWGEELTE TQHMIQRRIM ESVNGLKSLS AGRVVVVKNQ EHHNALGVIL QVSSNSTSRV FTTLVLCDKP LSQDPQDRG PATAEVPYPD DLVGFKLFLP EGPCDHTVVK LQPGDMAAIT TKVLRVNGEK ILEDFSKRQQ PKFKKDPPLA A VTTAVQEL LRLAQAHPAG PPTLDPVNDL QLKDMSVVEG GLRARKLEEL IQGAQCVHSP RFPAQYLKLR ERMQIQKEME RL RFLLSDQ SLLLLPEYHQ RVEVLRTLGY VDEAGTVKLA GRVACAMSSH ELLLTELMFD NALSTLRPEE IAALLSGLVC QSP GDAGDQ LPNTLKQGIE RVRAVAKRIG EVQVACGLNQ TVEEFVGELN FGLVEVVYEW ARGMPFSELA GLSGTPEGLV VRCI QRLAE MCRSLRGAAR LVGEPVLGAK METAATLLRR DIVFAASLYT Q

UniProtKB: Superkiller complex protein 2

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Macromolecule #2: Tetratricopeptide repeat protein 37

MacromoleculeName: Tetratricopeptide repeat protein 37 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 178.651641 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKHHHHHHHH HHSAGLEVLF QGPDSMSSKE VKTALKSARD AIRNKEYKEA LKHCKTVLKQ EKNNYNAWVF IGVAAAELEQ PDQAQSAYK KAAELEPDQL LAWQGLANLY EKYNHINAKD DLPGVYQKLL DLYESVDKQK WCDVCKKLVD LYYQEKKHLE V ARTWHKLI ...String:
MKHHHHHHHH HHSAGLEVLF QGPDSMSSKE VKTALKSARD AIRNKEYKEA LKHCKTVLKQ EKNNYNAWVF IGVAAAELEQ PDQAQSAYK KAAELEPDQL LAWQGLANLY EKYNHINAKD DLPGVYQKLL DLYESVDKQK WCDVCKKLVD LYYQEKKHLE V ARTWHKLI KTRQEQGAEN EELHQLWRKL TQFLAESTED QNNETQQLLF TAFENALGLS DKIPSEDHQV LYRHFIQSLS KF PHESARL KKACEGMINI YPTVQYPLEV LCLHLIESGN LTDEGQQYCC RLVEMDSKSG PGLIGLGIKA LQDKKYEDAV RNL TEGLKE SPVCTSGWYH LAEAQVKMHR PKEAVLSCSQ ALKIVDNLGA SGNSLYQRNL CLHLKAEALI KLSDYDSSEE AIRT LDQIS DADNIPGLLV LKSLAYRNKG SFDEAAKIME DLLSSYPDLA EVHALEALIH FTKKDYLQAE KCFQRALEKD TEVAE YHYQ LGLTYWFMGE ETRKDKTKAL THFLKAARLD TYMGKVFCYL GHYYRDVVGD KNRARGCYRK AFELDDTDAE SGAAAV DLS VELEDMEMAL AILTTVTQKA SAGTAKWAWL RRGLYYLKAG QHSQAVADLQ AALRADPKDF NCWESLGEAY LSRGGYT TA LKSFTKASEL NPESIYSVFK VAAIQQILGK YKEAVAQYQM IIKKKEDYVP ALKGLGECHL MMAKAALVDY LDGKAVDY I EKALEYFTCA LQHRADVSCL WKLAGDACTC LYAVAPSKVN VHVLGVLLGQ KEGKQVLKKN ELLHLGGRCY GRALKLMST SNTWCDLGIN YYRQAQHLAE TGSNMNDLKE LLEKSLHCLK KAVRLDSNNH LYWNALGVVA CYSGIGNYAL AQHCFIKSIQ SEQINAVAW TNLGVLYLTN ENIEQAHEAF KMAQSLDPSY LMCWIGQALI AEAVGSYDTM DLFRHTTELN MHTEGALGYA Y WVCTTLQD KSNRETELYQ YNILQMNAIP AAQVILNKYV ERIQNYAPAF TMLGYLNEHL QLKKEAANAY QRAILLLQTA ED QDTYNVA IRNYGRLLCS TGEYDKAIQA FKSTPLEVLE DIIGFALALF MKGLYKESSK AYERALSIVE SEQDKAHILT ALA ITEYKQ GKTDVAKTLL FKCSILKEPT TESLQALCAL GLAMQDATLS KAALNELLKH IKHKDSNYQR CLLTSAIYAL QGRS VAVQK QISKAVHSNP GDPALWSLLS RVVAQYAQRN AKGGVVAGNV AHILDSNHGK KALLYTAVNQ LAMGSSSAED EKNTA LKTI QKAALLSPGD PAIWAGLMAA CHADDKLALV NNTQPKRIDL YLALLSAVSA SIKDEKFFEN YNQSLEKWSL SQAVTG LID TGRISEAETL CTKNLKSNPD QPAVILLLRQ VQCKPLLESQ KPLPDAVLEE LQKTVMSNST SVPAWQWLAH VYQSQGM MR AAEMCYRKSL QLASQRGSWS GKLSSLLRLA LLALKVCMAN ISNDHWPSLV QEATTEALKL CFCPLAVLLQ ALLQFKRK M GARETRRLLE RVVYQPGYPK SIASTARWYL LRHLYAKDDY ELIDVLVNNA KTHGDTRALE LNQRLSSQ

UniProtKB: Superkiller complex protein 3

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Macromolecule #3: WD repeat-containing protein 61

MacromoleculeName: WD repeat-containing protein 61 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.617465 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MTNQYGILFK QEQAHDDAIW SVAWGTNKKE NSETVVTGSL DDLVKVWKWR DERLDLQWSL EGHQLGVVSV DISHTLPIAA SSSLDAHIR LWDLENGKQI KSIDAGPVDA WTLAFSPDSQ YLATGTHVGK VNIFGVESGK KEYSLDTRGK FILSIAYSPD G KYLASGAI ...String:
MTNQYGILFK QEQAHDDAIW SVAWGTNKKE NSETVVTGSL DDLVKVWKWR DERLDLQWSL EGHQLGVVSV DISHTLPIAA SSSLDAHIR LWDLENGKQI KSIDAGPVDA WTLAFSPDSQ YLATGTHVGK VNIFGVESGK KEYSLDTRGK FILSIAYSPD G KYLASGAI DGIINIFDIA TGKLLHTLEG HAMPIRSLTF SPDSQLLVTA SDDGYIKIYD VQHANLAGTL SGHASWVLNV AF CPDDTHF VSSSSDKSVK VWDVGTRTCV HTFFDHQDQV WGVKYNGNGS KIVSVGDDQE IHIYDCPI

UniProtKB: Superkiller complex protein 8

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Macromolecule #4: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')

MacromoleculeName: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3') / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.792037 KDa
SequenceString:
UUUUUU

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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

Concentration0.2 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE
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 exposure time: 5.0 sec. / Average electron dose: 55.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4buj

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 51048
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: BACKBONE TRACE / Target criteria: CORRELATION COEFFICIENT
Output model

PDB-7qdz:
80S-bound human SKI complex in the closed state

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