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- EMDB-10837: Rix1-Rea1 pre-60S particle - Rea1, body 3 (rigid body refinement,... -

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Basic information

Entry
Database: EMDB / ID: EMD-10837
TitleRix1-Rea1 pre-60S particle - Rea1, body 3 (rigid body refinement, composite structure of Rea1 ring and tail)
Map dataLocal resolution filtered composite map of the Rea1 Ring and Tail of the nucleoplasmic Rix1-Rea1 pre-60S particle
Sample
  • Complex: Rix1-Rea1 pre-60S assembly particle - Rea1 with the Rsa4-UBL domain
    • Protein or peptide: MidasinMDN1
    • Protein or peptide: Ribosome assembly protein 4
Function / homology
Function and homology information


protein-RNA complex remodeling / regulation of ribosomal subunit export from nucleus / Antigen processing: Ubiquitination & Proteasome degradation / preribosome, large subunit precursor / ribosomal large subunit export from nucleus / ribosomal large subunit assembly / rRNA processing / nucleolus / ATP hydrolysis activity / mitochondrion ...protein-RNA complex remodeling / regulation of ribosomal subunit export from nucleus / Antigen processing: Ubiquitination & Proteasome degradation / preribosome, large subunit precursor / ribosomal large subunit export from nucleus / ribosomal large subunit assembly / rRNA processing / nucleolus / ATP hydrolysis activity / mitochondrion / nucleoplasm / ATP binding / nucleus
Similarity search - Function
Midasin / Midasin, AAA lid domain 7 / Midasin AAA lid domain 5 / : / Midasin AAA lid domain / Midasin AAA lid domain / Midasin AAA+ ATPase lid domain / ATPase, dynein-related, AAA domain / AAA domain (dynein-related subfamily) / Sigma-54 interaction domain, ATP-binding site 1 ...Midasin / Midasin, AAA lid domain 7 / Midasin AAA lid domain 5 / : / Midasin AAA lid domain / Midasin AAA lid domain / Midasin AAA+ ATPase lid domain / ATPase, dynein-related, AAA domain / AAA domain (dynein-related subfamily) / Sigma-54 interaction domain, ATP-binding site 1 / NLE / NLE (NUC135) domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Ribosome assembly protein 4 / Midasin
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Baker's yeast (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsKater L / Beckmann R
CitationJournal: Mol Cell / Year: 2020
Title: Construction of the Central Protuberance and L1 Stalk during 60S Subunit Biogenesis.
Authors: Lukas Kater / Valentin Mitterer / Matthias Thoms / Jingdong Cheng / Otto Berninghausen / Roland Beckmann / Ed Hurt /
Abstract: Ribosome assembly is driven by numerous assembly factors, including the Rix1 complex and the AAA ATPase Rea1. These two assembly factors catalyze 60S maturation at two distinct states, triggering ...Ribosome assembly is driven by numerous assembly factors, including the Rix1 complex and the AAA ATPase Rea1. These two assembly factors catalyze 60S maturation at two distinct states, triggering poorly understood large-scale structural transitions that we analyzed by cryo-electron microscopy. Two nuclear pre-60S intermediates were discovered that represent previously unknown states after Rea1-mediated removal of the Ytm1-Erb1 complex and reveal how the L1 stalk develops from a pre-mature nucleolar to a mature-like nucleoplasmic state. A later pre-60S intermediate shows how the central protuberance arises, assisted by the nearby Rix1-Rea1 machinery, which was solved in its pre-ribosomal context to molecular resolution. This revealed a Rix1-Ipi3 tetramer anchored to the pre-60S via Ipi1, strategically positioned to monitor this decisive remodeling. These results are consistent with a general underlying principle that temporarily stabilized immature RNA domains are successively remodeled by assembly factors, thereby ensuring failsafe assembly progression.
History
DepositionApr 7, 2020-
Header (metadata) releaseJul 29, 2020-
Map releaseJul 29, 2020-
UpdateSep 2, 2020-
Current statusSep 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ylf
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10837.png

Downloads & links

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Map

FileDownload / File: emd_10837.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal resolution filtered composite map of the Rea1 Ring and Tail of the nucleoplasmic Rix1-Rea1 pre-60S particle
Voxel sizeX=Y=Z: 1.059 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.0015304224 - 0.14313743
Average (Standard dev.)0.00037300837 (±0.0035066353)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 370.65 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0591.0591.059
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z370.650370.650370.650
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS350350350
D min/max/mean-0.0020.1430.000

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Supplemental data

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Additional map: Local resolution filtered map of the Tail of...

Fileemd_10837_additional_1.map
AnnotationLocal resolution filtered map of the Tail of Rea1 of the nucleoplasmic Rix1-Rea1 pre-60S particle
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local resolution filtered map of the Ring of...

Fileemd_10837_additional_2.map
AnnotationLocal resolution filtered map of the Ring of Rea1 of the nucleoplasmic Rix1-Rea1 pre-60S particle
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Rix1-Rea1 pre-60S assembly particle - Rea1 with the Rsa4-UBL domain

EntireName: Rix1-Rea1 pre-60S assembly particle - Rea1 with the Rsa4-UBL domain
Components
  • Complex: Rix1-Rea1 pre-60S assembly particle - Rea1 with the Rsa4-UBL domain
    • Protein or peptide: MidasinMDN1
    • Protein or peptide: Ribosome assembly protein 4

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Supramolecule #1: Rix1-Rea1 pre-60S assembly particle - Rea1 with the Rsa4-UBL domain

SupramoleculeName: Rix1-Rea1 pre-60S assembly particle - Rea1 with the Rsa4-UBL domain
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Rix1-TAP Flag-Rea1 derived pre-60S assembly complex
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Midasin

MacromoleculeName: Midasin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast)
Molecular weightTheoretical: 559.951438 KDa
SequenceString: MSQDRILLDL DVVNQRLILF NSAFPSDAIE APFHFSNKES TSENLDNLAG TILHSRSITG HVFLYKHIFL EIVARWIKDS KKKDYVLVI EKLASIITIF PVAMPLIEDY LDKENDHFIT ILQNPSTQKD SDMFKILLAY YRLLYHNKEV FARFIQPDIL Y QLVDLLTK ...String:
MSQDRILLDL DVVNQRLILF NSAFPSDAIE APFHFSNKES TSENLDNLAG TILHSRSITG HVFLYKHIFL EIVARWIKDS KKKDYVLVI EKLASIITIF PVAMPLIEDY LDKENDHFIT ILQNPSTQKD SDMFKILLAY YRLLYHNKEV FARFIQPDIL Y QLVDLLTK EQENQVVIFL ALKVLSLYLD MGEKTLNDML DTYIKSRDSL LGHFEGDSGI DYSFLELNEA KRCANFSKLP SV PECFTIE KKSSYFIIEP QDLSTKVASI CGVIVPKVHT IHDKVFYPLT FVPTHKTVSS LRQLGRKIQN STPIMLIGKA GSG KTFLIN ELSKYMGCHD SIVKIHLGEQ TDAKLLIGTY TSGDKPGTFE WRAGVLATAV KEGRWVLIED IDKAPTDVLS ILLS LLEKR ELTIPSRGET VKAANGFQLI STVRINEDHQ KDSSNKIYNL NMIGMRIWNV IELEEPSEED LTHILAQKFP ILTNL IPKL IDSYKNVKSI YMNTKFISLN KGAHTRVVSV RDLIKLCERL DILFKNNGIN KPDQLIQSSV YDSIFSEAAD CFAGAI GEF KALEPIIQAI GESLDIASSR ISLFLTQHVP TLENLDDSIK IGRAVLLKEK LNIQKKSMNS TLFAFTNHSL RLMEQIS VC IQMTEPVLLV GETGTGKTTV VQQLAKMLAK KLTVINVSQQ TETGDLLGGY KPVNSKTVAV PIQENFETLF NATFSLKK N EKFHKMLHRC FNKNQWKNVV KLWNEAYKMA QSILKITNTE NENENAKKKK RRLNTHEKKL LLDKWADFND SVKKFEAQS SSIENSFVFN FVEGSLVKTI RAGEWLLLDE VNLATADTLE SISDLLTEPD SRSILLSEKG DAEPIKAHPD FRIFACMNPA TDVGKRDLP MGIRSRFTEI YVHSPERDIT DLLSIIDKYI GKYSVSDEWV GNDIAELYLE AKKLSDNNTI VDGSNQKPHF S IRTLTRTL LYVTDIIHIY GLRRSLYDGF CMSFLTLLDQ KSEAILKPVI EKFTLGRLKN VKSIMSQTPP SPGPDYVQFK HY WMKKGPN TIQEQAHYII TPFVEKNMMN LVRATSGKRF PVLIQGPTSS GKTSMIKYLA DITGHKFVRI NNHEHTDLQE YLG TYVTDD TGKLSFKEGV LVEALRKGYW IVLDELNLAP TDVLEALNRL LDDNRELFIP ETQEVVHPHP DFLLFATQNP PGIY GGRKI LSRAFRNRFL ELHFDDIPQD ELEIILRERC QIAPSYAKKI VEVYRQLSIE RSASRLFEQK NSFATLRDLF RWALR DAVG YEQLAASGYM LLAERCRTPQ EKVTVKKTLE KVMKVKLDMD QYYASLEDKS LEAIGSVTWT KGMRRLSVLV SSCLKN KEP VLLVGETGCG KTTICQLLAQ FMGRELITLN AHQNTETGDI LGAQRPVRNR SEIQYKLIKS LKTALNIAND QDVDLKE LL QLYSKSDNKN IAEDVQLEIQ KLRDSLNVLF EWSDGPLIQA MRTGNFFLLD EISLADDSVL ERLNSVLEPE RSLLLAEQ G SSDSLVTASE NFQFFATMNP GGDYGKKELS PALRNRFTEI WVPSMEDFND VNMIVSSRLL EDLKDLANPI VKFSEWFGK KLGGGNATSG VISLRDILAW VEFINKVFPK IQNKSTALIQ GASMVFIDAL GTNNTAYLAE NENDLKSLRT ECIIQLLKLC GDDLELQQI ETNEIIVTQD ELQVGMFKIP RFPDAQSSSF NLTAPTTASN LVRVVRAMQV HKPILLEGSP GVGKTSLITA L ANITGNKL TRINLSEQTD LVDLFGADAP GERSGEFLWH DAPFLRAMKK GEWVLLDEMN LASQSVLEGL NACLDHRGEA YI PELDISF SCHPNFLVFA AQNPQYQGGG RKGLPKSFVN RFSVVFIDML TSDDLLLIAK HLYPSIEPDI IAKMIKLMST LED QVCKRK LWGNSGSPWE FNLRDTLRWL KLLNQYSICE DVDVFDFVDI IVKQRFRTIS DKNKAQLLIE DIFGKFSTKE NFFK LTEDY VQINNEVALR NPHYRYPITQ NLFPLECNVA VYESVLKAIN NNWPLVLVGP SNSGKTETIR FLASILGPRV DVFSM NSDI DSMDILGGYE QVDLTRQISY ITEELTNIVR EIISMNMKLS PNATAIMEGL NLLKYLLNNI VTPEKFQDFR NRFNRF FSH LEGHPLLKTM SMNIEKMTEI ITKEASVKFE WFDGMLVKAV EKGHWLILDN ANLCSPSVLD RLNSLLEIDG SLLINEC SQ EDGQPRVLKP HPNFRLFLTM DPKYGELSRA MRNRGVEIYI DELHSRSTAF DRLTLGFELG ENIDFVSIDD GIKKIKLN E PDMSIPLKHY VPSYLSRPCI FAQVHDILLL SDEEPIEESL AAVIPISHLG EVGKWANNVL NCTEYSEKKI AERLYVFIT FLTDMGVLEK INNLYKPANL KFQKALGLHD KQLTEETVSL TLNEYVLPTV SKYSDKIKSP ESLYLLSSLR LLLNSLNALK LINEKSTHG KIDELTYIEL SAAAFNGRHL KNIPRIPIFC ILYNILTVMS ENLKTESLFC GSNQYQYYWD LLVIVIAALE T AVTKDEAR LRVYKELIDS WIASVKSKSD IEITPFLNIN LEFTDVLQLS RGHSITLLWD IFRKNYPTTS NSWLAFEKLI NL SEKFDKV RLLQFSESYN SIKDLMDVFR LLNDDVLNNK LSEFNLLLSK LEDGINELEL ISNKFLNKRK HYFADEFDNL IRY TFSVDT AELIKELAPA SSLATQKLTK LITNKYNYPP IFDVLWTEKN AKLTSFTSTI FSSQFLEDVV RKSNNLKSFS GNQI KQSIS DAELLLSSTI KCSPNLLKSQ MEYYKNMLLS WLRKVIDIHV GGDCLKLTLK ELCSLIEEKT ASETRVTFAE YIFPA LDLA ESSKSLEELG EAWITFGTGL LLLFVPDSPY DPAIHDYVLY DLFLKTKTFS QNLMKSWRNV RKVISGDEEI FTEKLI NTI SDDDAPQSPR VYRTGMSIDS LFDEWMAFLS STMSSRQIKE LVSSYKCNSD QSDRRLEMLQ QNSAHFLNRL ESGYSKF AD LNDILAGYIY SINFGFDLLK LQKSKDRASF QISPLWSMDP INISCAENVL SAYHELSRFF KKGDMEDTSI EKVLMYFL T LFKFHKRDTN LLEIFEAALY TLYSRWSVRR FRQEQEENEK SNMFKFNDNS DDYEADFRKL FPDYEDTALV TNEKDISSP ENLDDIYFKL ADTYISVFDK DHDANFSSEL KSGAIITTIL SEDLKNTRIE ELKSGSLSAV INTLDAETQS FKNTEVFGNI DFYHDFSIP EFQKAGDIIE TVLKSVLKLL KQWPEHATLK ELYRVSQEFL NYPIKTPLAR QLQKIEQIYT YLAEWEKYAS S EVSLNNTV KLITDLIVSW RKLELRTWKG LFNSEDAKTR KSIGKWWFYL YESIVISNFV SEKKETAPNA TLLVSSLNLF FS KSTLGEF NARLDLVKAF YKHIQLIGLR SSKIAGLLHN TIKFYYQFKP LIDERITNGK KSLEKEIDDI ILLASWKDVN VDA LKQSSR KSHNNLYKIV RKYRDLLNGD AKTIIEAGLL YSNENKLKLP TLKQHFYEDP NLEASKNLVK EISTWSMRAA PLRN IDTVA SNMDSYLEKI SSQEFPNFAD LASDFYAEAE RLRKETPNVY TKENKKRLAY LKTQKSKLLG DALKELRRIG LKVNF REDI QKVQSSTTTI LANIAPFNNE YLNSSDAFFF KILDLLPKLR SAASNPSDDI PVAAIERGMA LAQSLMFSLI TVRHPL SEF TNDYCKINGM MLDLEHFTCL KGDIVHSSLK ANVDNVRLFE KWLPSLLDYA AQTLSVISKY SATSEQQKIL LDAKSTL SS FFVHFNSSRI FDSSFIESYS RFELFINELL KKLENAKETG NAFVFDIIIE WIKANKGGPI KKEQKRGPSV EDVEQAFR R TFTSIILSFQ KVIGDGIESI SETDDNWLSA SFKKVMVNVK LLRSSVVSKN IETALSLLKD FDFTTTESIY VKSVISFTL PVITRYYNAM TVVLERSRIY YTNTSRGMYI LSTILHSLAK NGFCSPQPPS EEVDDKNLQE GTGLGDGEGA QNNNKDVEQD EDLTEDAQN ENKEQQDKDE RDDENEDDAV EMEGDMAGEL EDLSNGEEND DEDTDSEEEE LDEEIDDLNE DDPNAIDDKM W DDKASDNS KEKDTDQNLD GKNQEEDVQA AENDEQQRDN KEGGDEDPNA PEDGDEEIEN DENAEEENDV GEQEDEVKDE EG EDLEANV PEIETLDLPE DMNLDSEHEE SDEDVDMSDG MPDDLNKEEV GNEDEEVKQE SGIESDNEND EPGPEEDAGE TET ALDEEE GAEEDVDMTN DEGKEDEENG PEEQAMSDEE ELKQDAAMEE NKEKGGEQNT EGLDGVEEKA DTEDIDQEAA VQQD SGSKG AGADATDTQE QDDVGGSGTT QNTYEEDQED VTKNNEESRE EATAALKQLG DSMKEYHRRR QDIKEAQTNG EEDEN LEKN NERPDEFEHV EGANTETDTQ ALGSATQDQL QTIDEDMAID DDREEQEVDQ KELVEDADDE KMDIDEEEML SDIDAH DAN NDVDSKKSGF IGKRKSEEDF ENELSNEHFS ADQEDDSEIQ SLIENIEDNP PDASASLTPE RSLEESRELW HKSEIST AD LVSRLGEQLR LILEPTLATK LKGDYKTGKR LNMKRIIPYI ASQFRKDKIW LRRTKPSKRQ YQIMIALDDS KSMSESKC V KLAFDSLCLV SKTLTQLEAG GLSIVKFGEN IKEVHSFDQQ FSNESGARAF QWFGFQETKT DVKKLVAEST KIFERARAM VHNDQWQLEI VISDGICEDH ETIQKLVRRA RENKIMLVFV IIDGITSNES ILDMSQVNYI PDQYGNPQLK ITKYLDTFPF EFYVVVHDI SELPEMLSLI LRQYFTDLAS S

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Macromolecule #2: Ribosome assembly protein 4

MacromoleculeName: Ribosome assembly protein 4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast)
Molecular weightTheoretical: 57.106781 KDa
SequenceString: MSTLIPPPSK KQKKEAQLPR EVAIIPKDLP NVSIKFQALD TGDNVGGALR VPGAISEKQL EELLNQLNGT SDDPVPYTFS CTIQGKKAS DPVKTIDITD NLYSSLIKPG YNSTEDQITL LYTPRAVFKV KPVTRSSSAI AGHGSTILCS AFAPHTSSRM V TGAGDNTA ...String:
MSTLIPPPSK KQKKEAQLPR EVAIIPKDLP NVSIKFQALD TGDNVGGALR VPGAISEKQL EELLNQLNGT SDDPVPYTFS CTIQGKKAS DPVKTIDITD NLYSSLIKPG YNSTEDQITL LYTPRAVFKV KPVTRSSSAI AGHGSTILCS AFAPHTSSRM V TGAGDNTA RIWDCDTQTP MHTLKGHYNW VLCVSWSPDG EVIATGSMDN TIRLWDPKSG QCLGDALRGH SKWITSLSWE PI HLVKPGS KPRLASSSKD GTIKIWDTVS RVCQYTMSGH TNSVSCVKWG GQGLLYSGSH DRTVRVWDIN SQGRCINILK SHA HWVNHL SLSTDYALRI GAFDHTGKKP STPEEAQKKA LENYEKICKK NGNSEEMMVT ASDDYTMFLW NPLKSTKPIA RMTG HQKLV NHVAFSPDGR YIVSASFDNS IKLWDGRDGK FISTFRGHVA SVYQVAWSSD CRLLVSCSKD TTLKVWDVRT RKLSV DLPG HKDEVYTVDW SVDGKRVCSG GKDKMVRLWT H

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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
GridModel: Quantifoil R3/3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.3 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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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
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-48 / Number grids imaged: 1 / Average exposure time: 10.0 sec. / Average electron dose: 75.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 273799
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: EMDB MAP
EMDB ID:

3319

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)
Final 3D classificationSoftware - Name: RELION (ver. 3.0.8)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number images used: 55397

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Atomic model buiding 1

Initial model(PDB ID:

6hyp

,

6hyd

,

6or5

,

6qta

)
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6ylf:
Rix1-Rea1 pre-60S particle - Rea1, body 3 (rigid body refinement, composite structure of Rea1 ring and tail)

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