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- EMDB-0328: Rea1 Wild type AMPPNP state -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-0328
TitleRea1 Wild type AMPPNP state
Map data
Sample
  • Complex: Rea1-WT AMPPNP density map
    • Protein or peptide: Midasin,Midasin,Midasin,Midasin
KeywordsRea1 / Mdn1 / Midasin / AAA+ protein / ribosome maturation / molecular machine / MOTOR PROTEIN
Function / homology
Function and homology information


protein-RNA complex remodeling / regulation of ribosomal subunit export from nucleus / preribosome, large subunit precursor / ribosomal large subunit export from nucleus / ribosomal large subunit assembly / rRNA processing / nucleolus / ATP hydrolysis activity / mitochondrion / nucleoplasm ...protein-RNA complex remodeling / regulation of ribosomal subunit export from nucleus / 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 / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsSosnowski P / Urnavicius L
Funding support France, 1 items
OrganizationGrant numberCountry
French National Research AgencyATIP-Avenir France
CitationJournal: Elife / Year: 2018
Title: The CryoEM structure of the ribosome maturation factor Rea1.
Authors: Piotr Sosnowski / Linas Urnavicius / Andreas Boland / Robert Fagiewicz / Johan Busselez / Gabor Papai / Helgo Schmidt /
Abstract: The biogenesis of 60S ribosomal subunits is initiated in the nucleus where rRNAs and proteins form pre-60S particles. These pre-60S particles mature by transiently interacting with various assembly ...The biogenesis of 60S ribosomal subunits is initiated in the nucleus where rRNAs and proteins form pre-60S particles. These pre-60S particles mature by transiently interacting with various assembly factors. The ~5000 amino-acid AAA+ ATPase Rea1 (or Midasin) generates force to mechanically remove assembly factors from pre-60S particles, which promotes their export to the cytosol. Here we present three Rea1 cryoEM structures. We visualise the Rea1 engine, a hexameric ring of AAA+ domains, and identify an α-helical bundle of AAA2 as a major ATPase activity regulator. The α-helical bundle interferes with nucleotide-induced conformational changes that create a docking site for the substrate binding MIDAS domain on the AAA +ring. Furthermore, we reveal the architecture of the Rea1 linker, which is involved in force generation and extends from the AAA+ ring. The data presented here provide insights into the mechanism of one of the most complex ribosome maturation factors.
History
DepositionOct 31, 2018-
Header (metadata) releaseDec 12, 2018-
Map releaseDec 12, 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: 0.0156
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0156
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6i26
  • Surface level: 0.0156
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0328.png

Downloads & links

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Map

FileDownload / File: emd_0328.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.09 Å
Density
Contour LevelBy AUTHOR: 0.0156 / Movie #1: 0.0156
Minimum - Maximum-0.029409813 - 0.06672308
Average (Standard dev.)0.00012702298 (±0.0014525586)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 418.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z418.560418.560418.560
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0290.0670.000

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Supplemental data

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Sample components

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Entire : Rea1-WT AMPPNP density map

EntireName: Rea1-WT AMPPNP density map
Components
  • Complex: Rea1-WT AMPPNP density map
    • Protein or peptide: Midasin,Midasin,Midasin,Midasin

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Supramolecule #1: Rea1-WT AMPPNP density map

SupramoleculeName: Rea1-WT AMPPNP density map / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Midasin,Midasin,Midasin,Midasin

MacromoleculeName: Midasin,Midasin,Midasin,Midasin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 546.623375 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)PSVPECFTI E KKSSYFII EPQDLSTKVA SICGVIVPKV HTIHDKVFYP LTFVPTHKTV SSLRQLGRKI QNSTPIMLIG KAGSGKTFLI NE LSKYMGC HDSIVKIHLG EQTDAKLLIG TYTSGDKPGT FEWRAGVLAT AVKEGRWVLI EDIDKAPTDV LSILLSLLEK REL TIPSRG ETVKAANGFQ LISTVRINED HQKDSSNKIY NLNMIGMRIW NVIELEEPSE EDLTHILAQK FPILTNLIPK LIDS YKNVK SIYMNTKFIS LNKGAHTRVV SVRDLIKLCE RLDILFKNNG INKPDQLIQS SVYDSIFSEA ADCFAGAIGE FKALE PIIQ AIGESLDIAS SRISLFLTQH VPTLENLDDS IKIGRAVLLK EKLNIQKKSM NSTLFAFTNH SLRLMEQISV CIQMTE PVL LVGETGTGKT TVVQQLAKML AKKLTVINVS QQTETGDLLG GYKPVNSKTV AVPIQENFET LFNATFSLKK NEKFHKM LH RCFNKNQWKN VVKLWNEAYK MAQSILKITN TENENENAKK KKRRLNTHEK KLLLDKWADF NDSVKKFEAQ SSSIENSF V FNFVEGSLVK TIRAGEWLLL DEVNLATADT LESISDLLTE PDSRSILLSE KGDAEPIKAH PDFRIFACMN PATDVGKRD LPMGIRSRFT EIYVHSPERD ITDLLSIIDK YIGKYSVSDE WVGNDIAELY LEAKKLSDNN TIVDGSNQKP HFSIRTLTRT LLYVTDIIH IYGLRRSLYD GFCMSFLTLL DQKSEAILKP VIEKFTLGRL KNVKSIMSQT PPSPGPDYVQ FKHYWMKKGP N TIQEQAHY IITPFVEKNM MNLVRATSGK RFPVLIQGPT SSGKTSMIKY LADITGHKFV RINNHEHTDL QEYLGTYVTD DT GKLSFKE GVLVEALRKG YWIVLDELNL APTDVLEALN RLLDDNRELF IPETQEVVHP HPDFLLFATQ NPPGIYGGRK ILS RAFRNR FLELHFDDIP QDELEIILRE RCQIAPSYAK KIVEVYRQLS IERSASRLFE QKNSFATLRD LFRWALRDAV GYEQ LAASG YMLLAERCRT PQEKVTVKKT LEKVMKVKLD MDQYYASLED KSLEAIGSVT WTKGMRRLSV LVSSCLKNKE PVLLV GETG CGKTTICQLL AQFMGRELIT LNAHQNTETG DILGAQRPVR NRSEIQYKLI KSLKTALNIA NDQDVDLKEL LQLYSK SDN KNIAEDVQLE IQKLRDSLNV LFEWSDGPLI QAMRTGNFFL LDEISLADDS VLERLNSVLE PERSLLLAEQ GSSDSLV TA SENFQFFATM NPGGDYGKKE LSPALRNRFT EIWVPSMEDF NDVNMIVSSR LLEDLKDLAN PIVKFSEWFG KKLGGGNA T SGVISLRDIL AWVEFINKVF PKIQNKSTAL IQGASMVFID ALGTNNTAYL AENENDLKSL RTECIIQLLK LCGDDLELQ QIETNEIIVT QDELQVGMFK IPRFPDAQSS SFNLTAPTTA SNLVRVVRAM QVHKPILLEG SPGVGKTSLI TALANITGNK LTRINLSEQ TDLVDLFGAD APGERSGEFL WHDAPFLRAM KKGEWVLLDE MNLASQSVLE GLNACLDHRG EAYIPELDIS F SCHPNFLV FAAQNPQYQG GGRKGLPKSF VNRFSVVFID MLTSDDLLLI AKHLYPSIEP DIIAKMIKLM STLEDQVCKR KL WGNSGSP WEFNLRDTLR WLKLLNQYSI CEDVDVFDFV DIIVKQRFRT ISDKNKAQLL IEDIFGKFST KENFFKLTED YVQ INNEVA LRNPHYRYPI TQNLFPLECN VAVYESVLKA INNNWPLVLV GPSNSGKTET IRFLASILGP RVDVFSMNSD IDSM DILGG YEQVDLTRQI SYITEELTNI VREIISMNMK LSPNATAIME GLNLLKYLLN NIVTPEKFQD FRNRFNRFFS HLEGH PLLK TMSMNIEKMT EIITKEASVK FEWFDGMLVK AVEKGHWLIL DNANLCSPSV LDRLNSLLEI DGSLLINECS QEDGQP RVL KPHPNFRLFL TMDPKYGELS RAMRNRGVEI YIDELHSRST AFDRLTLGFE LGENIDFVSI DDGIKKIKLN EPDMSIP LK HYVPSYLSRP CIFAQVHDIL LLSDEEPIEE SLAAVIPISH LGEVGKWANN VLNCTEYSEK KIAERLYVFI TFLTDMGV L EKINNLYKPA NLKFQKALGL HDKQLTEETV SLTLNEYVLP TVSKYSDKIK SPESLYLLSS LRLLLNSLNA LKLINEKST HGKIDELTYI ELSAAAFNGR HLKNIPRIPI FCILYNILTV MSENLKTESL FCGSNQYQYY WDLLVIVIAA LETAVTKDEA RLRVYKELI DSWIASVKSK SDIEITPFLN INLEFTDVLQ LSRGHSITLL WDIFRKNYPT TSNSWLAFEK LINLSEKFDK V RLLQFSES YNSIKDLMDV FRLLNDDVLN NKLSEFNLLL SKLEDGINEL ELISNKFLNK RKHYFADEFD NLIRYTFSVD TA ELIKELA PASSLATQKL TKLITNKYNY PPIFDVLWTE KNAKLTSFTS TIFSSQFLED VVRKSNNLKS FSGNQIKQSI SDA ELLLSS TIKCSPNLLK SQMEYYKNML LSWLRKVIDI HVGGDCLKLT LKELCSLIEE KTASETRVTF AEYIFPALDL AESS KSLEE LGEAWITFGT GLLLLFVPDS PYDPAIHDYV LYDLFLKTKT FSQNLMKSWR NVRKVISGDE EIFTEKLINT ISDDD APQS PRVYRTGMSI DSLFDEWMAF LSSTMSSRQI KELVSSYKCN SDQSDRRLEM LQQNSAHFLN RLESGYSKFA DLNDIL AGY IYSINFGFDL LKLQKSKDRA SFQISPLWSM DPINISCAEN VLSAYHELSR FFKKGDMEDT SIEKVLMYFL TLFKFHK RD TNLLEIFEAA LYTLYSRWSV RRFRQEQEEN EKSNMFKFND NSDDYEADFR KLFPDYEDTA LVTNEKDISS PENLDDIY F KLADTYISVF DKDHDANFSS ELKSGAIITT ILSEDLKNTR IEELKSGSLS AVINTLDAET QSFKNTEVFG NIDFYHDFS IPEFQKAGDI IETVLKSVLK LLKQWPEHAT LKELYRVSQE FLNYPIKTPL ARQLQKIEQI YTYLAEWEKY ASSEVSLNNT VKLITDLIV SWRKLELRTW KGLFNSEDAK TRKSIGKWWF YLYESIVISN FVSEKKETAP NATLLVSSLN LFFSKSTLGE F NARLDLVK AFYKHIQLIG LRSSKIAGLL HNTIKFYYQF KPLIDERITN GKKSLEKEID DIILLASWKD VNVDALKQSS RK SHNNLYK IVRKYRDLLN GDAKTIIEAG LLY(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)RNI DTVASNMDSY LEKISSQEFP NFADLASDFY AEAERLRKET PNVYTKE NK KRLAYLKTQK SKLLGDALKE LRRIGLKVNF REDIQKVQSS TTTILANIAP FNNEYLNSSD AFFFKILDLL PKLRSAAS N PSDDIPVAAI ERGMALAQSL MFSLITVRHP LSEFTNDYCK INGMMLDLEH FTCLKGDIVH SSLKANVDNV RLFEKWLPS LLDYAAQTLS VISKYSATSE QQKILLDAKS TLSSFFVHFN SSRIFDSSFI ESYSRFELFI NELLKKLENA KETGNAFVFD IIIEWIKAN KGGPIKKEQK RGPSVEDVEQ AFRRTFTSII LSFQKVIGDG IESISETDDN WLSASFKKVM VNVKLLRSSV V SKNIETAL SLLKDFDFTT TESIYVKSVI SFTLPVITRY YNAMTVVLER SRIYYTNTSR GMYILSTILH SLAKNGFCSP QP PSEEVDD KNLQEGTGLG DGEGAQNNNK DVEQDEDLTE DAQNENKEQQ DKDERDDENE DDAVEMEGDM AGELEDLSNG EEN DDEDTD SEEEELDEEI DDLNEDDPNA IDDKMWDDKA SDNSKEKDTD QNLDGKNQEE DVQAAENDEQ QRDNKEGGDE DPNA PEDGD EEIENDENAE EENDVGEQED EVKDEEGEDL EANVPEIETL DLPEDMNLDS EHEESDEDVD MSDGMPDDLN KEEVG NEDE EVKQESGIES DNENDEPGPE EDAGETETAL DEEEGAEEDV DMTNDEGKED EENGPEEQAM SDEEELKQDA AMEENK EKG GEQNTEGLDG VEEKADTEDI DQEAAVQQDS GSKGAGADAT DTQEQDDVGG SGTTQNTYEE DQEDVTKNNE ESREEAT AA LKQLGDSMKE YHRRRQDIKE AQTNGEEDEN LEKNNERPDE FEHVEGANTE TDTQALGSAT QDQLQTIDED MAIDDDRE E QEVDQKELVE DADDEKMDID EEEMLSDIDA HDANNDVDSK KSGFIGKRKS EEDFENELSN EHFSADQEDD SEIQSLIEN IEDNPPDASA SLTPERSLEE SRELWHKSEI STADLVSRLG EQLRLILEPT LATKLKGDYK TGKRLNMKRI IPYIASQFRK DKIWLRRTK PSKRQYQIMI ALDDSKSMSE SKCVKLAFDS LCLVSKTLTQ LEAGGLSIVK FGENIKEVHS FDQQFSNESG A RAFQWFGF QETKTDVKKL VAESTKIFER ARAMVHNDQW QLEIVISDGI CEDHETIQKL VRRARENKIM LVFVIIDGIT SN ESILDMS QVNYIPDQYG NPQLKITKYL DTFPFEFYVV VHDISELPEM LSLILRQYFT DLASS

UniProtKB: Midasin, Midasin

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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 mg/mL
BufferpH: 7.2
Component:
ConcentrationFormulaName
150.0 mMC8H18N2O4SHEPES
10.0 mMMg(CH3COO)2Magnesium Acetate
5.0 mMC14H24N2O10EGTA
5.0 mMC4H10O2S2DTT
3.0 mMC10H17N6O12P3AMP-PNP

Details: AMP-PNP was added 5 minute before the plunging
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 280 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsSpherical aberration corrector: Titan Krios Cs Corrector / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3712 pixel / Digitization - Dimensions - Height: 3840 pixel / Digitization - Frames/image: 2-38 / Number grids imaged: 2 / Number real images: 6797 / Average exposure time: 0.2 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 3.4 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 790775
Startup modelType of model: INSILICO MODEL
In silico model: Low pass filter of the Rea1 ADP state (see emd-0308, emd-0309)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 55442
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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