[English] 日本語
Yorodumi
- EMDB-17003: Chaetomium thermophilum Methionine Aminopeptidase 2 at the 80S ri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-17003
TitleChaetomium thermophilum Methionine Aminopeptidase 2 at the 80S ribosome
Map data
Sample
  • Complex: MAP2 at the 80S ribosome
    • Protein or peptide: Ribosomal protein L19
    • Protein or peptide: 60S ribosomal protein L25-like proteinRibosome
    • Protein or peptide: 60S ribosomal protein L26-like proteinRibosome
    • Protein or peptide: dolichyl-diphosphooligosaccharide--protein glycotransferase
    • Protein or peptide: 60S ribosomal protein L38-like proteinRibosome
    • RNA: 28S rRNA28S ribosomal RNA
    • RNA: 5.8S rRNA5.8S ribosomal RNA
    • Protein or peptide: Methionine aminopeptidase 2Methionyl aminopeptidase
KeywordsRibosome Associated Factor / Protease / Tunnel exit / Protein Maturation / Proteostasis / NME / p67 / MAP / MetAP / MAP2 / MetAP2 / ES27L / PTE / METAL BINDING PROTEIN
Function / homology
Function and homology information


dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / initiator methionyl aminopeptidase activity / methionyl aminopeptidase / metalloaminopeptidase activity / protein glycosylation / large ribosomal subunit / cytosolic large ribosomal subunit / rRNA binding / ribosome ...dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / initiator methionyl aminopeptidase activity / methionyl aminopeptidase / metalloaminopeptidase activity / protein glycosylation / large ribosomal subunit / cytosolic large ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / proteolysis / RNA binding / membrane / metal ion binding / cytoplasm
Similarity search - Function
Gcn1, N-terminal / Generalcontrol nonderepressible 1 (Gcn1) N-terminal / Centrosomal protein CEP104-like, TOG domain / E-Z type HEAT repeats / PBS lyase HEAT-like repeat / Peptidase M24A, methionine aminopeptidase, subfamily 2 / Parkin co-regulated protein / Parkin co-regulated protein / TOG domain / TOG ...Gcn1, N-terminal / Generalcontrol nonderepressible 1 (Gcn1) N-terminal / Centrosomal protein CEP104-like, TOG domain / E-Z type HEAT repeats / PBS lyase HEAT-like repeat / Peptidase M24A, methionine aminopeptidase, subfamily 2 / Parkin co-regulated protein / Parkin co-regulated protein / TOG domain / TOG / : / STT3/PglB/AglB core domain / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / : / Oligosaccharyl transferase, STT3 subunit / Oligosaccharyl transferase STT3, N-terminal / HEAT-like repeat / HEAT repeat profile. / HEAT, type 2 / Peptidase M24, methionine aminopeptidase / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal protein L23/L25, N-terminal / Ribosomal L38e protein family / Ribosomal protein L23, N-terminal domain / Ribosomal protein L19, eukaryotic / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L26/L24, eukaryotic/archaeal / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e / Ribosomal proteins L26 eukaryotic, L24P archaeal / Armadillo-like helical / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal L29 protein / KOW (Kyprides, Ouzounis, Woese) motif. / Ribosomal protein L25/L23 / Ribosomal protein L23 / Ribosomal protein L26/L24, KOW domain / Translation protein SH3-like domain superfamily / Ribosomal protein L23/L15e core domain superfamily / KOW / KOW motif / Ribosomal protein L2, domain 2 / Armadillo-type fold / Winged helix DNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
60S ribosomal protein L26-like protein / dolichyl-diphosphooligosaccharide--protein glycotransferase / 60S ribosomal protein L25-like protein / Ribosomal protein L19 / Methionine aminopeptidase 2 / 60S ribosomal protein L38-like protein
Similarity search - Component
Biological speciesThermochaetoides thermophila (fungus) / Thermochaetoides thermophila DSM 1495 (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsKlein MA / Wild K / Kisonaite M / Sinning I
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SI 586-6 Germany
CitationJournal: Nat Commun / Year: 2024
Title: Methionine aminopeptidase 2 and its autoproteolysis product have different binding sites on the ribosome.
Authors: Marius A Klein / Klemens Wild / Miglė Kišonaitė / Irmgard Sinning /
Abstract: Excision of the initiator methionine is among the first co-translational processes that occur at the ribosome. While this crucial step in protein maturation is executed by two types of methionine ...Excision of the initiator methionine is among the first co-translational processes that occur at the ribosome. While this crucial step in protein maturation is executed by two types of methionine aminopeptidases in eukaryotes (MAP1 and MAP2), additional roles in disease and translational regulation have drawn more attention to MAP2. Here, we report several cryo-EM structures of human and fungal MAP2 at the 80S ribosome. Irrespective of nascent chains, MAP2 can occupy the tunnel exit. On nascent chain displaying ribosomes, the MAP2-80S interaction is highly dynamic and the MAP2-specific N-terminal extension engages in stabilizing interactions with the long rRNA expansion segment ES27L. Loss of this extension by autoproteolytic cleavage impedes interactions at the tunnel, while promoting MAP2 to enter the ribosomal A-site, where it engages with crucial functional centers of translation. These findings reveal that proteolytic remodeling of MAP2 severely affects ribosome binding, and set the stage for targeted functional studies.
History
DepositionApr 4, 2023-
Header (metadata) releaseFeb 21, 2024-
Map releaseFeb 21, 2024-
UpdateFeb 21, 2024-
Current statusFeb 21, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_17003.png

Downloads & links

-
Map

FileDownload / File: emd_17003.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.868 Å
Density
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-1.3803455 - 3.064435
Average (Standard dev.)-0.0030497613 (±0.106239274)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720720720
Spacing720720720
CellA=B=C: 624.95996 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_17003_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_17003_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : MAP2 at the 80S ribosome

EntireName: MAP2 at the 80S ribosome
Components
  • Complex: MAP2 at the 80S ribosome
    • Protein or peptide: Ribosomal protein L19
    • Protein or peptide: 60S ribosomal protein L25-like proteinRibosome
    • Protein or peptide: 60S ribosomal protein L26-like proteinRibosome
    • Protein or peptide: dolichyl-diphosphooligosaccharide--protein glycotransferase
    • Protein or peptide: 60S ribosomal protein L38-like proteinRibosome
    • RNA: 28S rRNA28S ribosomal RNA
    • RNA: 5.8S rRNA5.8S ribosomal RNA
    • Protein or peptide: Methionine aminopeptidase 2Methionyl aminopeptidase

-
Supramolecule #1: MAP2 at the 80S ribosome

SupramoleculeName: MAP2 at the 80S ribosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Thermochaetoides thermophila (fungus)

-
Macromolecule #1: Ribosomal protein L19

MacromoleculeName: Ribosomal protein L19 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 317.092281 KDa
Recombinant expressionOrganism: Thermochaetoides thermophila DSM 1495 (fungus)
SequenceString: MSEPVANDAA PGSFDLEQAR TALTSSSTTV RIAQLRAIDE KISHNSLDRP ALLGLLKVLF WTHTFYADRP SRRAVQKCLT SITKCSEAE SFVPPLVAAI RQEAQKQAIA QANSFALVEW CSLLIQNLAG TSLWEKCSKD LVLATADALE KSLQPTARGS V GHSALVIT ...String:
MSEPVANDAA PGSFDLEQAR TALTSSSTTV RIAQLRAIDE KISHNSLDRP ALLGLLKVLF WTHTFYADRP SRRAVQKCLT SITKCSEAE SFVPPLVAAI RQEAQKQAIA QANSFALVEW CSLLIQNLAG TSLWEKCSKD LVLATADALE KSLQPTARGS V GHSALVIT RRGFRKLVQA DQAAVSTAIG VLAAKDAKPT AKNSVLLGVI AGVCARQPEA KAVVEDLKGQ YFTFYAREII GS RTALPSH IADGLHDFFA AFVSLEDLDK EVFPAIEKGL LRAPEVVLND LITPLVKALP KLDLSKALNS RFVKPLLSNI KSS NAVIRS GAVRAFREIA TVCRDFADLE KTADEVLGPL KTNKLASADH RVLHSEMLSG LPLSASIATK IATGLPAVTS KEAN EAALS AETLALNASA LFLLRTPEVP KALLDAYVKG LGDKKVSSRR IWILRTGDLL QAFAQEAELP AGFVAFAEAV VPSLL TIFN EVVANPTAAV QSGLVTGALV VAGLSGLLQR LENANIQALL KKAAVQKNSL ILDPKPSFVL SQRLYSKYPE DDLKWF CRA LSAIVEGLLS SSDAIKLAWT QAFIFLICSA TTPSAVRRQA IDALSDLSAR SLKPGCQFVA TEIIKGLWHW IATSEAA EK ESAAVLAKSG TSNLHLVLKA ICLSPAELNR RSGGDVDKAQ LQAQMCSLLV LAKQQLIPRA SWIDLCLKVQ VDPGQLAK D HEDALIDEIV RCTGHEQKSE ATKQAAYSAA AELVFVSPEN MTSRIVALIQ DDLDAAVVST VGPLEAAIFR TPEGTTFVD VLAKRQNVVP NKNVKDYDLL KWEEELRQQL AEKKGIQKKL TAEEQAKVSA QLKKEAEIRE NVRKIAAKLL RGFGVVKALA TGPPTDATR WMGAAVSSTL AAINAGATRI TGETGPLAFV SLSEQITSRI GSFIRPFMGV ATLRAYEVTA LPENLTEEPF E ELITRVLY RLRFVGEQRP LDTVSLIYVL PLVLYVLEKG GFAKDADEKD AQLVLAIEIL SFHTDVAFDE ALPRAEILSS LI SSMQKYS QHYKILKDCF SDMVRCIAPN ISPAEIGVLA RGAIVPQTSV RTAVLQAISA DVDMSDVNAS EEIWLACHDD IDE NAELGR EIWEESEWKT SEELGHKMIP YLESKDVQLR RAAAKSLAEV AGQHPDVVAP ILEKLRESYV ELAKPRVQQL DEFG MPKKM DLSDPWEARH GIALAFKGLA PHLEKRQLEP YFNFLIEQGP LGDQSAGVRA EMLEAANMTI EIHGKEILDR LMKTF EKVL EAPDKNSEAA DRVNEAVIIM YGALARHLKP GDKKIPVVIE RLLATLSTPS EAVQYAIAEC LPPLVRTCAD KSSKYF DEM MEILLTSKKY SEQRGAAYGL AGLVLGRGIN VLKEYRIMTQ LNSALENKKE IRQRESAMIA YELLSTILGR LFEPYVI QI VPQLLAGFGD GNADVREAAL AAAKACFAKL SSYGVKQILP TLLNGLDDDQ WRSKKGACDL LGAMAYLDPQ QLAQNLPE I IPPLTAVLND SHKEVRAAAN RSLKRFGEVI TNPEIKSLID ILLKALSDPT KYTDDALDAL IKVQFVHYLD APSLALVSR ILQRGLGDRS NTKRKASQVI GSLAHLTERK DLIAHLPVLV AGLKVAVVDP VPTTRATASR ALGSLVEKLG EDALPDLIPN LMQTLKSDT SAGDRLGSAQ ALSEVLAGLG TSRLEETLPT ILQNVESPKP AVREGFMSLF IFLPVCFGNS FANYLGKIIP P ILSGLADD VESIRETALR AGRLLVKNFA VRAVDLLLPE LERGLADDNY RIRLSSVELV GDLLFNLAGV KASANKEEDE AD QDITKEA GASLREVLGE EKRNKILSAL YVCRCDTAGA VRAAAVTVWK QLVHSPRTLK ELVPTLTQLL IKRLGSSNME HKV IASNAL GELIKKAGDG VLATLLPTLE EGLQTSRDVN AKQGICLALK ELISSASPEA LEDHEKTLIS VVRTALTDSD SDVR EAAAE AFDSLQQIIG KRAIDQVLPF LLNLLRSEEE ANNALAALLT LLTEPTRANI ILPNLIPTLI TPPISAFNAK ALASL SKVA GAAMNRRLPN IINSLMDNIV GCADETLREE LDTSFDTVIL SIDDTDGLNV VMNVLLQLIK HEDHRKRAAT GRHLAK FFS AATVNYSRYN QDIIRALLIS FDDKDMEVVK ASWNALNEFT KRLKKEEMEG LVISTRQTLL QVGVAGRELA GFELPKG IN AILPIFLQGL MNGTAEQRVA AALGISDIVD RTTEASLKPF VTQITGPLIR VVSERSTEVR SAILLTLNHL LEKMPTAL K PFLPQLQRTF AKSLADTSSE ILRSRAARAL GTLIKYTPRV DPLIAELVTG SKTTDAGVKT AMLKALYEVI SKAGSNMGE SSRAAVLGLI DMEPDENDKA MTITNAKLFG ALMKNVPADM AVGLLKNRVM VREFTTSSVL ALNAVLLESP SSLLDSPLAE DLPELLCQG IESKDAFIAD NFIMATGKYL LHDSPKAFET TKAIFTSLAK LIPPGNPGDS RRLSLVLVRT MARKQPDMVR P HLSLLAPP IFSSVRDMVI PVKLAAEAAF VQLFAVADEE SKVFDKWITA ATDLAPNVKR SMQDYFKRVT LRLGAQARER RE AEGGAGT LGLSADEVED EKELMAVGKP RVSWNRNPEK LKKPRAQSEV DPGPVPLKTV ARARQKSFKM VNLRTQKRLA ASV LGCGEG KVWLDPNEVS EISNANSRQS IRKLVADGLI IKKPVTMHSR SRARELNLAR RIGRHRGFGK RKGTADARMP QQVL WMRRQ RVLRRLLVKY RASGKIDKHL YHELYHLAKG NTFKHKRALV EHIHRAKAEK ARERQIKEEM DAKRARTKAA RERKQ ERQA AKRNALLGEE EESK

UniProtKB: Ribosomal protein L19

-
Macromolecule #2: 60S ribosomal protein L25-like protein

MacromoleculeName: 60S ribosomal protein L25-like protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 17.175334 KDa
Recombinant expressionOrganism: Thermochaetoides thermophila DSM 1495 (fungus)
SequenceString:
MAPKDVKKGG ASKAAKGAQA KKAAQAALKG VHSHKKTKVR KSTTFHRPKT LVLSRAPKYP RKSIPHEPRL DEHKIIIHPL NTEGALKKI EEQNTLVFIV DVKANKAQIK QALKKLYDID TVKINTLIRP DGTKKAFARL TPDVDALDIA ATKLGLV

UniProtKB: 60S ribosomal protein L25-like protein

-
Macromolecule #3: 60S ribosomal protein L26-like protein

MacromoleculeName: 60S ribosomal protein L26-like protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 15.565322 KDa
Recombinant expressionOrganism: Thermochaetoides thermophila DSM 1495 (fungus)
SequenceString:
MKVRPTVSSS RRKARKAHFS APSSVRRVIM SAPLSKELRE KYNVRSIPIR KGDEVQIVRG AHKDKEGKVT SVYRLKYVIH VERVTREKA TGQTVPIGIH PSNVVITKLH LDKDRENILA RIKAGREQVA KAKGKKTAA

UniProtKB: 60S ribosomal protein L26-like protein

-
Macromolecule #4: dolichyl-diphosphooligosaccharide--protein glycotransferase

MacromoleculeName: dolichyl-diphosphooligosaccharide--protein glycotransferase
type: protein_or_peptide / ID: 4
Details: This protein is wrongly annoted as dolichyl-diphosphooligosaccharide-protein glycotransferase in uniprotKB, which explains the long non-matching C-terminus.
Number of copies: 1 / Enantiomer: LEVO
EC number: dolichyl-diphosphooligosaccharide-protein glycotransferase
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 105.169227 KDa
Recombinant expressionOrganism: Thermochaetoides thermophila DSM 1495 (fungus)
SequenceString: MSSNGKVKAG QLWSKNKEEL TKILGELKTE LSQLRIQKIS SSGAKLNKIH DLRKSIARVL TVINAKQRAQ LRLFYKNKKY LPLDLRPKL TRALRRRLSK EDASRVLEKT KKRLTHFPQR KYAVKAATYS EGPALSIYHS HQREARCSLV QCCTFEPELR E SLLLLPVA ...String:
MSSNGKVKAG QLWSKNKEEL TKILGELKTE LSQLRIQKIS SSGAKLNKIH DLRKSIARVL TVINAKQRAQ LRLFYKNKKY LPLDLRPKL TRALRRRLSK EDASRVLEKT KKRLTHFPQR KYAVKAATYS EGPALSIYHS HQREARCSLV QCCTFEPELR E SLLLLPVA ASLKGPNFTR RERQHRNPSE ATMSAAEPLK LLASAGKGKS TRSVLRVAIL VLIAGAAVAS RLFSVIRFES II HEFDPWF NFRATKYLVA NGFYKFWDWF DDRTWHPLGR VTGGTLYPGL MVTSGVIYHL LRFLTVPVDI RNICVLLAPG FSG LTAIAA YLLTNEMTTS PSAGLLAAAF MGIAPGYISR SVAGSYDNEA IAIFLLVFTF FLWIKALKQG SMLWGALCAL FYGY MVASW GGYAFITCLL PLHSFVLICM GRYSTRLYVA YTTWYALGTL ASMQIPFVGF LPVKTSEHMP ALGIFGFLQL LAFLD YVRS TISSRQFQTF LWLFAGGIFG LGLLGLVIAT SAGLIAPWSG RFYSLWDTGY AKIHIPIIAS VSEHQPTAWP AFFFDL NML VWLFPVGVYL CFQQLGDEHV FIIVYALFGS YFAGVMVRLM LTLTPVVCVA AAIAFSSLLD TYLNLKTPNP GQAQATE DA GKKKSGLKAA SKPAVGVYAL WGKTMMISGL TIYLLLFVLH CTWVTSNAYS SPSVVLASRL PDGSQHIIDD YREAYQWL R QNTREDAKIM SWWDYGYQIG GMADRPTLVD NNTWNNTHIA TVGKAMASRE EVSYPIMRQH EVDYVLVVFG GLLGYSGDD INKFLWMVRI AEGIWPDEVS ERAFFTPRGE YRVDAEATDT MKNSLMYKMC YYNYNNLFPP GQAVDRMRGV RLPEVGPTLN TLEEAFTSE NWIIRIYKVK DLDNLGRDHA SAAAFERGHK KKKATKKRGP RVLRVE

UniProtKB: dolichyl-diphosphooligosaccharide--protein glycotransferase

-
Macromolecule #5: 60S ribosomal protein L38-like protein

MacromoleculeName: 60S ribosomal protein L38-like protein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 10.902031 KDa
Recombinant expressionOrganism: Thermochaetoides thermophila DSM 1495 (fungus)
SequenceString:
MPQEVSDIKK FIEICRRKDA SSKILTIAFP PPLTAARIKK NPKTQQIKFK VRCQRFLYTL VLKDSDKAEK LKQSLPPNLQ IKDVPKRNK RKSSA

UniProtKB: 60S ribosomal protein L38-like protein

-
Macromolecule #8: Methionine aminopeptidase 2

MacromoleculeName: Methionine aminopeptidase 2 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 48.912805 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAAQVPTEEL SKLSVQDAAA VKPGADAPEP ANGKENESDD EEDEAEEAAA APESGAGGAK KKKKKKNKKK KKKPTQQSDP PRVLISHLF PDGKYPAGEE VEYVNENRYR TTSEEKRYLD NMQSEFLNDY RQAAEVHRQV RKWAQGFVKP GKSLIEISEG I EDSVRALV ...String:
MAAQVPTEEL SKLSVQDAAA VKPGADAPEP ANGKENESDD EEDEAEEAAA APESGAGGAK KKKKKKNKKK KKKPTQQSDP PRVLISHLF PDGKYPAGEE VEYVNENRYR TTSEEKRYLD NMQSEFLNDY RQAAEVHRQV RKWAQGFVKP GKSLIEISEG I EDSVRALV GHPGLEEGDA LKAGMGFPVG LSINHCAAHY NPNSGNKIVL QQDDVIKIDI GVHVNGRIVD SAFTMAWNDQ FN PLLEAVR AATNAGIREA GIDARVGEIG GVIQEVMESY EVEINGKTYP VKPIRNLNGH NILPYSIHGT KSVPIVKTHD QTK MEEGDV FAIETFGSTG KGYVIESGEV SHYALRGDAP KVDLRLSSAK SLLNVIKRHF GTLPFCRRFL DRLGQEKYLL GLNN LVSNG IVEDYPPLVD EKGSYTAQFE HTILIRPTVK EVISRGDDY

UniProtKB: Methionine aminopeptidase 2

-
Macromolecule #6: 28S rRNA

MacromoleculeName: 28S rRNA / type: rna / ID: 6
Details: alignment does not work properly here in context of 28S rRNA sequence ... to be redone
Number of copies: 1
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 1.078716125 MDa
SequenceString: AGGUUGACCU CGGAUCAGGU AGGAGGACCC GCUGAACUUA AGCAUAUCAA UAAGCGGAGG AAAAGAAACC AACAGGGAUU GCCCUAGUA ACGGCGAGUG AAGCGGCAAC AGCUCAAAUU UGAAAGCUGG CUUCGGCCCG CGUUGUAAUU UGGAGAGGAU G CUUUGGGC ...String:
AGGUUGACCU CGGAUCAGGU AGGAGGACCC GCUGAACUUA AGCAUAUCAA UAAGCGGAGG AAAAGAAACC AACAGGGAUU GCCCUAGUA ACGGCGAGUG AAGCGGCAAC AGCUCAAAUU UGAAAGCUGG CUUCGGCCCG CGUUGUAAUU UGGAGAGGAU G CUUUGGGC GAGGCUCCUU CUGAGUUCCC UGGAACGGGA CGCCACAGAG GGUGAGAGCC CCGUAUAGUU GGAAGCCAAG CC UGUGUAA AGCUCCUUCG ACGAGUCGAG UAGUUUGGGA AUGCUGCUCA AAAUGGGAGG UAAAUUUCUU CUAAAGCUAA AUA CCGGCC AGAGACCGAU AGCGCACAAG UAGAGUGAUC GAAAGAUGAA AAGCACUUUG AAAAGAGGGU UAAAUAGCAC GUGA AAUUG UUGAAAGGGA AGCGCUUGUG ACCAGACUUG CGCCCGGCGG AUCAUCCGGU GUUCUCACCG GUGCACUCCG CCGGG CUCA GGCCAGCAUC GGUUCUGGCG GGGGGAUAAA GGCCCAGGGA AUGUGGCUCC UCCGGGAGUG UUAUAGCCCU GGGUGU AAU ACCCUCGCCG GGACCGAGGA CCGCGCUCUG CAAGGAUGCU GGCGUAAUGG UCACCAGCGA CCCGUCUUGA AACACGG AC CAAGGAGUCA AGGUUUUGCG CGAGUGUUUG GGUGUAAAAC CCGCACGCGU AAUGAAAGUG AACGUAGGUG AGAGCUUC G GCGCAUCAUC GACCGAUCCU GAUGUAUUCG GAUGGAUUUG AGUAGGAGCG UUAAGCCUUG GACCCGAAAG AUGGUGAAC UAUGCUUGGA UAGGGUGAAG CCAGAGGAAA CUCUGGUGGA GGCUCGCAGC GGUUCUGACG UGCAAAUCGA UCGUCAAAUC UGAGCAUGG GGGCGAAAGA CUAAUCGAAC CAUCUAGUAG CUGGUUACCG CCGAAGUUUC CCUCAGGAUA GCAGUGUCGA C CUUCAGUU UUAUGAGGUA AAGCGAAUGA UUAGGGACUC GGGGGCGAUU UUUAGCCUUC AUCCAUUCUC AAACUUUAAA UA UGUAAGA AGCCCUUGUU ACUUAACUGA ACGUGGGCAU UCGAAUGUAU CGACACUAGU GGGCCAUUUU UGGUAAGCAG AAC UGGCGA UGCGGGAUGA ACCGAACGCG GGGUUAAGGU GCCGGAGUGG ACGCUCAUCA GACACCACAA AAGGCGUUAG UACA UCUUG ACAGCAGGAC GGUGGCCAUG GAAGUCGGAA UCCGCUAAGG ACUGUGUAAC AACUCACCUG CCGAAUGUAC UAGCC CUGA AAAUGGAUGG CGCUCAAGCG UCCCACCCAU ACCCCGCCCU CAGGGUAGAA ACGAUGCCCU GAGGAGUAGG CGGCCG UGG AGGUCAGUGA CGAAGCCUAG GGCGUGAGCC CGGGUCGAAC GGCCUCUAGU GCAGAUCUUG GUGGUAGUAG CAAAUAC UU CAAUGAGAAC UUGAAGGACC GAAGUGGGGA AAGGUUCCAU GUGAACAGCG GUUGGACAUG GGUUAGUCGA UCCUAAGC C AUAGGGAAGU UCCGUUUCAA AGGGGCACUC GUGCCCCGUG UGGCGAAAGG GAAGCCGGUU AAUAUUCCGG CACCUGGAU GUGGGUUUUG CGCGGCAACG CAACUGAACG CGGAGACGAC GGCGGGGGCC CCGGGCAGAG UUCUCUUUUC UUCUUAACGG UCUAUCACC CUGGAAACAG UUUGUCUGGA GAUAGGGUUU AAUGGCCGGA AGAGCCCGAC ACUUCUGUCG GGUCCGGUGC G CUCUCGAC GUCCCUUGAA AAUCCGCGGG AGGGAAUAAU UCUCACGCCA GGUCGUACUC AUAACCGCAG CAGGUCCCCA AG GUGAACA GCCUCUGGUU GAUAGAACAA UGUAGAUAAG GGAAGUCGGC AAAAUAGAUC CGUAACUUCG GGAAAAGGAU UGG CUCUAA GGGUUGGGCA CGUUGGGCUU UGGGCGGACG CCCUGGGAGC AGAGGGCCUC UAGCCGGGCA ACCGGCCGGC GGCC CUCAG CACCCGGGGU UGAAGCCCUU AGCAGGCUUC GGCCGUCCGG CGUGCGGUUA ACAACCAACU UAGAACUGGU ACGGA CAGG GGGAAUCUGA CUGUCUAAUU AAAACAUAGC AUUGCGAUGG CCAGAAAGUG GUGUUGACGC AAUGUGAUUU CUGCCC AGU GCUCUGAAUG UCAAAGUGAA GAAAUUCAAC CAAGCGCGGG UAAACGGCGG GAGUAACUAU GACUCUCUUA AGGUAGC CA AAUGCCUCGU CAUCUAAUUA GUGACGCGCA UGAAUGGAUU AACGAGAUUC CCACUGUCCC UAUCUACUAU CUAGCGAA A CCACAGCCAA GGGAACGGGC UUGGCAAAAU CAGCGGGGAA AGAAGACCCU GUUGAGCUUG ACUCUAGUUU GACAUUGUG AAAAGACAUA GGAGGUGUAG AAUAGGUGGG AGCUUCGGCG CCAGUGAAAU ACCACUACUC CUAUUGUUUU UUUACUUAUU CAAUGAAGC GGGGCUGGAC UUGCGUCCAA CUUCUGGAGU UAAGGUCCUU CGCGGGCCGA CCCGGGUUGA AGACAUUGUC A GGUGGGGA GUUUGGCUGG GGCGGCACAU CUGUUAAACC AUAACGCAGG UGUCCUAAGG GGGGCUCAUG GAGAACAGAA AU CUCCAGU AGAACAAAAG GGUAAAAGUC CCCUUGAUUU UGAUUUUCAG UGUGAAUACA AACCAUGAAA GUGUGGCCUA UCG AUCCUU UAGUCCCUCG AAAUUUGAGG CUAGAGGUGC CAGAAAAGUU ACCACAGGGA UAACUGGCUU GUGGCGGCCA AGCG UUCAU AGCGACGUCG CUUUUUGAUC CUUCGAUGUC GGCUCUUCCU AUCAUACCGA AGCAGAAUUC GGUAAGCGUU GGAUU GUUC ACCCACUAAU AGGGAACGUG AGCUGGGUUU AGACCGUCGU GAGACAGGUU AGUUUUACCC UACUGAUGAA CUCGUC GCA AUGGUAAUUC AGCUUAGUAC GAGAGGAACC GCUGAUUCAG AUAAUUGGUU UUUGCGGUUG UCCGACCGGG CAGUGCC GC GAAGCUACCA UCUGCUGGAU AAUGGCUGAA CGCCUCUAAG UCAGAAUCCA UGCCAGAACG CGACGAUACU ACCCGCAC G UUGUAGACGU AUAAGAAUAG GCUCCGGCCU CGUAUCCUAG CAGGCGAUUC CUCCGCCGGC CUCGAAGUGG CCGUCGGUA AUUCGCGUAU UGCAAUUUAG ACACGCGCGG GAUCAAAUCC UUUGCAGACG ACUUAGAUGU GCGAAAGGGU CCUGUAAGCA GUAGAGUAG CCUUGUUGUU ACGAUCUGCU GAGGGUAAGC CCUCCUUCGC CUAGAUUU

GENBANK: GENBANK: XR_002966752.1

-
Macromolecule #7: 5.8S rRNA

MacromoleculeName: 5.8S rRNA / type: rna / ID: 7 / Number of copies: 1
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 50.147688 KDa
SequenceString:
AAACUUUCAA CAACGGAUCU CUUGGUUCUG GCAUCGAUGA AGAACGCAGC GAAAUGCGAU AAGUAAUGUG AAUUGCAGAA UUCCGUGAA UCAUCGAAUC UUUGAACGCA CAUUGCGCCC GCCGGUAUUC CGGCGGGCAU GCCUGUUCGA GCGUCAU

GENBANK: GENBANK: XR_002966750.1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
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 / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.1 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 42.7 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

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

7olc

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 61734

+
About Yorodumi

-
News

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

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more