[English] 日本語
Yorodumi
- EMDB-24271: State E2 nucleolar 60S ribosomal biogenesis intermediate - Spb1-M... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-24271
TitleState E2 nucleolar 60S ribosomal biogenesis intermediate - Spb1-MTD locally refined map
Map dataState E2 Spb1-MTD locally refined map
Sample
  • Complex: Nucleolar 60S intermediate purified with tags on Ytm1 and Spb4.
    • RNA: x 1 types
    • Protein or peptide: x 15 types
  • Ligand: x 2 types
Function / homology
Function and homology information


25S rRNA (cytosine2870-C5)-methyltransferase / Noc1p-Noc2p complex / 27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / Noc2p-Noc3p complex / rRNA (guanosine-2'-O-)-methyltransferase activity / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (cytosine-C5-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / rRNA base methylation / positive regulation of ATP-dependent activity ...25S rRNA (cytosine2870-C5)-methyltransferase / Noc1p-Noc2p complex / 27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / Noc2p-Noc3p complex / rRNA (guanosine-2'-O-)-methyltransferase activity / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (cytosine-C5-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / rRNA base methylation / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methylation / maturation of 5.8S rRNA / ribosomal subunit export from nucleus / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / ATPase activator activity / Formation of a pool of free 40S subunits / ribosomal large subunit binding / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit export from nucleus / regulation of translational fidelity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / translation initiation factor activity / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / maintenance of translational fidelity / ribosomal large subunit assembly / rRNA processing / large ribosomal subunit rRNA binding / protein transport / cytoplasmic translation / cytosolic large ribosomal subunit / ATPase binding / structural constituent of ribosome / translation / mRNA binding / GTPase activity / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Nucleolar complex protein 2 / Noc2p family / RNA (C5-cytosine) methyltransferase, NOP2 / Ribosomal RNA small subunit methyltransferase F, N-terminal / N-terminal domain of 16S rRNA methyltransferase RsmF / Nop2p / Bacterial Fmu (Sun)/eukaryotic nucleolar NOL1/Nop2p, conserved site / NOL1/NOP2/sun family signature. / Ribosomal RNA methyltransferase, SPB1-like, C-terminal / Ribosomal RNA methyltransferase Spb1, domain of unknown function DUF3381 ...Nucleolar complex protein 2 / Noc2p family / RNA (C5-cytosine) methyltransferase, NOP2 / Ribosomal RNA small subunit methyltransferase F, N-terminal / N-terminal domain of 16S rRNA methyltransferase RsmF / Nop2p / Bacterial Fmu (Sun)/eukaryotic nucleolar NOL1/Nop2p, conserved site / NOL1/NOP2/sun family signature. / Ribosomal RNA methyltransferase, SPB1-like, C-terminal / Ribosomal RNA methyltransferase Spb1, domain of unknown function DUF3381 / AdoMet-dependent rRNA methyltransferase SPB1-like / Spb1 C-terminal domain / Ribosomal RNA methyltransferase Spb1, DUF3381 / Ribosomal RNA large subunit methyltransferase E / : / Domain of unknown function DUF2423 / Protein of unknown function (DUF2423) / SAM-dependent methyltransferase RsmB/NOP2-type / RNA (C5-cytosine) methyltransferase / 16S rRNA methyltransferase RsmB/F / SAM-dependent MTase RsmB/NOP-type domain profile. / Guanine nucleotide-binding protein-like 3, N-terminal domain / GNL3L/Grn1 putative GTPase / GTP-binding protein, orthogonal bundle domain superfamily / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / Translation initiation factor IF6 / eIF-6 family / translation initiation factor 6 / 50S ribosome-binding GTPase / GTP binding domain / metallochaperone-like domain / TRASH domain / Ribosomal protein L31e, conserved site / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal_L31e / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Ribosomal protein L3, domain 3, archaeal type superfamily / Ribosomal protein L3, archaeal/eukaryotic type / Ribosomal protein L31e / Ribosomal protein L24e-related / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L24e / Ribosomal protein L31e signature. / Ribosomal protein L14P, conserved site / Ribosomal protein L14 signature. / Ribosomal protein L14p/L23e / Ribosomal protein L14P / Ribosomal protein L14 superfamily / Ribosomal protein L3, conserved site / Ribosomal protein L14p/L23e / Ribosomal protein L3 / Ribosomal protein L3 / Ribosomal protein L3 signature. / Translation protein, beta-barrel domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Large ribosomal subunit protein eL31A / Large ribosomal subunit protein uL14A / Large ribosomal subunit protein uL3 / 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase / UPF0642 protein YBL028C / Nucleolar complex protein 2 / Nuclear GTP-binding protein NUG1 / 25S rRNA (cytosine(2870)-C(5))-methyltransferase / Ribosome biogenesis protein RLP24 / Eukaryotic translation initiation factor 6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae BY4741 (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsCruz VE / Sekulski K / Peddada N / Erzberger JP
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM135617-01 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR150074 United States
Robert A. Welch FoundationI-1897 United States
CitationJournal: Nat Struct Mol Biol / Year: 2022
Title: Sequence-specific remodeling of a topologically complex RNP substrate by Spb4.
Authors: Victor Emmanuel Cruz / Kamil Sekulski / Nagesh Peddada / Carolin Sailer / Sahana Balasubramanian / Christine S Weirich / Florian Stengel / Jan P Erzberger /
Abstract: DEAD-box ATPases are ubiquitous enzymes essential in all aspects of RNA biology. However, the limited in vitro catalytic activities described for these enzymes are at odds with their complex cellular ...DEAD-box ATPases are ubiquitous enzymes essential in all aspects of RNA biology. However, the limited in vitro catalytic activities described for these enzymes are at odds with their complex cellular roles, most notably in driving large-scale RNA remodeling steps during the assembly of ribonucleoproteins (RNPs). We describe cryo-EM structures of 60S ribosomal biogenesis intermediates that reveal how context-specific RNA unwinding by the DEAD-box ATPase Spb4 results in extensive, sequence-specific remodeling of rRNA secondary structure. Multiple cis and trans interactions stabilize Spb4 in a post-catalytic, high-energy intermediate that drives the organization of the three-way junction at the base of rRNA domain IV. This mechanism explains how limited strand separation by DEAD-box ATPases is leveraged to provide non-equilibrium directionality and ensure efficient and accurate RNP assembly.
History
DepositionJun 21, 2021-
Header (metadata) releaseNov 9, 2022-
Map releaseNov 9, 2022-
UpdateDec 28, 2022-
Current statusDec 28, 2022Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_24271.png

Downloads & links

-
Map

FileDownload / File: emd_24271.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationState E2 Spb1-MTD locally refined map
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.018
Minimum - Maximum-0.048888553 - 0.10175384
Average (Standard dev.)3.6645804e-05 (±0.0018181521)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 453.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: State E2 Spb1-MTD locally refined half map 2

Fileemd_24271_half_map_1.map
AnnotationState E2 Spb1-MTD locally refined half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: State E2 Spb1-MTD locally refined half map 1

Fileemd_24271_half_map_2.map
AnnotationState E2 Spb1-MTD locally refined half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Nucleolar 60S intermediate purified with tags on Ytm1 and Spb4.

EntireName: Nucleolar 60S intermediate purified with tags on Ytm1 and Spb4.
Components
  • Complex: Nucleolar 60S intermediate purified with tags on Ytm1 and Spb4.
    • RNA: 25S rRNA
    • Protein or peptide: Ribosomal RNA-processing protein 17
    • Protein or peptide: Nucleolar complex protein 2
    • Protein or peptide: 60S ribosomal protein L23-ARibosome
    • Protein or peptide: Ribosome biogenesis protein RLP24
    • Protein or peptide: 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase
    • Protein or peptide: 60S ribosome biogenesis factor Nog1
    • Protein or peptide: 60S ribosomal protein L31-ARibosome
    • Protein or peptide: 60S ribosomal protein L22-ARibosome
    • Protein or peptide: 60S ribosome ribosomal protein L19A
    • Protein or peptide: 60S ribosomal protein L30
    • Protein or peptide: 60S ribosomal protein L3
    • Protein or peptide: UPF0642 protein YBL028C
    • Protein or peptide: Nuclear GTP-binding protein NUG1
    • Protein or peptide: Eukaryotic translation initiation factor 6
    • Protein or peptide: 25S rRNA (cytosine(2870)-C(5))-methyltransferase
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
  • Ligand: water

+
Supramolecule #1: Nucleolar 60S intermediate purified with tags on Ytm1 and Spb4.

SupramoleculeName: Nucleolar 60S intermediate purified with tags on Ytm1 and Spb4.
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#16
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast)
Molecular weightTheoretical: 3.3 MDa

+
Macromolecule #1: 25S rRNA

MacromoleculeName: 25S rRNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 121.655477 KDa
SequenceString: AUAGGGUGAA GCCAGAGGAA ACUCUGGUGG AGGCUCGAAA AUGGAAUUAG ACUGAAGGUC GGCGCCCUGG AGUUAUCUUU UCUUGUUUA UCCCGCUUCG GCCCCAAGGU GAACAGCCUC UAAUGUAGAU AAGGGAAGUC GGGGGAAUCU GACUGUUAAC G AGAUUCCC ...String:
AUAGGGUGAA GCCAGAGGAA ACUCUGGUGG AGGCUCGAAA AUGGAAUUAG ACUGAAGGUC GGCGCCCUGG AGUUAUCUUU UCUUGUUUA UCCCGCUUCG GCCCCAAGGU GAACAGCCUC UAAUGUAGAU AAGGGAAGUC GGGGGAAUCU GACUGUUAAC G AGAUUCCC ACUGUCCCUA UCUACUCGGG GAACUGGCUU GUCGGCUCUU CCUAUCAUAC CAUUCGGUAA GCGUUGGAU (OMU)(OMG)(PSU)UCACCCA CUAAUAGGGA ACGUG(A2M)GCUG AAUUGAACUU AGGAACAGUU CAUUCGGAUA AUUG GUUUU UGCGGCUGUC UGAUCAGGCA UUGCCGCGAA GCUACCAUCC GAAUCUAUAU AUUGUAAGCU GAGAUUAAGC CU

+
Macromolecule #2: Ribosomal RNA-processing protein 17

MacromoleculeName: Ribosomal RNA-processing protein 17 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 13.077044 KDa
SequenceString:
NRQILTRGKQ SKKFGTDEVT FDKDSRLDYL TGFHKRKLQR QKKAQEFIKE QERLRKIEER QKIRQERKEV MEEQLKTFKE SLNLKFRYL TKNERRINQR KANDNK

+
Macromolecule #3: Nucleolar complex protein 2

MacromoleculeName: Nucleolar complex protein 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 4.74966 KDa
SequenceString:
KVSKSTKKFQ SKHLKHTLDQ RRKEKIQKKR IQGRRGNKT

+
Macromolecule #4: 60S ribosomal protein L23-A

MacromoleculeName: 60S ribosomal protein L23-A / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 14.218625 KDa
SequenceString:
NGAQGTKFRI SLGLPVGAIM NCADNSGARN LYIIAVKGSG SRLNRLPAAS LGDMVMATVK KGKPELRKKV MPAIVVRQAK SWRRRDGVF LYFEDNAGVI ANPKGEMKGS AITGPVGKEC ADLWPRVASN SGVVV

+
Macromolecule #5: Ribosome biogenesis protein RLP24

MacromoleculeName: Ribosome biogenesis protein RLP24 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 7.786305 KDa
SequenceString:
MRIYQCHFCS SPCYPGHGIM FVRNDAKEFR FCRSKCHKAF KQRRNPRKLK WTKAFRKAAG KELAV

+
Macromolecule #6: 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase

MacromoleculeName: 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
EC number: 27S pre-rRNA (guanosine2922-2'-O)-methyltransferase
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 45.405633 KDa
SequenceString: MGKTQKKNSK GRLDRYYYLA KEKGYRARSS FKIIQINEKY GHFLEKSKVV IDLCAAPGSW CQVASKLCPV NSLIIGVDIV PMKPMPNVI TFQSDITTED CRSKLRGYMK TWKADTVLHD GAPNVGLGWV QDAFTQSQLT LQALKLAVEN LVVNGTFVTK I FRSKDYNK ...String:
MGKTQKKNSK GRLDRYYYLA KEKGYRARSS FKIIQINEKY GHFLEKSKVV IDLCAAPGSW CQVASKLCPV NSLIIGVDIV PMKPMPNVI TFQSDITTED CRSKLRGYMK TWKADTVLHD GAPNVGLGWV QDAFTQSQLT LQALKLAVEN LVVNGTFVTK I FRSKDYNK LIWVFQQLFE KVEATKPPAS RNVSAEIFVV CKGFKAPKRL DPRLLDPKEV FEELPDGQQN MESKIYNPEK KV RKRQGYE EGDNLLYHET SILDFVRTED PISMLGEMNK FTIDENDHEW KILKKLKQTT DEFRSCIEDL KVLGKKDFKM ILR WRKIAR EILGIEVKDD AKTEIEVVPL TEEEQIEKDL QGLQEKQRLN VKRERRRKNE MKQKELQRMQ MNM

+
Macromolecule #7: 60S ribosome biogenesis factor Nog1

MacromoleculeName: 60S ribosome biogenesis factor Nog1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
EC number: 27S pre-rRNA (guanosine2922-2'-O)-methyltransferase
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 8.783554 KDa
SequenceString:
IVLNRTQRKT PTVIRPGFKI TRIRAFYMRK VKYTGEGMPE ILDGKNVYIR NRQKTMIAEA RNRKSLKNKA IMPR

+
Macromolecule #8: 60S ribosomal protein L31-A

MacromoleculeName: 60S ribosomal protein L31-A / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 7.025393 KDa
SequenceString:
TINLHKRLHG VSFKKRAPRA VKEIKKFAKL HMGTDDVRLA PELNQAIWKR GVKGVEYRLR

+
Macromolecule #9: 60S ribosomal protein L22-A

MacromoleculeName: 60S ribosomal protein L22-A / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 2.350864 KDa
SequenceString:
KYLKYLTKKY LKKNQLRD

+
Macromolecule #10: 60S ribosome ribosomal protein L19A

MacromoleculeName: 60S ribosome ribosomal protein L19A / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 7.490019 KDa
SequenceString:
KAVTVHSKRL PSQVVWIRRL RVLRRLLAKY RIDKHLYHVL YKESKGNAFK HKRALVEHII QA

+
Macromolecule #11: 60S ribosomal protein L30

MacromoleculeName: 60S ribosomal protein L30 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 4.390093 KDa
SequenceString:
LGYIIIAANT PVLRKSVYYF QGGNNELGTA VGKLFRVGVV S

+
Macromolecule #12: 60S ribosomal protein L3

MacromoleculeName: 60S ribosomal protein L3 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 42.452184 KDa
SequenceString: GHLGFLPRKR AASIRARVKA FPKDDRSKPV ALTSFLGYKA GMTTIVRDLD RPGSKFHKRE VVEAVTVVDT PPVVVVGVVG YVETPRGLR SLTTVWAEHL SDEVKRRFYK NWYKSKKKAF TKYSAKYAQD GAGIERELAR IKKYASVVRV LVHTQIRKTP L AQKKAHLA ...String:
GHLGFLPRKR AASIRARVKA FPKDDRSKPV ALTSFLGYKA GMTTIVRDLD RPGSKFHKRE VVEAVTVVDT PPVVVVGVVG YVETPRGLR SLTTVWAEHL SDEVKRRFYK NWYKSKKKAF TKYSAKYAQD GAGIERELAR IKKYASVVRV LVHTQIRKTP L AQKKAHLA EIQLNGGSIS EKVDWAREHF EKTVAVDSVF EQNEMIDAIA VTKGHGFEGV THRWGTKKLP RKTHRGLRKV AC IGAWHPA HVMWSVARAG QRGYHSRTSI NHKIYRVGKG DDEANGATSF DRTKKTITPM GGFVHYGEIK NDFIMVKGCI PGN RKRIVT LRKSLYTNTS RKALEEVSLK WIDTASKFGK GRFQTPAEKH AFMGTLKKDL

+
Macromolecule #13: UPF0642 protein YBL028C

MacromoleculeName: UPF0642 protein YBL028C / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 646.78 Da
SequenceString:
AKSLRA

+
Macromolecule #14: Nuclear GTP-binding protein NUG1

MacromoleculeName: Nuclear GTP-binding protein NUG1 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 977.232 Da
SequenceString:
MRVRKRQ

+
Macromolecule #15: Eukaryotic translation initiation factor 6

MacromoleculeName: Eukaryotic translation initiation factor 6 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 26.476605 KDa
SequenceString: MATRTQFENS NEIGVFSKLT NTYCLVAVGG SENFYSAFEA ELGDAIPIVH TTIAGTRIIG RMTAGNRRGL LVPTQTTDQE LQHLRNSLP DSVKIQRVEE RLSALGNVIC CNDYVALVHP DIDRETEELI SDVLGVEVFR QTISGNILVG SYCSLSNQGG L VHPQTSVQ ...String:
MATRTQFENS NEIGVFSKLT NTYCLVAVGG SENFYSAFEA ELGDAIPIVH TTIAGTRIIG RMTAGNRRGL LVPTQTTDQE LQHLRNSLP DSVKIQRVEE RLSALGNVIC CNDYVALVHP DIDRETEELI SDVLGVEVFR QTISGNILVG SYCSLSNQGG L VHPQTSVQ DQEELSSLLQ VPLVAGTVNR GSSVVGAGMV VNDYLAVTGL DTTAPELSVI ESIFRLQDAQ PESISGNLRD TL IETYS

+
Macromolecule #16: 25S rRNA (cytosine(2870)-C(5))-methyltransferase

MacromoleculeName: 25S rRNA (cytosine(2870)-C(5))-methyltransferase / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO / EC number: 25S rRNA (cytosine2870-C5)-methyltransferase
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 3.821383 KDa
SequenceString:
LAQTLVNRGV NLQPIGSWTK VGLQIFDSQV PIGATP

+
Macromolecule #17: S-ADENOSYL-L-HOMOCYSTEINE

MacromoleculeName: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 17 / Number of copies: 1 / Formula: SAH
Molecular weightTheoretical: 384.411 Da
Chemical component information

ChemComp-SAH:
S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine

+
Macromolecule #18: water

MacromoleculeName: water / type: ligand / ID: 18 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.45 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMCH2[CH2NHC(CH2OH)3]2Bis-Tris-Propane
150.0 mMNaClSodium chlorideSodium Chloride
10.0 mMMgCl2Magnesium Chloride
1.0 mMC9H15O6PHClTCEP
0.01 % (w/v)NP-40
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.30000000000000004 nm
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 4523 / Average exposure time: 0.05 sec. / Average electron dose: 1.2 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 825096
Startup modelType of model: EMDB MAP
EMDB ID:

3891

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 4 / Avg.num./class: 118000 / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 198000
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-7naf:
State E2 nucleolar 60S ribosomal biogenesis intermediate - Spb1-MTD local model

+
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