[English] 日本語
Yorodumi
- EMDB-12736: Ribosomal methyltransferase KsgA bound to small ribosomal subunit -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12736
TitleRibosomal methyltransferase KsgA bound to small ribosomal subunit
Map dataKsgA bound to bacterial ribosomal small subunit 30S
Sample
  • Complex: KsgA bound to bacterial ribosomal small subunit 30S
    • Protein or peptide: x 14 types
    • RNA: x 1 types
  • Ligand: x 1 types
Function / homology
Function and homology information


16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase / 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity / mRNA 5'-UTR binding / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / cytoplasmic translation / small ribosomal subunit / tRNA binding / rRNA binding ...16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase / 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity / mRNA 5'-UTR binding / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / cytoplasmic translation / small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / RNA binding / cytosol / cytoplasm
Similarity search - Function
rRNA adenine dimethylase-like, C-terminal / Ribosomal RNA adenine dimethylase / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. / Ribosomal protein S21, conserved site ...rRNA adenine dimethylase-like, C-terminal / Ribosomal RNA adenine dimethylase / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S15, bacterial-type / Ribosomal protein S2 signature 2. / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / Ribosomal protein S17, conserved site / Ribosomal protein S2 signature 1. / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4, conserved site / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S5 / Ribosomal protein S5, N-terminal / Ribosomal S11, conserved site / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, C-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S8 / Ribosomal protein S17 signature. / Ribosomal protein S5, C-terminal domain / S4 RNA-binding domain / Ribosomal protein S11 / RNA-binding S4 domain / RNA-binding S4 domain superfamily / Ribosomal protein S8 signature. / Ribosomal protein S11 / S4 domain / Ribosomal protein S17/S11 / Ribosomal protein S4 signature. / Ribosomal_S15 / Ribosomal protein S15 signature. / Ribosomal protein S15 / Ribosomal protein S12/S23 / S4 RNA-binding domain profile. / Ribosomal protein S12/S23 / Ribosomal protein S17 / Ribosomal protein S15 / Ribosomal protein S11 signature. / Ribosomal protein S11 superfamily / Ribosomal protein S12 signature. / S15/NS1, RNA-binding / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
30S ribosomal protein S2 / Ribosomal RNA small subunit methyltransferase A / 30S ribosomal protein S21 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS5 / 30S ribosomal protein S18 / Small ribosomal subunit protein bS16 / 30S ribosomal protein S15 / 30S ribosomal protein S8 / Small ribosomal subunit protein uS12 ...30S ribosomal protein S2 / Ribosomal RNA small subunit methyltransferase A / 30S ribosomal protein S21 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS5 / 30S ribosomal protein S18 / Small ribosomal subunit protein bS16 / 30S ribosomal protein S15 / 30S ribosomal protein S8 / Small ribosomal subunit protein uS12 / 30S ribosomal protein S20 / Small ribosomal subunit protein bS6 / 30S ribosomal protein S17 / Small ribosomal subunit protein uS4
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsStephan NC / Ries AB / Boehringer D / Ban N
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_182341 Switzerland
CitationJournal: Nucleic Acids Res / Year: 2021
Title: Structural basis of successive adenosine modifications by the conserved ribosomal methyltransferase KsgA.
Authors: Niklas C Stephan / Anne B Ries / Daniel Boehringer / Nenad Ban /
Abstract: Biogenesis of ribosomal subunits involves enzymatic modifications of rRNA that fine-tune functionally important regions. The universally conserved prokaryotic dimethyltransferase KsgA sequentially ...Biogenesis of ribosomal subunits involves enzymatic modifications of rRNA that fine-tune functionally important regions. The universally conserved prokaryotic dimethyltransferase KsgA sequentially modifies two universally conserved adenosine residues in helix 45 of the small ribosomal subunit rRNA, which is in proximity of the decoding site. Here we present the cryo-EM structure of Escherichia coli KsgA bound to an E. coli 30S at a resolution of 3.1 Å. The high-resolution structure reveals how KsgA recognizes immature rRNA and binds helix 45 in a conformation where one of the substrate nucleotides is flipped-out into the active site. We suggest that successive processing of two adjacent nucleotides involves base-flipping of the rRNA, which allows modification of the second substrate nucleotide without dissociation of the enzyme. Since KsgA is homologous to the essential eukaryotic methyltransferase Dim1 involved in 40S maturation, these results have also implications for understanding eukaryotic ribosome maturation.
History
DepositionApr 8, 2021-
Header (metadata) releaseJun 16, 2021-
Map releaseJun 16, 2021-
UpdateJun 30, 2021-
Current statusJun 30, 2021Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.081
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.081
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7o5h
  • Surface level: 0.081
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12736.png

Downloads & links

-
Map

FileDownload / File: emd_12736.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationKsgA bound to bacterial ribosomal small subunit 30S
Voxel sizeX=Y=Z: 1.39 Å
Density
Contour LevelBy AUTHOR: 0.081 / Movie #1: 0.081
Minimum - Maximum-0.079294406 - 0.24466532
Average (Standard dev.)0.00036297398 (±0.005544969)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 444.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z444.800444.800444.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ280280280
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0790.2450.000

-
Supplemental data

-
Mask #1

Fileemd_12736_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_12736_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_12736_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : KsgA bound to bacterial ribosomal small subunit 30S

EntireName: KsgA bound to bacterial ribosomal small subunit 30S
Components
  • Complex: KsgA bound to bacterial ribosomal small subunit 30S
    • Protein or peptide: Ribosomal RNA small subunit methyltransferase A
    • RNA: 16S rRNA
    • Protein or peptide: 30S ribosomal protein S2
    • Protein or peptide: 30S ribosomal protein S4
    • Protein or peptide: 30S ribosomal protein S5
    • Protein or peptide: 30S ribosomal protein S6, fully modified isoformRibosome
    • Protein or peptide: 30S ribosomal protein S8
    • Protein or peptide: 30S ribosomal protein S11
    • Protein or peptide: 30S ribosomal protein S12
    • Protein or peptide: 30S ribosomal protein S15
    • Protein or peptide: 30S ribosomal protein S16
    • Protein or peptide: 30S ribosomal protein S17
    • Protein or peptide: 30S ribosomal protein S18
    • Protein or peptide: 30S ribosomal protein S20
    • Protein or peptide: 30S ribosomal protein S21
  • Ligand: MAGNESIUM ION

+
Supramolecule #1: KsgA bound to bacterial ribosomal small subunit 30S

SupramoleculeName: KsgA bound to bacterial ribosomal small subunit 30S / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#15
Source (natural)Organism: Escherichia coli (E. coli)

+
Macromolecule #1: Ribosomal RNA small subunit methyltransferase A

MacromoleculeName: Ribosomal RNA small subunit methyltransferase A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: 16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 27.988273 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: QNFLNDQFVI DSIVSAINPQ KGQAMVEIGP GLAALTEPVG ERLDQLTVIE LDRDLAARLQ THPFLGPKLT IYQQDAMTFN FGELAEKMG QPLRVFGNLP YNISTPLMFH LFSYTDAIAD MHFMLQKEVV NRLVAGPNSK AYGRLSVMAQ YYCNVIPVLE V PPSAFTPP ...String:
QNFLNDQFVI DSIVSAINPQ KGQAMVEIGP GLAALTEPVG ERLDQLTVIE LDRDLAARLQ THPFLGPKLT IYQQDAMTFN FGELAEKMG QPLRVFGNLP YNISTPLMFH LFSYTDAIAD MHFMLQKEVV NRLVAGPNSK AYGRLSVMAQ YYCNVIPVLE V PPSAFTPP PKVDSAVVRL VPHATMPHPV KDVRVLSRIT TEAFNQRRKT IRNSLGNLFS VEVLTGMGID PAMRAENISV AQ YCQMANY LAENA

+
Macromolecule #3: 30S ribosomal protein S2

MacromoleculeName: 30S ribosomal protein S2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: JW0050.3
Molecular weightTheoretical: 25.072867 KDa
SequenceString: TVSMRDMLKA GVHFGHQTRY WNPKMKPFIF GARNKVHIIN LEKTVPMFNE ALAELNKIAS RKGKILFVGT KRAASEAVKD AALSCDQFF VNHRWLGGML TNWKTVRQSI KRLKDLETQS QDGTFDKLTK KEALMRTREL EKLENSLGGI KDMGGLPDAL F VIDADHEH ...String:
TVSMRDMLKA GVHFGHQTRY WNPKMKPFIF GARNKVHIIN LEKTVPMFNE ALAELNKIAS RKGKILFVGT KRAASEAVKD AALSCDQFF VNHRWLGGML TNWKTVRQSI KRLKDLETQS QDGTFDKLTK KEALMRTREL EKLENSLGGI KDMGGLPDAL F VIDADHEH IAIKEANNLG IPVFAIVDTN SDPDGVDFVI PGNDDAIRAV TLYLGAVAAT VREGRSQ

+
Macromolecule #4: 30S ribosomal protein S4

MacromoleculeName: 30S ribosomal protein S4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: JW0050.3
Molecular weightTheoretical: 23.383002 KDa
SequenceString: ARYLGPKLKL SRREGTDLFL KSGVRAIDTK CKIEQAPGQH GARKPRLSDY GVQLREKQKV RRIYGVLERQ FRNYYKEAAR LKGNTGENL LALLEGRLDN VVYRMGFGAT RAEARQLVSH KAIMVNGRVV NIASYQVSPN DVVSIREKAK KQSRVKAALE L AEQREKPT ...String:
ARYLGPKLKL SRREGTDLFL KSGVRAIDTK CKIEQAPGQH GARKPRLSDY GVQLREKQKV RRIYGVLERQ FRNYYKEAAR LKGNTGENL LALLEGRLDN VVYRMGFGAT RAEARQLVSH KAIMVNGRVV NIASYQVSPN DVVSIREKAK KQSRVKAALE L AEQREKPT WLEVDAGKME GTFKRKPERS DLSADINEHL IVELYSK

+
Macromolecule #5: 30S ribosomal protein S5

MacromoleculeName: 30S ribosomal protein S5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: JW0050.3
Molecular weightTheoretical: 16.661268 KDa
SequenceString:
ELQEKLIAVN RVSKTVKGGR IFSFTALTVV GDGNGRVGFG YGKAREVPAA IQKAMEKARR NMINVALNNG TLQHPVKGVH TGSRVFMQP ASEGTGIIAG GAMRAVLEVA GVHNVLAKAY GSTNPINVVR ATIDGLENMN SPEMVAAKRG KSVEEILGK

+
Macromolecule #6: 30S ribosomal protein S6, fully modified isoform

MacromoleculeName: 30S ribosomal protein S6, fully modified isoform / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: JW0050.3
Molecular weightTheoretical: 12.326251 KDa
SequenceString:
MRHYEIVFMV HPDQSEQVPG MIERYTAAIT GAEGKIHRLE DWGRRQLAYP INKLHKAHYV LMNVEAPQEV IDELETTFRF NDAVIRSMV MRTKHAVTEA SPMVKAK

+
Macromolecule #7: 30S ribosomal protein S8

MacromoleculeName: 30S ribosomal protein S8 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: JW0050.3
Molecular weightTheoretical: 14.015361 KDa
SequenceString:
SMQDPIADML TRIRNGQAAN KAAVTMPSSK LKVAIANVLK EEGFIEDFKV EGDTKPELEL TLKYFQGKAV VESIQRVSRP GLRIYKRKD ELPKVMAGLG IAVVSTSKGV MTDRAARQAG LGGEIICYVA

+
Macromolecule #8: 30S ribosomal protein S11

MacromoleculeName: 30S ribosomal protein S11 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: JW0050.3
Molecular weightTheoretical: 12.4872 KDa
SequenceString:
RKQVSDGVAH IHASFNNTIV TITDRQGNAL GWATAGGSGF RGSRKSTPFA AQVAAERCAD AVKEYGIKNL EVMVKGPGPG RESTIRALN AAGFRITNIT DVTPIPHNGC RPPKKRRV

+
Macromolecule #9: 30S ribosomal protein S12

MacromoleculeName: 30S ribosomal protein S12 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: JW0050.3
Molecular weightTheoretical: 13.636961 KDa
SequenceString:
ATVNQLVRKP RARKVAKSNV PALEACPQKR GVCTRVYTTT PKKPNSALRK VCRVRLTNGF EVTSYIGGEG HNLQEHSVIL IRGGRVKDL PGVRYHTVRG ALDCSGVKDR KQARSKYGVK RPKA

+
Macromolecule #10: 30S ribosomal protein S15

MacromoleculeName: 30S ribosomal protein S15 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: JW0050.3
Molecular weightTheoretical: 10.159621 KDa
SequenceString:
SLSTEATAKI VSEFGRDAND TGSTEVQVAL LTAQINHLQG HFAEHKKDHH SRRGLLRMVS QRRKLLDYLK RKDVARYTQL IERLGLRR

+
Macromolecule #11: 30S ribosomal protein S16

MacromoleculeName: 30S ribosomal protein S16 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: JW0050.3
Molecular weightTheoretical: 9.207572 KDa
SequenceString:
MVTIRLARHG AKKRPFYQVV VADSRNARNG RFIERVGFFN PIASEKEEGT RLDLDRIAHW VGQGATISDR VAALIKEVNK AA

+
Macromolecule #12: 30S ribosomal protein S17

MacromoleculeName: 30S ribosomal protein S17 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: JW0050.3
Molecular weightTheoretical: 9.263946 KDa
SequenceString:
KIRTLQGRVV SDKMEKSIVV AIERFVKHPI YGKFIKRTTK LHVHDENNEC GIGDVVEIRE CRPLSKTKSW TLVRVVEKAV

+
Macromolecule #13: 30S ribosomal protein S18

MacromoleculeName: 30S ribosomal protein S18 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: JW0050.3
Molecular weightTheoretical: 6.466477 KDa
SequenceString:
EIDYKDIATL KNYITESGKI VPSRITGTRA KYQRQLARAI KRARYLSLLP YTDRH

+
Macromolecule #14: 30S ribosomal protein S20

MacromoleculeName: 30S ribosomal protein S20 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: JW0050.3
Molecular weightTheoretical: 9.577268 KDa
SequenceString:
ANIKSAKKRA IQSEKARKHN ASRRSMMRTF IKKVYAAIEA GDKAAAQKAF NEMQPIVDRQ AAKGLIHKNK AARHKANLTA QINKLA

+
Macromolecule #15: 30S ribosomal protein S21

MacromoleculeName: 30S ribosomal protein S21 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: JW0050.3
Molecular weightTheoretical: 6.629744 KDa
SequenceString:
PVIKVRENEP FDVALRRFKR SCEKAGVLAE VRRREFYEKP TTERKRAKAS AVKRHA

+
Macromolecule #2: 16S rRNA

MacromoleculeName: 16S rRNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli) / Strain: JW0050.3
Molecular weightTheoretical: 312.980562 KDa
SequenceString: AAAUUGAAGA GUUUGAUCAU GGCUCAGAUU GAACGCUGGC GGCAGGCCUA ACACAUGCAA GUCGAACGGU AACAGGAUUG CUGACGAGU GGCGGACGGG UGAGUAAUGU CUGGGAAACU GCCUGAUGGA GGGGGAUAAC UACUGGAAAC GGUAGCUAAU A CCGCAUAA ...String:
AAAUUGAAGA GUUUGAUCAU GGCUCAGAUU GAACGCUGGC GGCAGGCCUA ACACAUGCAA GUCGAACGGU AACAGGAUUG CUGACGAGU GGCGGACGGG UGAGUAAUGU CUGGGAAACU GCCUGAUGGA GGGGGAUAAC UACUGGAAAC GGUAGCUAAU A CCGCAUAA CGUCGCAAGA CCAAAGAGGG GGACCUUCGG GCCUCUUGCC AUCGGAUGUG CCCAGAUGGG AUUAGCUAGU AG GUGGGGU AACGGCUCAC CUAGGCGACG AUCCCUAGCU GGUCUGAGAG GAUGACCAGC CACACUGGAA CUGAGACACG GUC CAGACU CCUACGGGAG GCAGCAGUGG GGAAUAUUGC ACAAUGGGCG CAAGCCUGAU GCAGCCAUGC CGCGUGUAUG AAGA AGGCC UUCGGGUUGU AAAGUACUUU CAGCGGGGAG GAAGGGAGUA AAGUUAAUAC CUUUGCUCAU UGACGUUACC CGCAG AAGA AGCACCGGCU AACUCCGUGC CAGCAGCCGC GGUAAUACGG AGGGUGCAAG CGUUAAUCGG AAUUACUGGG CGUAAA GCG CACGCAGGCG GUUUGUUAAG UCAGAUGUGA AAUCCCCGGG CUCAACCUGG GAACUGCAUC UGAUACUGGC AAGCUUG AG UCUCGUAGAG GGGGGUAGAA UUCCAGGUGU AGCGGUGAAA UGCGUAGAGA UCUGGAGGAA UACCGGUGGC GAAGGCGG C CCCCUGGACG AAGACUGACG CUCAGGUGCG AAAGCGUGGG GAGCAAACAG GAUCCUGGUA GUCCACGCCG UAAACGAUG UCGACUUGGA GGUUGUGCCG GCGUGGCUUC CGGAGCUAAC GCGUUAAGUC GACCGCCUGG GGAGUACGGC CGCAAGGUUA AAACUCAAA UGAAUUGACG CUCGUGUUGU GAAAUGUUGG GUUCCCGCAA CGAGCGGUAC AAACCGUAGG GGAACCUGCG G UUGG

+
Macromolecule #16: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 16 / Number of copies: 167 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE-PROPANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 35.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 165073
FSC plot (resolution estimation)

+
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