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- EMDB-7340: Conformation of methylated GGQ in the peptidyl transferase center... -

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Basic information

Entry
Database: EMDB / ID: EMD-7340
TitleConformation of methylated GGQ in the peptidyl transferase center during translation termination (PTC region)
Map dataConformation of methylated GGQ in the peptidyl transferase center during translation termination
Sample
  • Complex: nonstop ribosomal complex with ArfA/RF2
    • Complex: 50S subunit
      • Organelle or cellular component: 23S rRNA
        • RNA: 23S rRNA
      • Organelle or cellular component: 50S ribosomal protein L2
        • Protein or peptide: 50S ribosomal protein L2
      • Organelle or cellular component: 50S ribosomal protein L3
        • Protein or peptide: 50S ribosomal protein L3
      • Organelle or cellular component: 50S ribosomal protein L16
        • Protein or peptide: 50S ribosomal protein L16
      • Organelle or cellular component: 50S ribosomal protein L27
        • Protein or peptide: 50S ribosomal protein L27
    • Organelle or cellular component: P-site tRNA fMet
      • RNA: P-site tRNA fMet
    • Organelle or cellular component: Peptide chain release factor 2
      • Protein or peptide: Peptide chain release factor RF2
  • Ligand: MAGNESIUM ION
Function / homology
Function and homology information


translation release factor activity, codon specific / positive regulation of ribosome biogenesis / translational termination / DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / regulation of cell growth / ribosome binding / transferase activity ...translation release factor activity, codon specific / positive regulation of ribosome biogenesis / translational termination / DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / regulation of cell growth / ribosome binding / transferase activity / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / viral translational frameshifting / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Peptide chain release factor 2 / Peptide chain release factor / PCRF domain / PCRF / Peptide chain release factor class I superfamily / Prokaryotic-type class I peptide chain release factors signature. / Peptide chain release factor class I / RF-1 domain / Ribosomal protein L16 signature 1. / Ribosomal protein L16, conserved site ...Peptide chain release factor 2 / Peptide chain release factor / PCRF domain / PCRF / Peptide chain release factor class I superfamily / Prokaryotic-type class I peptide chain release factors signature. / Peptide chain release factor class I / RF-1 domain / Ribosomal protein L16 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L16 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L2 signature. / Ribosomal protein L2, conserved site / : / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e / Ribosomal protein L2, domain 3 / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, C-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2 / Ribosomal protein L3, conserved site / Ribosomal protein L3 signature. / Ribosomal protein L3 / Ribosomal protein L3 / Translation protein SH3-like domain superfamily / Translation protein, beta-barrel domain superfamily / Ribosomal protein L2, domain 2 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Peptide chain release factor RF2 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsZeng F / Jin H
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM120552 United States
CitationJournal: Sci Rep / Year: 2018
Title: Conformation of methylated GGQ in the Peptidyl Transferase Center during Translation Termination.
Authors: Fuxing Zeng / Hong Jin /
Abstract: The universally conserved Gly-Gly-Gln (GGQ) tripeptide in release factors or release factor-like surveillance proteins is required to catalyze the release of nascent peptide in the ribosome. The ...The universally conserved Gly-Gly-Gln (GGQ) tripeptide in release factors or release factor-like surveillance proteins is required to catalyze the release of nascent peptide in the ribosome. The glutamine of the GGQ is methylated post-translationally at the N position in vivo; this covalent modification is essential for optimal cell growth and efficient translation termination. However, the precise conformation of the methylated-GGQ tripeptide in the ribosome remains unknown. Using cryoEM and X-ray crystallography, we report the conformation of methylated-GGQ in the peptidyl transferase center of the ribosome during canonical translational termination and co-translation quality control. It has been suggested that the GGQ motif arose independently through convergent evolution among otherwise unrelated proteins that catalyze peptide release. The requirement for this tripeptide in the highly conserved peptidyl transferase center suggests that the conformation reported here is likely shared during termination of protein synthesis in all domains of life.
History
DepositionJan 12, 2018-
Header (metadata) releaseFeb 21, 2018-
Map releaseFeb 21, 2018-
UpdateJan 8, 2020-
Current statusJan 8, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
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  • Surface view colored by height
  • Surface level: 0.04
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  • Surface view with fitted model
  • Atomic models: PDB-6c4h
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6c4h
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7340.png

Downloads & links

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Map

FileDownload / File: emd_7340.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConformation of methylated GGQ in the peptidyl transferase center during translation termination
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 384 pix.
= 460.8 Å		1.2 Å/pix.
x 384 pix.
= 460.8 Å		1.2 Å/pix.
x 384 pix.
= 460.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.2639116 - 0.39169636
Average (Standard dev.)0.0000735994 (±0.011791689)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 460.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.21.21.2
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z460.800460.800460.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.2640.3920.000

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Supplemental data

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Sample components

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Entire : nonstop ribosomal complex with ArfA/RF2

EntireName: nonstop ribosomal complex with ArfA/RF2
Components
  • Complex: nonstop ribosomal complex with ArfA/RF2
    • Complex: 50S subunit
      • Organelle or cellular component: 23S rRNA
        • RNA: 23S rRNA
      • Organelle or cellular component: 50S ribosomal protein L2
        • Protein or peptide: 50S ribosomal protein L2
      • Organelle or cellular component: 50S ribosomal protein L3
        • Protein or peptide: 50S ribosomal protein L3
      • Organelle or cellular component: 50S ribosomal protein L16
        • Protein or peptide: 50S ribosomal protein L16
      • Organelle or cellular component: 50S ribosomal protein L27
        • Protein or peptide: 50S ribosomal protein L27
    • Organelle or cellular component: P-site tRNA fMet
      • RNA: P-site tRNA fMet
    • Organelle or cellular component: Peptide chain release factor 2
      • Protein or peptide: Peptide chain release factor RF2
  • Ligand: MAGNESIUM ION

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Supramolecule #1: nonstop ribosomal complex with ArfA/RF2

SupramoleculeName: nonstop ribosomal complex with ArfA/RF2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Details: nonstop termination complex with 70S, ArfA, RF2, tRNA and nonstop mRNA

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Supramolecule #2: 50S subunit

SupramoleculeName: 50S subunit / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#5
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #3: P-site tRNA fMet

SupramoleculeName: P-site tRNA fMet / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #6
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #4: Peptide chain release factor 2

SupramoleculeName: Peptide chain release factor 2 / type: organelle_or_cellular_component / ID: 4 / Parent: 1 / Macromolecule list: #7
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #5: 23S rRNA

SupramoleculeName: 23S rRNA / type: organelle_or_cellular_component / ID: 5 / Parent: 2 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #6: 50S ribosomal protein L2

SupramoleculeName: 50S ribosomal protein L2 / type: organelle_or_cellular_component / ID: 6 / Parent: 2 / Macromolecule list: #2
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #7: 50S ribosomal protein L3

SupramoleculeName: 50S ribosomal protein L3 / type: organelle_or_cellular_component / ID: 7 / Parent: 2 / Macromolecule list: #3
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #8: 50S ribosomal protein L16

SupramoleculeName: 50S ribosomal protein L16 / type: organelle_or_cellular_component / ID: 8 / Parent: 2 / Macromolecule list: #4
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #9: 50S ribosomal protein L27

SupramoleculeName: 50S ribosomal protein L27 / type: organelle_or_cellular_component / ID: 9 / Parent: 2 / Macromolecule list: #5
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: 23S rRNA

MacromoleculeName: 23S rRNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 941.818625 KDa
SequenceString: GGUUAAGCGA CUAAGCGUAC ACGGUGGAUG CCCUGGCAGU CAGAGGCGAU GAAGGACGUG CUAAUCUGCG AUAAGCGUCG GUAAGGUGA UAUGAACCGU UAUAACCGGC GAUUUCCGAA UGGGGAAACC CAGUGUGUUU CGACACACUA UCAUUAACUG A AUCCAUAG ...String:
GGUUAAGCGA CUAAGCGUAC ACGGUGGAUG CCCUGGCAGU CAGAGGCGAU GAAGGACGUG CUAAUCUGCG AUAAGCGUCG GUAAGGUGA UAUGAACCGU UAUAACCGGC GAUUUCCGAA UGGGGAAACC CAGUGUGUUU CGACACACUA UCAUUAACUG A AUCCAUAG GUUAAUGAGG CGAACCGGGG GAACUGAAAC AUCUAAGUAC CCCGAGGAAA AGAAAUCAAC CGAGAUUCCC CC AGUAGCG GCGAGCGAAC GGGGAGCAGC CCAGAGCCUG AAUCAGUGUG UGUGUUAGUG GAAGCGUCUG GAAAGGCGCG CGA UACAGG GUGACAGCCC CGUACACAAA AAUGCACAUG CUGUGAGCUC GAUGAGUAGG GCGGGACACG UGGUAUCCUG UCUG AAUAU GGGGGGACCA UCCUCCAAGG CUAAAUACUC CUGACUGACC GAUAGUGAAC CAGUACCGUG AGGGAAAGGC GAAAA GAAC CCCGGCGAGG GGAGUGAAAA AGAACCUGAA ACCGUGUACG UACAAGCAGU GGGAGCACGC UUAGGCGUGU GACUGC GUA CCUUUUGUAU AAUGGGUCAG CGACUUAUAU UCUGUAGCAA GGUUAACCGA AUAGGGGAGC CGAAGGGAAA CCGAGUC UU AACUGGGCGU UAAGUUGCAG GGUAUAGACC CGAAACCCGG UGAUCUAGCC AUGGGCAGGU UGAAGGUUGG GUAACACU A ACUGGAGGAC CGAACCGACU AAU(1MG)(PSU)(5MU)GAAA AAUUAGCGGA UGACUUGUGG CUGGGGGUGA AAGGCCA AU CAAACCGGGA GAUAGCUGGU UCUCCCCGAA AGCUAUUUAG GUAGCGCCUC GUGAAUUCAU CUCCGGGGGU AGAGCACU G UUUCGGCAAG GGGGUCAACC CGACUUACCA ACCCGAUGCA AACUGCGAAU ACCGGAGAAU GUUAUCACGG GAGACACAC GGCGGG(PSU)GCU AACGUCCGUC GUGAAGAGGG AAACAACCCA GACCGCCAGC UAAGGUCCCA AAGUCAUGGU UAAGUG GGA AACGAUGUGG GAAGGCCCAG ACAGCCAGGA UGUUGGCUUA GAAGCAGCCA UCAUUUAAAG AAAGCGUAAU AGCUCAC UG GUCGAGUCGG CCUGCGCGGA AGAUGUAACG GGGCUAAACC AUGCACCGAA GCUGCGGCAG CGACGCUUAU GCGUUGUU G GGUAGGGGAG CGUUCUGUAA GCCUGCGAAG GUGUGCUGUG AGGCAUGCUG GAGGUAUCAG AAGUGCGAAU GCUGACAUA AGUAACGAUA AAGCGGGUGA AAAGCCCGCU CGCCGGAAGA CCAAGGGUUC CUGUCCAACG UUAAUCGGGG CAGGGUGAGU CGACCCCUA AGGCGAGGCC GAAAGGCGUA GUCGAUGGGA AACAGGUUAA UAUUCCUGUA CUUGGUGUUA CUGCGAAGGG G GGACGGAG AAGGCUAUGU UGGCCGGGCG ACGGUUGUCC CGGUUUAAGC GUGUAGGCUG GUUUUCCAGG CAAAUCCGGA AA AUCAAGG CUGAGGCGUG AUGACGAGGC ACUACGGUGC UGAAGCAACA AAUGCCCUGC UUCCAGGAAA AGCCUCUAAG CAU CAGGUA ACAUCAAAUC GUACCCCAAA CCGACAC(6MZ)GG UGGUCAGGUA GAGAAUACCA AGGCGCUUGA GAGAACUCGG GUGAAGGAA CUAGGCAAAA UGGUGCCGUA ACUUCGGGAG AAGGCACGCU GAUAUGUAGG UGAGGUCCCU CGCGGAUGGA G CUGAAAUC AGUCGAAGAU ACCAGCUGGC UGCAACUGUU UAUUAAAAAC ACAGCACUGU GCAAACACGA AAGUGGACGU AU ACGGUGU GACGCCU(2MG)CC CGGUGCCGGA AGGUUAAUUG AUGGGGUUAG CGCAAGCGAA GCUCUUGAUC GAAGCCCCG GUAAACGGCG GCCG(PSU)AAC(3TD)A (PSU)AACGGUCCU AAGGUAGCGA AA(5MU)UCCUUGU CGGGUAAGUU CCGA C(5MC)UGC ACGAAUGGCG UAAUGAUGGC CAGGCUGUCU CCACCCGAGA CUCAGUGAAA UUGAACUCGC UGUGAAGAUG C AGUGUACC CGCGGCAAGA CGGAAAGACC CCGU(G7M)AACCU UUACUAUAGC UUGACACUGA ACAUUGAGCC UUGAUGUG U AGGAUAGGUG GGAGGCUUUG AAGUGUGGAC GCCAGUCUGC AUGGAGCCGA CCUUGAAAUA CCACCCUUUA AUGUUUGAU GUUCUAACGU UGACCCGUAA UCCGGGUUGC GGACAGUGUC UGGUGGGUAG UUUGACUG(OMG)G GCGGUCUCCU CCUAAA GAG UAACGGAGGA GCACGAAGGU UGGCUAAUCC UGGUCGGACA UCAGGAGGUU AGUGCAAUGG CAUAAGCCAG CUUGACU GC GAGCGUGACG GCGCGAGCAG GUGCGAAAGC AGGUCAUAGU GAUCCGGUGG UUCUGAAUGG AAGGGCCAUC GCUCAACG G AUAAAAGGUA CUCCG(2MG)GGAU AACAGGC(PSU)GA UACCGCCCAA GAGUUCAUAU CGACGGCGGU GUUUGGCA (OMC) CUCG(2MA)(PSU)GUCG GCUCAUCACA UCCUGGGGCU GAAGUAGGUC CCAAGGGUAU GGC(OMU)GUUCGC CAU UUAAAG UGGUACGCGA GC(PSU)GGGUUUA GAACGUCGUG AGACAGU(PSU)CG GUCCCUAUCU GCCGUGGGCG CUGGAG AAC UGAGGGGGGC UGCUCCUAGU ACGAGAGGAC CGGAGUGGAC GCAUCACUGG UGUUCGGGUU GUCAUGCCAA UGGCACU GC CCGGUAGCUA AAUGCGGAAG AGAUAAGUGC UGAAAGCAUC UAAGCACGAA ACUUGCCCCG AGAUGAGUUC UCCCUGAC C CUUUAAGGGU CCUGAAGGAA CGUUGAAGAC GACGACGUUG AUAGGCCGGG UGUGUAAGCG CAGCGAUGCG UUGAGCUAA CCGGUACUAA UGAACCGUGA GGCUUAACCU U

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Macromolecule #6: P-site tRNA fMet

MacromoleculeName: P-site tRNA fMet / type: rna / ID: 6 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 24.786785 KDa
SequenceString:
CGCGGGGUGG AGCAGCCUGG UAGCUCGUCG GGCUCAUAAC CCGAAGAUCG UCGGUUCAAA UCCGGCCCCC GCAACCA

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Macromolecule #2: 50S ribosomal protein L2

MacromoleculeName: 50S ribosomal protein L2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 29.923619 KDa
SequenceString: MAVVKCKPTS PGRRHVVKVV NPELHKGKPF APLLEKNSKS GGRNNNGRIT TRHIGGGHKQ AYRIVDFKRN KDGIPAVVER LEYDPNRSA NIALVLYKDG ERRYILAPKG LKAGDQIQSG VDAAIKPGNT LPMRNIPVGS TVHNVEMKPG KGGQLARSAG T YVQIVARD ...String:
MAVVKCKPTS PGRRHVVKVV NPELHKGKPF APLLEKNSKS GGRNNNGRIT TRHIGGGHKQ AYRIVDFKRN KDGIPAVVER LEYDPNRSA NIALVLYKDG ERRYILAPKG LKAGDQIQSG VDAAIKPGNT LPMRNIPVGS TVHNVEMKPG KGGQLARSAG T YVQIVARD GAYVTLRLRS GEMRKVEADC RATLGEVGNA EHMLRVLGKA GAARWRGVRP TVRGTAMNPV DHPHGGGEGR NF GKHPVTP WGVQTKGKKT RSNKRTDKFI VRRRSK

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Macromolecule #3: 50S ribosomal protein L3

MacromoleculeName: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 22.277535 KDa
SequenceString: MIGLVGKKVG MTRIFTEDGV SIPVTVIEVE ANRVTQVKDL ANDGYRAIQV TTGAKKANRV TKPEAGHFAK AGVEAGRGLW EFRLAEGEE FTVGQSISVE LFADVKKVDV TGTSKGKGFA GTVKRWNFRT QDATHGNSLS HRVPGSIGQN QTPGKVFKGK K MAGQMGNE ...String:
MIGLVGKKVG MTRIFTEDGV SIPVTVIEVE ANRVTQVKDL ANDGYRAIQV TTGAKKANRV TKPEAGHFAK AGVEAGRGLW EFRLAEGEE FTVGQSISVE LFADVKKVDV TGTSKGKGFA GTVKRWNFRT QDATHGNSLS HRVPGSIGQN QTPGKVFKGK K MAGQMGNE RVTVQSLDVV RVDAERNLLL VKGAVPGATG SDLIVKPAVK A

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Macromolecule #4: 50S ribosomal protein L16

MacromoleculeName: 50S ribosomal protein L16 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 15.312269 KDa
SequenceString:
MLQPKRTKFR KMHKGRNRGL AQGTDVSFGS FGLKAVGRGR LTARQIEAAR RAMTRAVKRQ GKIWIRVFPD KPITEKPLAV RMGKGKGNV EYWVALIQPG KVLYEMDGVP EELAREAFKL AAAKLPIKTT FVTKTVM

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Macromolecule #5: 50S ribosomal protein L27

MacromoleculeName: 50S ribosomal protein L27 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 9.14654 KDa
SequenceString:
MAHKKAGGST RNGRDSEAKR LGVKRFGGES VLAGSIIVRQ RGTKFHAGAN VGCGRDHTLF AKADGKVKFE VKGPKNRKFI SIEAE

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Macromolecule #7: Peptide chain release factor RF2

MacromoleculeName: Peptide chain release factor RF2 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 43.384945 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AHHHHHHSAA LEVLFQGPGM FEINPVNNRI QDLTERSDVL RGYLDYDAKK ERLEEVNAEL EQPDVWNEPE RAQALGKERS SLEAVVDTL DQMKQGLEDV SGLLELAVEA DDEETFNEAV AELDALEEKL AQLEFRRMFS GEYDSADCYL DIQAGSGGTE A QDWASMLE ...String:
AHHHHHHSAA LEVLFQGPGM FEINPVNNRI QDLTERSDVL RGYLDYDAKK ERLEEVNAEL EQPDVWNEPE RAQALGKERS SLEAVVDTL DQMKQGLEDV SGLLELAVEA DDEETFNEAV AELDALEEKL AQLEFRRMFS GEYDSADCYL DIQAGSGGTE A QDWASMLE RMYLRWAESR GFKTEIIEES EGEVAGIKSV TIKISGDYAY GWLRTETGVH RLVRKSPFDS GGRRHTSFSS AF VYPEVDD DIDIEINPAD LRIDVYRTSG AGG(MEQ)HVNRTE SAVRITHIPT GIVTQCQNDR SQHKNKDQAM KQMKAKLYE LEMQKKNAEK QAMEDNKSDI GWGSQIRSYV LDDSRIKDLR TGVETRNTQA VLDGSLDQFI EASLKAGL

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 34 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4S4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
15.0 mMMg(CH3COO)2magnesium acetate
150.0 mMCH3CO2Kpotassium acetate
4.0 mMHOCH2CH2SHbeta-mercapthoethanol
2.0 mMC7H19N3spermidine
0.05 mMC10H26N4spermine
GridModel: C-flat-2/0.5 4C / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Grids were blotted for 3.5 seconds..

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Electron microscopy

MicroscopeJEOL 3200FS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 83822 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageCooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: EMDB MAP
EMDB ID:

8505

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 143372
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2)
Final 3D classificationSoftware - Name: RELION (ver. 2)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT / Target criteria: Average FSC
Output model

PDB-6c4h:
Conformation of methylated GGQ in the peptidyl transferase center during translation termination (PTC region)

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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

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