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- EMDB-10324: IC2 head of cryo-EM structure of a full archaeal ribosomal transl... -

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Basic information

Entry
Database: EMDB / ID: EMD-10324
TitleIC2 head of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi
Map dataIC2 head map
Sample
  • Complex: Archaeal translation initiation complex devoid of aIF1 - IC2 head
    • Complex: 30S
      • RNA: x 1 types
      • Protein or peptide: x 12 types
    • Complex: initiator Met-tRNA fMet from E. coli (A1U72 variant)
      • RNA: x 1 types
    • Complex: translation initiation factor 1A
      • Protein or peptide: x 1 types
  • Ligand: x 3 types
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / translation initiation factor activity / ribosome biogenesis / small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex ...ribonuclease P activity / tRNA 5'-leader removal / translation initiation factor activity / ribosome biogenesis / small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein S27ae / Ribosomal protein S9, archaeal / Ribosomal protein S13, archaeal / Ribosomal protein S3, archaeal / Ribosomal protein S7, archaeal / Ribosomal protein S19e, archaeal / Ribosomal protein S14, type Z, archaeal / Translation initiation factor 1A (eIF-1A), conserved site / Eukaryotic initiation factor 1A signature. / eukaryotic translation initiation factor 1A ...Ribosomal protein S27ae / Ribosomal protein S9, archaeal / Ribosomal protein S13, archaeal / Ribosomal protein S3, archaeal / Ribosomal protein S7, archaeal / Ribosomal protein S19e, archaeal / Ribosomal protein S14, type Z, archaeal / Translation initiation factor 1A (eIF-1A), conserved site / Eukaryotic initiation factor 1A signature. / eukaryotic translation initiation factor 1A / Translation initiation factor 1A (eIF-1A) / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / Ribosomal protein L7Ae, archaea / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S19A/S15e / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal protein S28e conserved site / Ribosomal protein S28e signature. / Ribosomal protein S28e / Ribosomal protein S28e / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein S14/S29 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / K Homology domain / K homology RNA-binding domain / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / K homology domain superfamily, prokaryotic type / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / Ribosomal protein S14 / Ribosomal protein S14p/S29e / K homology domain-like, alpha/beta / Ribosomal protein S10p/S20e / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e / Ribosomal protein S9, conserved site / Ribosomal protein S9 signature. / Ribosomal protein S13-like, H2TH / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S7p/S5e / Ribosomal protein S9 / Ribosomal protein S9/S16 / Zinc-binding ribosomal protein / Ribosomal protein S5 domain 2-type fold, subgroup / Winged helix DNA-binding domain superfamily / Ribosomal protein S5 domain 2-type fold / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS31 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS7 / Translation initiation factor 1A / Small ribosomal subunit protein uS9 ...Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS31 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS7 / Translation initiation factor 1A / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS3
Similarity search - Component
Biological speciesPyrococcus abyssi (strain GE5 / Orsay) (archaea) / Escherichia coli (E. coli) / Pyrococcus abyssi GE5 (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsCoureux P-D / Mechulam Y / Schmitt E
Funding support France, 1 items
OrganizationGrant numberCountry
French National Research AgencyANR-17-CE11-0037 France
CitationJournal: Commun Biol / Year: 2020
Title: Cryo-EM study of an archaeal 30S initiation complex gives insights into evolution of translation initiation.
Authors: Pierre-Damien Coureux / Christine Lazennec-Schurdevin / Sophie Bourcier / Yves Mechulam / Emmanuelle Schmitt /
Abstract: Archaeal translation initiation occurs within a macromolecular complex containing the small ribosomal subunit (30S) bound to mRNA, initiation factors aIF1, aIF1A and the ternary complex aIF2:GDPNP: ...Archaeal translation initiation occurs within a macromolecular complex containing the small ribosomal subunit (30S) bound to mRNA, initiation factors aIF1, aIF1A and the ternary complex aIF2:GDPNP:Met-tRNA. Here, we determine the cryo-EM structure of a 30S:mRNA:aIF1A:aIF2:GTP:Met-tRNA complex from Pyrococcus abyssi at 3.2 Å resolution. It highlights archaeal features in ribosomal proteins and rRNA modifications. We find an aS21 protein, at the location of eS21 in eukaryotic ribosomes. Moreover, we identify an N-terminal extension of archaeal eL41 contacting the P site. We characterize 34 N-acetylcytidines distributed throughout 16S rRNA, likely contributing to hyperthermostability. Without aIF1, the 30S head is stabilized and initiator tRNA is tightly bound to the P site. A network of interactions involving tRNA, mRNA, rRNA modified nucleotides and C-terminal tails of uS9, uS13 and uS19 is observed. Universal features and domain-specific idiosyncrasies of translation initiation are discussed in light of ribosomal structures from representatives of each domain of life.
History
DepositionSep 20, 2019-
Header (metadata) releaseFeb 19, 2020-
Map releaseFeb 19, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.004
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.004
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6swe
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10324.png

Downloads & links

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Map

FileDownload / File: emd_10324.map.gz / Format: CCP4 / Size: 160.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIC2 head map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 348 pix.
= 379.32 Å		1.09 Å/pix.
x 348 pix.
= 379.32 Å		1.09 Å/pix.
x 348 pix.
= 379.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004 / Movie #1: 0.004
Minimum - Maximum-0.02097708 - 0.05286314
Average (Standard dev.)-0.00027031792 (±0.0014324628)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions348348348
Spacing348348348
CellA=B=C: 379.32 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z348348348
origin x/y/z0.0000.0000.000
length x/y/z379.320379.320379.320
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS348348348
D min/max/mean-0.0210.053-0.000

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Supplemental data

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Mask #1

Fileemd_10324_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: IC2 head postprocessed map

Fileemd_10324_additional.map
AnnotationIC2 head postprocessed map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: IC2 head half2 map

Fileemd_10324_half_map_1.map
AnnotationIC2 head half2 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: IC2 head half1 map

Fileemd_10324_half_map_2.map
AnnotationIC2 head half1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Archaeal translation initiation complex devoid of aIF1 - IC2 head

EntireName: Archaeal translation initiation complex devoid of aIF1 - IC2 head
Components
  • Complex: Archaeal translation initiation complex devoid of aIF1 - IC2 head
    • Complex: 30S
      • RNA: 16S ribosomal RNA
      • Protein or peptide: 30S ribosomal protein S7
      • Protein or peptide: 30S ribosomal protein S9
      • Protein or peptide: 30S ribosomal protein S10
      • Protein or peptide: 30S ribosomal protein S13
      • Protein or peptide: 30S ribosomal protein S14 type Z
      • Protein or peptide: 30S ribosomal protein S17e
      • Protein or peptide: 30S ribosomal protein S19
      • Protein or peptide: 30S ribosomal protein S19e
      • Protein or peptide: 30S ribosomal protein S28e
      • Protein or peptide: 30S ribosomal protein S27ae
      • Protein or peptide: 30S ribosomal protein S3
      • Protein or peptide: 50S ribosomal protein L7Ae
    • Complex: initiator Met-tRNA fMet from E. coli (A1U72 variant)
      • RNA: initiator Met-tRNA fMet from E. coli (A1U72 variant)
    • Complex: translation initiation factor 1A
      • Protein or peptide: Translation initiation factor 1A
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: Archaeal translation initiation complex devoid of aIF1 - IC2 head

SupramoleculeName: Archaeal translation initiation complex devoid of aIF1 - IC2 head
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#15
Molecular weightTheoretical: 1.05 MDa

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Supramolecule #2: 30S

SupramoleculeName: 30S / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#13
Source (natural)Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea)

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Supramolecule #3: initiator Met-tRNA fMet from E. coli (A1U72 variant)

SupramoleculeName: initiator Met-tRNA fMet from E. coli (A1U72 variant) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #14
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #4: translation initiation factor 1A

SupramoleculeName: translation initiation factor 1A / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #15
Source (natural)Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: 16S ribosomal RNA

MacromoleculeName: 16S ribosomal RNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea)
Molecular weightTheoretical: 152.069453 KDa
SequenceString: GUAAGGCGGG GGAGCACUAC AAGGGGUGGA GCGUGCGGUU UAAUUGGAU(B8H) (5MC)AACGCCGGG AACCUCAC (4AC) GGGGGCGACG GCAGGAUGAA GGCCAGGCUG AAGGUCUUGC CGGACGCGCC GAGAGGAGGU GCAUGGCCGC (4AC) GUCAGCUC GGCGUCCACU ...String:
GUAAGGCGGG GGAGCACUAC AAGGGGUGGA GCGUGCGGUU UAAUUGGAU(B8H) (5MC)AACGCCGGG AACCUCAC (4AC) GGGGGCGACG GCAGGAUGAA GGCCAGGCUG AAGGUCUUGC CGGACGCGCC GAGAGGAGGU GCAUGGCCGC (4AC) GUCAGCUC GGCGUCCACU UAAGUGUGGU AACGAGCGAG ACCCGCGCCC CCAGUUGCCA GUCCCUCCCG CUCGGGAGGG AG GCACUCU GGGGGGACUG CCGGCGAUAA GC(4AC)GGAGGAA GGGGCGGGCG ACGGUAGGUC AGUAUGCCC(4AC) GAAAC CCC(4AC) GGGCUACA(5MC)G CGCGCUACAA UGGGCGGGAC AAUGGGUGC(4AC) GACCC(4AC)GAAA GGGGGAGGUA AUCCCCUAA ACCCGCCCUC AGUUCGGAUC GCGGGCUGCA ACUCGCCCGC GUGAAGCUGG AAUCCCUAGU ACCCGCGCGU C AUCAUCGC GCGGCGAAUA CGUCCCUGCU CCUU

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Macromolecule #14: initiator Met-tRNA fMet from E. coli (A1U72 variant)

MacromoleculeName: initiator Met-tRNA fMet from E. coli (A1U72 variant) / type: rna / ID: 14 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 5.761509 KDa
SequenceString:
GUCGGG(OMC)UCA UAACCCGA

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Macromolecule #2: 30S ribosomal protein S7

MacromoleculeName: 30S ribosomal protein S7 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 24.662818 KDa
SequenceString: MAKPLSERFF IPHEIKVMGR WSTEDVEVRD PSLKPYINLE PRLLPHTHGR HAKKHFGKAN VHIVERLINK IMRSGGSHYK VAGHFMRRE HRSLNSKKVK AYEVVKEAFK IIEKRTGKNP IQVLVWAIEN AAPREDTTSV MFGGIRYHVA VDISPMRRLD V ALRNIALG ...String:
MAKPLSERFF IPHEIKVMGR WSTEDVEVRD PSLKPYINLE PRLLPHTHGR HAKKHFGKAN VHIVERLINK IMRSGGSHYK VAGHFMRRE HRSLNSKKVK AYEVVKEAFK IIEKRTGKNP IQVLVWAIEN AAPREDTTSV MFGGIRYHVA VDISPMRRLD V ALRNIALG ASAKCYRTKM SFAEALAEEI ILAANKDPKS YAYSKKLEIE RIAESSR

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Macromolecule #3: 30S ribosomal protein S9

MacromoleculeName: 30S ribosomal protein S9 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 15.293867 KDa
SequenceString:
MRIIQTTGKR KTAIARAVIR EGKGRVRING KPVELVEPEI ARFTILEPLI LAGEEIWNSV DIDVKVQGGG FMGQAEAARI AIARALVEW TGDMNLKEKF IKYDRTMLVG DPRRTEPHKP NRSTKGPRAK RQKSYR

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Macromolecule #4: 30S ribosomal protein S10

MacromoleculeName: 30S ribosomal protein S10 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 11.795769 KDa
SequenceString:
MQKARIKLAS TNVRSLEEVA NQIKQIAERT GVRMSGPIPL PTKRIRIVTR KSPDGEGSAT FDRWELRIHK RLIDIEADER AMRQIMRIR VPEDVTIEIE LIS

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Macromolecule #5: 30S ribosomal protein S13

MacromoleculeName: 30S ribosomal protein S13 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 16.992912 KDa
SequenceString:
MADFRHIVRV AGVDLDGNKQ LRWALTAIKG VGINFATMVC RVAGLDPFMK AGYLTDEQVK KIEEILQDPV AHGIPRWAVN RPKDYETGR DLHLITAKLD MAIREDIMRL RRIRAYRGIR HELGLPVRGQ RTRSNFRRGQ TVGVSRKKK

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Macromolecule #6: 30S ribosomal protein S14 type Z

MacromoleculeName: 30S ribosomal protein S14 type Z / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 6.644064 KDa
SequenceString:
MAKADYNKRK PRKFGKGARR CIRCGQYGPI IRIHGLMLCR HCFREVAPKL GFRKYE

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Macromolecule #7: 30S ribosomal protein S17e

MacromoleculeName: 30S ribosomal protein S17e / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 8.059528 KDa
SequenceString:
MGKIRQGFIK RVARELFNKY PNEFTRDFEH NKKKVEELTN VTSKKIRNRI AGYITKLVRM KEEGKIL

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Macromolecule #8: 30S ribosomal protein S19

MacromoleculeName: 30S ribosomal protein S19 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 15.307319 KDa
SequenceString:
MARKEFRYRG YTLEQLMNMS LEELAKLLPA RQRRSLKRGL TPEQKKLLRK IRLAKKGKYN KPIRTHCRDM IVLPEMVGLT IYVHNGKEF VPVEIKPEMI GHYLGEFAPT RKRVQHGAPG IGATRSSMFV AVK

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Macromolecule #9: 30S ribosomal protein S19e

MacromoleculeName: 30S ribosomal protein S19e / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 17.42225 KDa
SequenceString:
MATVYDVPGD LLVERVAQRL KEIPEIKPPE WAPFVKTGRH KERLPEQEDW WYYRVASILR RVYLDGPVGI ERLRTYYGGR KNRGHAPER FYKAGGSIIR KALQQLEAAG FVEKVPGKGR VITPKGRSFL DKIATELKKE LEEIIPELKK Y

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Macromolecule #10: 30S ribosomal protein S28e

MacromoleculeName: 30S ribosomal protein S28e / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 8.102305 KDa
SequenceString:
MAEDEGYPAE VIEIIGRTGT TGDVTQVKVR ILEGRDKGRV IRRNVRGPVR VGDILILRET EREAREIKSR R

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Macromolecule #11: 30S ribosomal protein S27ae

MacromoleculeName: 30S ribosomal protein S27ae / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 5.992168 KDa
SequenceString:
MGQKWKLYIV KDGKVIRKNK FCPRCGPGVF MADHGDRWAC GRCGYTEWKK K

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Macromolecule #12: 30S ribosomal protein S3

MacromoleculeName: 30S ribosomal protein S3 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 23.472309 KDa
SequenceString: MAIERYFIRE AVKEMLIDEF LEKELRRAGY GGLDIKKTPL GTKVIIFAAN PGYVIGRGGR RIRELTRILE RQFGLENPQI DVQEIKNPY LNAKVQAVRI AQALERGIHF RRAAYAAMRA IMSNGARGVE IRISGKLTGE RAKSVRFYQG YLAKVGNPAE T LVSKGYAQ ...String:
MAIERYFIRE AVKEMLIDEF LEKELRRAGY GGLDIKKTPL GTKVIIFAAN PGYVIGRGGR RIRELTRILE RQFGLENPQI DVQEIKNPY LNAKVQAVRI AQALERGIHF RRAAYAAMRA IMSNGARGVE IRISGKLTGE RAKSVRFYQG YLAKVGNPAE T LVSKGYAQ ALLKLGVIGV KVAIMPPDAR LPDEIEIIEK PVEEEVSSNE AE

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Macromolecule #13: 50S ribosomal protein L7Ae

MacromoleculeName: 50S ribosomal protein L7Ae / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 13.442678 KDa
SequenceString:
MAKPSYVKFE VPKELAEKAL QAVEIARDTG KIRKGTNETT KAVERGQAKL VIIAEDVDPE EIVAHLPPLC EEKEIPYIYV PSKKELGAA AGIEVAAASV AIIEPGKARD LVEEIAMKVR ELMK

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Macromolecule #15: Translation initiation factor 1A

MacromoleculeName: Translation initiation factor 1A / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 13.078265 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPKKERKVEG DEVIRVPLPE GNQLFGVVEQ ALGAGWMDVR CEDGKIRRCR IPGKLRRRVW IRVGDLVIVQ PWPVQSDKRG DIVYRYTQT QVDWLLRKGK ITQEFLTGGS LLVE

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Macromolecule #16: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 16 / Number of copies: 8 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #17: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 17 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #18: water

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

ChemComp-HOH:
WATER

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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: 6.7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 142000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
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  • 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

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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

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