[English] 日本語
Yorodumi
- EMDB-10320: IC2A cryo-EM map of a full archaeal ribosomal translation initiat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10320
TitleIC2A cryo-EM map of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi
Map dataPab IC2A map
Sample
  • Complex: Archaeal translation initiation complex devoid of aIF1 - IC2A state
    • Complex: Ribosome
      • RNA: x 1 types
      • Protein or peptide: x 28 types
    • Complex: tRNATransfer RNA
      • RNA: x 1 types
    • Complex: Translation initiation factor 1A
      • Protein or peptide: x 1 types
    • Complex: mRNAMessenger RNA
      • RNA: x 1 types
    • Complex: Translation initiation factor 2 subunits alpha, beta and gammaInitiation factor
      • Protein or peptide: x 3 types
  • Ligand: x 5 types
Function / homology
Function and homology information


protein-synthesizing GTPase / formation of cytoplasmic translation initiation complex / formation of translation preinitiation complex / ribonuclease P activity / tRNA 5'-leader removal / translation elongation factor activity / translational initiation / translation initiation factor activity / cytosolic ribosome / ribosome binding ...protein-synthesizing GTPase / formation of cytoplasmic translation initiation complex / formation of translation preinitiation complex / ribonuclease P activity / tRNA 5'-leader removal / translation elongation factor activity / translational initiation / translation initiation factor activity / cytosolic ribosome / ribosome binding / ribosome biogenesis / small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / GTPase activity / GTP binding / RNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
Translation initiation factor 2, alpha subunit, archaeal / Translation initiation factor 2, beta subunit / Small zinc finger protein HVO_2753-like, zinc-binding pocket / Small zinc finger protein HVO_2753-like / Small zinc finger protein HVO_2753-like, Zn-binding pocket / Ribosomal protein S27ae / Translation initiation factor 2, gamma subunit / : / Ribosomal protein S9, archaeal / Ribosomal protein S13, archaeal ...Translation initiation factor 2, alpha subunit, archaeal / Translation initiation factor 2, beta subunit / Small zinc finger protein HVO_2753-like, zinc-binding pocket / Small zinc finger protein HVO_2753-like / Small zinc finger protein HVO_2753-like, Zn-binding pocket / Ribosomal protein S27ae / Translation initiation factor 2, gamma subunit / : / Ribosomal protein S9, archaeal / Ribosomal protein S13, archaeal / Ribosomal protein S17, archaeal / Ribosomal protein S6e, archaeal / Ribosomal protein S4, archaeal / Ribosomal protein S12, archaea / Ribosomal protein S3, archaeal / 30S ribosomal protein S3Ae / Ribosomal protein S7, archaeal / Ribosomal protein S19e, archaeal / Ribosomal protein S11, archaeal / Ribosomal protein S2, archaeal / Ribosomal protein S14, type Z, archaeal / Ribosomal protein S8e, archaeal / Translation initiation factor IF2/IF5 / Translation initiation factor IF2/IF5 domain / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / Domain found in IF2B/IF5 / domain present in translation initiation factor eIF2B and eIF5 / Translation initiation factor 1A (eIF-1A), conserved site / Eukaryotic initiation factor 1A signature. / eukaryotic translation initiation factor 1A / Translation initiation factor 1A (eIF-1A) / IF2a, S1-like domain / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / Eukaryotic translation initiation factor 2 alpha subunit / Initiation factor eIF2 gamma, domain 2 / Initiation factor eIF2 gamma, GTP-binding domain / Initiation factor eIF2 gamma, C-terminal / Initiation factor eIF2 gamma, C terminal / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / Ribosomal protein L7Ae, archaea / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Ribosomal protein S19e, conserved site / S1 domain profile. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S17e, conserved site / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S19A/S15e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S8e, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal S17 / Ribosomal protein S19e signature. / Ribosomal protein S19e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S27 / Ribosomal protein S28e conserved site / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S28e / Ribosomal protein S4e, N-terminal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal protein S8e / Ribosomal protein S4, KOW domain / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S6e / Ribosomal protein S4/S9, eukaryotic/archaeal / RS4NT (NUC023) domain / Ribosomal protein S27 / Ribosomal S3Ae family / Ribosomal protein S17e signature. / Ribosomal protein S28e / Ribosomal family S4e / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S6e / Ribosomal protein S3Ae signature. / Ribosomal protein S27e signature.
Similarity search - Domain/homology
Zn-ribbon RNA-binding protein involved in translation / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS31 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein eS32 / Translation initiation factor 2 subunit beta ...Zn-ribbon RNA-binding protein involved in translation / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS31 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein eS32 / Translation initiation factor 2 subunit beta / Translation initiation factor 2 subunit alpha / Translation initiation factor 2 subunit gamma / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS8 / 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 uS2 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS15
Similarity search - Component
Biological speciesPyrococcus abyssi GE5 (archaea) / Escherichia coli (E. coli) / Saccharolobus solfataricus P2 (archaea) / Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 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

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.004
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.004
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6sw9
  • Surface level: 0.004
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10320.png

Downloads & links

-
Map

FileDownload / File: emd_10320.map.gz / Format: CCP4 / Size: 160.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPab IC2A map
Voxel sizeX=Y=Z: 1.09 Å
Density
Contour LevelBy AUTHOR: 0.004 / Movie #1: 0.004
Minimum - Maximum-0.007168596 - 0.044311192
Average (Standard dev.)0.00030256435 (±0.002654964)
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-0.0070.0440.000

-
Supplemental data

-
Additional map: Pab IC2A postprocessed map

Fileemd_10320_additional.map
AnnotationPab IC2A postprocessed map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Pab IC2A half2 map

Fileemd_10320_half_map_1.map
AnnotationPab IC2A half2 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Pab IC2A half1 map

Fileemd_10320_half_map_2.map
AnnotationPab IC2A half1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Archaeal translation initiation complex devoid of aIF1 - IC2A state

EntireName: Archaeal translation initiation complex devoid of aIF1 - IC2A state
Components
  • Complex: Archaeal translation initiation complex devoid of aIF1 - IC2A state
    • Complex: Ribosome
      • RNA: 16S ribosomal RNA
      • Protein or peptide: 30S ribosomal protein S3AeRibosome
      • Protein or peptide: 30S ribosomal protein S2
      • Protein or peptide: Zn-ribbon RNA-binding protein involved in translation
      • Protein or peptide: 30S ribosomal protein S4
      • Protein or peptide: 30S ribosomal protein S4eRibosome
      • Protein or peptide: 30S ribosomal protein S5
      • Protein or peptide: 30S ribosomal protein S6eRibosome
      • Protein or peptide: 30S ribosomal protein S7
      • Protein or peptide: 30S ribosomal protein S8
      • Protein or peptide: 30S ribosomal protein S8eRibosome
      • Protein or peptide: 30S ribosomal protein S9
      • Protein or peptide: 30S ribosomal protein S10
      • Protein or peptide: 30S ribosomal protein S11
      • Protein or peptide: 30S ribosomal protein S12
      • Protein or peptide: 30S ribosomal protein S13
      • Protein or peptide: 30S ribosomal protein S14 type ZRibosome
      • Protein or peptide: 30S ribosomal protein S15
      • Protein or peptide: 30S ribosomal protein S17
      • Protein or peptide: 30S ribosomal protein S17eRibosome
      • Protein or peptide: 30S ribosomal protein S19
      • Protein or peptide: 30S ribosomal protein S19eRibosome
      • Protein or peptide: 30S ribosomal protein S24eRibosome
      • Protein or peptide: 30S ribosomal protein S27eRibosome
      • Protein or peptide: 30S ribosomal protein S28eRibosome
      • Protein or peptide: 30S ribosomal protein S27aeRibosome
      • Protein or peptide: 30S ribosomal protein S3
      • Protein or peptide: 50S ribosomal protein L41eRibosome
      • Protein or peptide: 50S ribosomal protein L7AeRibosome
    • Complex: tRNATransfer RNA
      • RNA: initiator Met-tRNA fMet from E. coli (A1U72 variant)
    • Complex: Translation initiation factor 1A
      • Protein or peptide: Translation initiation factor 1A
    • Complex: mRNAMessenger RNA
      • RNA: mRNAMessenger RNA
    • Complex: Translation initiation factor 2 subunits alpha, beta and gammaInitiation factor
      • Protein or peptide: Translation initiation factor 2 subunit gammaInitiation factor
      • Protein or peptide: Translation initiation factor 2 subunit betaInitiation factor
      • Protein or peptide: Translation initiation factor 2 subunit alphaInitiation factor
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: METHIONINE
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
  • Ligand: water

+
Supramolecule #1: Archaeal translation initiation complex devoid of aIF1 - IC2A state

SupramoleculeName: Archaeal translation initiation complex devoid of aIF1 - IC2A state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#35
Molecular weightTheoretical: 1.05 MDa

+
Supramolecule #2: Ribosome

SupramoleculeName: Ribosome / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#29
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea)

+
Supramolecule #3: tRNA

SupramoleculeName: tRNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #31
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)

+
Supramolecule #4: Translation initiation factor 1A

SupramoleculeName: Translation initiation factor 1A / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #32
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea)
Recombinant expressionOrganism: Escherichia coli (E. coli)

+
Supramolecule #5: mRNA

SupramoleculeName: mRNA / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #30
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea)
Recombinant expressionOrganism: synthetic construct (others)

+
Supramolecule #6: Translation initiation factor 2 subunits alpha, beta and gamma

SupramoleculeName: Translation initiation factor 2 subunits alpha, beta and gamma
type: complex / ID: 6 / Parent: 1 / Macromolecule list: #33-#35
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Recombinant expressionOrganism: Escherichia coli (E. coli)

+
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: 487.700312 KDa
SequenceString: AUUC(4AC)GGUUG AUCCUGCCGG AGGCCACUGC UAUGGGGGUC (4AC)GACUAAGCC AUGCGAGUCA AGGGGGCGUC CC UUCUGGG ACGCCACCGG CGGACGGCUC AGUAACACGU CGGUAACCUA CCCUCGGGAG GGGGAUAACC CCGGGAAACU GGG GCUAAU ...String:
AUUC(4AC)GGUUG AUCCUGCCGG AGGCCACUGC UAUGGGGGUC (4AC)GACUAAGCC AUGCGAGUCA AGGGGGCGUC CC UUCUGGG ACGCCACCGG CGGACGGCUC AGUAACACGU CGGUAACCUA CCCUCGGGAG GGGGAUAACC CCGGGAAACU GGG GCUAAU CCCCCAUAGG CCUGGGGUAC UGGAAGGUCC CCAGGCCGAA AGGGAGCCGU AAGGCUCCGC CCGAGGAUGG GCCG GCGGC (LHH)GAUUAGGUA GUUGGUGGGG UAACGGCCCA CCAAGC(4AC)GAA GAUCGGUACG GGC(4AC)GUGAGA GCG GGAGCC (4AC)GGAGAUGGA CACUGAGACA CGGGUCCAGG CCCUACGGGG CGCAGCAGGC GCGA(A2M)ACCUC (4AC)G CAAUGCG GGAAAC(4AC)GCG ACGGGGGGAC CCCCAGUGCC GUGCCUCUGG CACGGCUUUU CCGGAGUGUA AAAAGCUCC GGGAAUAAGG GCUGGGCAAG GC(4AC)GGUGGCA GCCGCCGCGG UAAUACCGGC GGCC(4AC)GAGUG GUGGCCACUA UU AUUGGGC CUAAAGCGGC (4AC)GUAGCCGGG CCCGUAAGUC CCUGGCGAAA UCCCACGGCU CAAC(4AC)GUGGG GCUCG CUGG GGAUACUGCG GGCCUUGGGA C(4AC)GGGAGAGG C(4AC)GGGGGUAC CCC(4AC)GGGGUA GGGGUGAAAU CCUA UAAUC CCGGGGGGAC CGCCAGUGGC GAAGGCGCC(4AC) GGCUGGAACG GGUC(4AC)GACGG UGAGGGC(4AC)GA AGG CCAGGG GAGCGAAC(4AC)G GAUUAGAUAC CCGGGUAGUC CUGGCUGUAA AGGAUGCGGG CUAGGUGUCG GGCGAGCUUC GAGCUCGCC CGGUGC(4AC)GUA GGGAAGC(4AC)GU UAAGCC(4AC)GC(4AC) GCCUGGGGAG UACGGC(4AC)GCA A GGCUGAAA CUUAAAGGAA UUGGCGGGGG AGCACUACAA GGGGUGGAGC GUGCGGUUUA AUUGGAU(B8H)(5MC)A ACGC CGGGA ACCUCAC(4AC)GG GGGCGACGGC AGGAUGAAGG CCAGGCUGAA GGUCUUGCCG GACGCGCCGA GAGGAGGUGC A UGGCCGC(4AC) GUCAGCUCGU AC(4AC)GUGAGGC GUCCACUUAA GUGUGGUAAC GAGCGAGACC CGCGCCCCCA GUUG CCAGU CCCUCCCGCU CGGGAGGGAG GCACUCUGGG GGGACUGCCG GCGAUAAGC(4AC) GGAGGAAGGG GCGGGCGACG G UAGGUCAG UAUGCCC(4AC)GA AACCCC(4AC)GGG CUACA(5MC)GCGC GCUACAAUGG GCGGGACAAU GGGUGC (4AC)GA CCC(4AC)GAAAGG GGGAGGUAAU CCCCUAAACC CGCCCUCAGU UCGGAUCGCG GGCUGCAACU CGCCCGCGU GAAGCUGGAA UCCCUAGUAC CCGCGCGUCA UCAUCGCGCG GCGAAUACGU CCCUGCUCCU UGCACACACC G(OMC)C (5HM)GUCAC UCCACCCGAG CGGGGCCUAG GUGAGGCCCG AUCUCCUUCG GGAGGUCGGG UCGAGCCUAG GCUCCGUGAG GGGGGAGAA GUCG(UR3)A(6MZ)CAA GGUAGC(4AC)GUA GGGG(MA6)(MA6)CCUA CGGCUCGAUC ACCUCCU

+
Macromolecule #30: mRNA

MacromoleculeName: mRNA / type: rna / ID: 30 / Number of copies: 1
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea)
Molecular weightTheoretical: 6.448871 KDa
SequenceString:
UGGAGGUGAU UUAAAUGCCA

+
Macromolecule #31: initiator Met-tRNA fMet from E. coli (A1U72 variant)

MacromoleculeName: initiator Met-tRNA fMet from E. coli (A1U72 variant) / type: rna / ID: 31 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 24.504695 KDa
SequenceString:
GCGGGG(4SU)GGA GCAGCCUGG(H2U) AGCUCGUCGG G(OMC)UCAUAACC CGAAGAUCGU CGG(5MU)(PSU)CAAAU CCGGCCCCC GCUACCA

+
Macromolecule #2: 30S ribosomal protein S3Ae

MacromoleculeName: 30S ribosomal protein S3Ae / 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: 22.888068 KDa
SequenceString: MAAKRRVSAA KDKWKLKQWY VIYAPDFFGG VEVGLTPADD PEKVLNRVVE VTLKDITGDF LKGHVKLYFQ VYDVKGQNAY TKFKGMKLA RSYIRSLVRR RTTRIDGIFN ITTKDGYKLR VMAMVIAARR IQTSQERAIR KIMQEIIYKK AEELNFKDFV L EAVNGKIA ...String:
MAAKRRVSAA KDKWKLKQWY VIYAPDFFGG VEVGLTPADD PEKVLNRVVE VTLKDITGDF LKGHVKLYFQ VYDVKGQNAY TKFKGMKLA RSYIRSLVRR RTTRIDGIFN ITTKDGYKLR VMAMVIAARR IQTSQERAIR KIMQEIIYKK AEELNFKDFV L EAVNGKIA AEIAKEAKKI YPLKKAEIRK IKVLGEPEVA A

+
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: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 23.026865 KDa
SequenceString: MADEYLVPLD QYLAAGVHIG TQQKTKDMKK FIYRVRQDGL YVLDVRKTDE RLKVAGKFLA RFDPQSILAV SVRLYGQKPV KKFGEVTGA RAIPGRFLPG TMTNPAVKNF FEPDVIIITD PRADHQAMKE AIEIGIPIVA LVDTENLLSY VDLAIPTNNK G RKALALIY ...String:
MADEYLVPLD QYLAAGVHIG TQQKTKDMKK FIYRVRQDGL YVLDVRKTDE RLKVAGKFLA RFDPQSILAV SVRLYGQKPV KKFGEVTGA RAIPGRFLPG TMTNPAVKNF FEPDVIIITD PRADHQAMKE AIEIGIPIVA LVDTENLLSY VDLAIPTNNK G RKALALIY WILAREILYN RGEISSREEF KIPVEEFEMK IVRR

+
Macromolecule #4: Zn-ribbon RNA-binding protein involved in translation

MacromoleculeName: Zn-ribbon RNA-binding protein involved in translation / 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: 7.163395 KDa
SequenceString:
MAENVELKFE IPVCTSCGRE ITPREHATHF VCPNCGEAII WRCETCRLLA KPYKCPKCGW EGP

+
Macromolecule #5: 30S ribosomal protein S4

MacromoleculeName: 30S ribosomal protein S4 / 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: 21.38191 KDa
SequenceString:
MGDPKRQRKK YETPPHPWIK ERLDRERVLM DKYELKNKKE LWKHETQLKN FRRRARRLLA ARGKQAEIER EQLLARLKRL GLLPEDAVL DDVLSLTIED ILERRLQTIV YKKGLARTMR QARQLIVHGH IEVNGQIIRS PSYLVLKEEE DTITYARTSP F ANPQHPER MMIEKAKQGG EA

+
Macromolecule #6: 30S ribosomal protein S4e

MacromoleculeName: 30S ribosomal protein S4e / 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: 28.246119 KDa
SequenceString: MARKGPKRHL KRLAAPTSWY IERKAYKWAV RPRPGPHNMR TSIPLLYIVR DYLGYAKTAR EARKILNEGK FLVDGRVRKD YKFPVGIMD VVSIPETGEH YRVLPNRIGK LILHPISEEE ANIKPLRIRN KRMVKGAKIQ LNFHDGTNHL IPLSEKDNYF T SYTVLMKV ...String:
MARKGPKRHL KRLAAPTSWY IERKAYKWAV RPRPGPHNMR TSIPLLYIVR DYLGYAKTAR EARKILNEGK FLVDGRVRKD YKFPVGIMD VVSIPETGEH YRVLPNRIGK LILHPISEEE ANIKPLRIRN KRMVKGAKIQ LNFHDGTNHL IPLSEKDNYF T SYTVLMKV PEREILEVLP FEKGAYVFVT QGKNVARKGR IVEIKKFPMG WPDVVTIEDE EGELFDTLKE YAFVVGRDKP RI SLP

+
Macromolecule #7: 30S ribosomal protein S5

MacromoleculeName: 30S ribosomal protein S5 / 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: 26.523904 KDa
SequenceString: MSQEWKEYAK RVLDEWQPKT KLGMLVKEGQ ITDIHEIFRK GYQIKEPEII DVLLPEVNAR ENQEILDIAL TVRMTDSGRR VRFRVLAAV GNRDGYVGLG IGHGREVGIA IRKAINYAKL NIIEIKRGCG SWECRCRRPH SVPFTVEGKE GSVRVKLIPG P RGLGLVIG ...String:
MSQEWKEYAK RVLDEWQPKT KLGMLVKEGQ ITDIHEIFRK GYQIKEPEII DVLLPEVNAR ENQEILDIAL TVRMTDSGRR VRFRVLAAV GNRDGYVGLG IGHGREVGIA IRKAINYAKL NIIEIKRGCG SWECRCRRPH SVPFTVEGKE GSVRVKLIPG P RGLGLVIG DVGKKILRLA GIQDVWSQTL GETRTTVNFA KAVFNALYNT NKVVVTPEMI ERYGIVVGRA MPASFTLE

+
Macromolecule #8: 30S ribosomal protein S6e

MacromoleculeName: 30S ribosomal protein S6e / 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: 14.029461 KDa
SequenceString:
MATFKLVISD PKTGIAKQIE ITGPEAEKLI GKRIGDQIPV KELGINLNEL FGKEFPEDVK MEIRGGTDKD GFPMRPDIHG PRRVRILLS KGPGFRPKEK GERRKKTVRG NTISPEIVQV NVKLVY

+
Macromolecule #9: 30S ribosomal protein S7

MacromoleculeName: 30S ribosomal protein S7 / 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: 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

+
Macromolecule #10: 30S ribosomal protein S8

MacromoleculeName: 30S ribosomal protein S8 / 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: 14.772246 KDa
SequenceString:
MTLLDPLANA LSHITNSERV GKREVYIKPA SKLIGEVLRV MQKYGYIGEF EFIDDGRAGV YRVQLLGKIN KAGAIKPRFP VKARDYERW EKRFLPAFEF GILIVSTSQG VMSHKEAREK GIGGRLIAYV Y

+
Macromolecule #11: 30S ribosomal protein S8e

MacromoleculeName: 30S ribosomal protein S8e / 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: 14.293733 KDa
SequenceString:
MAIWQGRSLR KPSGGRIVLA RKKRKRELGR EPSNTRVAEQ DKRKIIRTYG GNKKVRLTAA AYANVFDKSG KGRKVRIIRV IENPANRQF ARRNIITKGA IIETEIGKAK VTSRPGQDGV VNAILLEE

+
Macromolecule #12: 30S ribosomal protein S9

MacromoleculeName: 30S ribosomal protein S9 / 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: 15.293867 KDa
SequenceString:
MRIIQTTGKR KTAIARAVIR EGKGRVRING KPVELVEPEI ARFTILEPLI LAGEEIWNSV DIDVKVQGGG FMGQAEAARI AIARALVEW TGDMNLKEKF IKYDRTMLVG DPRRTEPHKP NRSTKGPRAK RQKSYR

+
Macromolecule #13: 30S ribosomal protein S10

MacromoleculeName: 30S ribosomal protein S10 / 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: 11.795769 KDa
SequenceString:
MQKARIKLAS TNVRSLEEVA NQIKQIAERT GVRMSGPIPL PTKRIRIVTR KSPDGEGSAT FDRWELRIHK RLIDIEADER AMRQIMRIR VPEDVTIEIE LIS

+
Macromolecule #14: 30S ribosomal protein S11

MacromoleculeName: 30S ribosomal protein S11 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 14.77295 KDa
SequenceString:
MSEEQVNIKK KEKWGIAHIY SSYNNTIIHI TDITGAETIS RWSGGMVVKA DRDEPSPYAA MLAARRAAEE ALEKGIVGVH IRVRAPGGS KSKTPGPGAQ AAIRALARAG LKIGRVEDVT PIPHDGTRPK GGRRGRRV

+
Macromolecule #15: 30S ribosomal protein S12

MacromoleculeName: 30S ribosomal protein S12 / 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: 16.477621 KDa
SequenceString:
MPGKKAPNGE FAGRKLKLKR KKFRWSDIRY KRRVLRLKEK SDPLEGAPQA RGIVLEKIAV EAKQPNSGMR KAVRVQLIKN GKVVTAFCP GDGAIKFIDE HDEVIIEGIG GPKGGSMGDI PGIRYKVVKV NRVSLKELVK GRKEKPRR

+
Macromolecule #16: 30S ribosomal protein S13

MacromoleculeName: 30S ribosomal protein S13 / type: protein_or_peptide / ID: 16 / 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

+
Macromolecule #17: 30S ribosomal protein S14 type Z

MacromoleculeName: 30S ribosomal protein S14 type Z / type: protein_or_peptide / ID: 17 / 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

+
Macromolecule #18: 30S ribosomal protein S15

MacromoleculeName: 30S ribosomal protein S15 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 18.697143 KDa
SequenceString:
MARMHARKRG KSGSKRPPRT APPIWLEYTV EDIENLVVKL RKEGYSTAMI GTILRDQYGI PTVKLFRDPD NPNRKLTITR ILEKHGLAP EIPEDLMFLI KRAVNLRKHL EQHPKDLHSM RGLQLIESKI RRLVKYYKRK GKLPKDWRYD PEQAKLLVR

+
Macromolecule #19: 30S ribosomal protein S17

MacromoleculeName: 30S ribosomal protein S17 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 13.364604 KDa
SequenceString:
MVRDIGLRIQ PPAEKCDDPK CPWHGHLKIH GRVFEGIVVS DKPRKTVTVE RQYYHYLKKY ERYELRRSRI HAHNPPCINA KVGDRVLIA ETRPLSKTKH FVVVAVLERA EERR

+
Macromolecule #20: 30S ribosomal protein S17e

MacromoleculeName: 30S ribosomal protein S17e / type: protein_or_peptide / ID: 20 / 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

+
Macromolecule #21: 30S ribosomal protein S19

MacromoleculeName: 30S ribosomal protein S19 / type: protein_or_peptide / ID: 21 / 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

+
Macromolecule #22: 30S ribosomal protein S19e

MacromoleculeName: 30S ribosomal protein S19e / type: protein_or_peptide / ID: 22 / 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

+
Macromolecule #23: 30S ribosomal protein S24e

MacromoleculeName: 30S ribosomal protein S24e / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 11.798637 KDa
SequenceString:
MEIKITEVKE NKLIGRKEIY FEIYHPGEPT PSRKDVKGKL VAMLDLNPET TVIQYIRSYF GSYKSKGYAK YYYDKDRMLY IEPEYILIR DGIIEKKEGE

+
Macromolecule #24: 30S ribosomal protein S27e

MacromoleculeName: 30S ribosomal protein S27e / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 7.186609 KDa
SequenceString:
MALPRNVIPM PRSRFLRVKC IDCGNEQIVF SHPATRVRCN VCGATLVEPT GGKGIIRAKI LEVLE

+
Macromolecule #25: 30S ribosomal protein S28e

MacromoleculeName: 30S ribosomal protein S28e / type: protein_or_peptide / ID: 25 / 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

+
Macromolecule #26: 30S ribosomal protein S27ae

MacromoleculeName: 30S ribosomal protein S27ae / type: protein_or_peptide / ID: 26 / 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

+
Macromolecule #27: 30S ribosomal protein S3

MacromoleculeName: 30S ribosomal protein S3 / type: protein_or_peptide / ID: 27 / 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

+
Macromolecule #28: 50S ribosomal protein L41e

MacromoleculeName: 50S ribosomal protein L41e / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea)
Molecular weightTheoretical: 4.910237 KDa
SequenceString:
MKRRPRKWKK KGRMRWKWIK KRIRRLKRQR KKERGL

+
Macromolecule #29: 50S ribosomal protein L7Ae

MacromoleculeName: 50S ribosomal protein L7Ae / type: protein_or_peptide / ID: 29 / 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

+
Macromolecule #32: Translation initiation factor 1A

MacromoleculeName: Translation initiation factor 1A / type: protein_or_peptide / ID: 32 / 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

+
Macromolecule #33: Translation initiation factor 2 subunit gamma

MacromoleculeName: Translation initiation factor 2 subunit gamma / type: protein_or_peptide / ID: 33
Details: Model from high resolution structures of aIF2 gamma Saccharolobus solfataricus
Number of copies: 1 / Enantiomer: LEVO / EC number: protein-synthesizing GTPase
Source (natural)Organism: Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2
Molecular weightTheoretical: 45.718035 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AWPKVQPEVN IGVVGHVDHG KTTLVQAITG IWTSKHSEEL KRGMTIKLGY AETNIGVCES CKKPEAYVTE PSCKSCGSDD EPKFLRRIS FIDAPGHEVL MATMLSGAAL MDGAILVVAA NEPFPQPQTR EHFVALGIIG VKNLIIVQNK VDVVSKEEAL S QYRQIKQF ...String:
AWPKVQPEVN IGVVGHVDHG KTTLVQAITG IWTSKHSEEL KRGMTIKLGY AETNIGVCES CKKPEAYVTE PSCKSCGSDD EPKFLRRIS FIDAPGHEVL MATMLSGAAL MDGAILVVAA NEPFPQPQTR EHFVALGIIG VKNLIIVQNK VDVVSKEEAL S QYRQIKQF TKGTWAENVP IIPVSALHKI NIDSLIEGIE EYIKTPYRDL SQKPVMLVIR SFDVNKPGTQ FNELKGGVIG GS IIQGLFK VDQEIKVLPG LRVEKQGKVS YEPIFTKISS IRFGDEEFKE AKPGGLVAIG TYLDPSLTKA DNLLGSIITL ADA EVPVLW NIRIKYNLLE RVVGAKEMLK VDPIRAKETL MLSVGSSTTL GIVTSVKKDE IEVELRRPVA VWSNNIRTVI SRQI AGRWR MIGWGLVEI

+
Macromolecule #34: Translation initiation factor 2 subunit beta

MacromoleculeName: Translation initiation factor 2 subunit beta / type: protein_or_peptide / ID: 34
Details: Model from high resolution structures of aIF2 beta Saccharolobus solfataricus
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2
Molecular weightTheoretical: 14.835475 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SEKEYVEMLD RLYSKLPQSL PNMIILNIGN TTIIRNFAEY CDRIRREDKI CMKYLLKELA APGNVDDKGE LVIQGKFSSQ VINTLMERF LKAYVECSTC KSLDTILKKE KKSWYIVCLA CGAQTPVKPL

+
Macromolecule #35: Translation initiation factor 2 subunit alpha

MacromoleculeName: Translation initiation factor 2 subunit alpha / type: protein_or_peptide / ID: 35
Details: Model from high resolution structures of aIF2 alpha Saccharolobus solfataricus
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2
Molecular weightTheoretical: 28.946588 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIYSRSKLPS EGEILIATVK QVFDYGSYVS LDEYGGLQAF LPWSEVSNIR DVLKENRKVI VKVIRVDRRK GTVDVSLKKV TDDERRKKN LQWKKIQRLD KILELVSQKL KLSEKDAWEQ VAWKLEAKYG DPITAIEKAV KEGEKILIDA GVPEIWVKPL L EEASRKVK ...String:
MIYSRSKLPS EGEILIATVK QVFDYGSYVS LDEYGGLQAF LPWSEVSNIR DVLKENRKVI VKVIRVDRRK GTVDVSLKKV TDDERRKKN LQWKKIQRLD KILELVSQKL KLSEKDAWEQ VAWKLEAKYG DPITAIEKAV KEGEKILIDA GVPEIWVKPL L EEASRKVK MSGLITVRTN EPLGVEKIKE VISKALENIE QDYESLLNIK IYTIGAPRYR VDVVGTNPKE ASEALNQIIS NL IKIGKEE NVDISVV

+
Macromolecule #36: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 36 / Number of copies: 34 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #37: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 37 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #38: METHIONINE

MacromoleculeName: METHIONINE / type: ligand / ID: 38 / Number of copies: 1 / Formula: MET
Molecular weightTheoretical: 149.211 Da
Chemical component information

ChemComp-MET:
METHIONINE / Methionine

+
Macromolecule #39: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / type: ligand / ID: 39 / Number of copies: 1 / Formula: GNP
Molecular weightTheoretical: 522.196 Da
Chemical component information

ChemComp-GNP:
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GppNHp, GMPPNP, energy-carrying molecule analogue*YM / 5'-Guanylyl imidodiphosphate

+
Macromolecule #40: water

MacromoleculeName: water / type: ligand / ID: 40 / Number of copies: 42 / 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

BufferpH: 6.7
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.0 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: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 34000
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