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- EMDB-25543: Structure of the wt IRES eIF5B-containing 48S initiation complex,... -

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Basic information

Entry
Database: EMDB / ID: EMD-25543
TitleStructure of the wt IRES eIF5B-containing 48S initiation complex, closed conformation. Structure 15(wt)
Map dataPost processed map
Sample
  • Complex: 40S ribosomal small subunit with HCV IRES
    • RNA: x 3 types
    • Protein or peptide: x 35 types
  • Protein or peptide: x 1 types
  • Ligand: x 4 types
Function / homology
Function and homology information


multi-eIF complex / translation factor activity, RNA binding / eukaryotic 43S preinitiation complex / ribosomal subunit / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / laminin receptor activity / Ribosomal scanning and start codon recognition / Translation initiation complex formation / mammalian oogenesis stage ...multi-eIF complex / translation factor activity, RNA binding / eukaryotic 43S preinitiation complex / ribosomal subunit / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / laminin receptor activity / Ribosomal scanning and start codon recognition / Translation initiation complex formation / mammalian oogenesis stage / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / ubiquitin ligase inhibitor activity / phagocytic cup / GTP hydrolysis and joining of the 60S ribosomal subunit / 90S preribosome / L13a-mediated translational silencing of Ceruloplasmin expression / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / T cell proliferation involved in immune response / erythrocyte development / ribosomal small subunit export from nucleus / translation regulator activity / laminin binding / rough endoplasmic reticulum / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / gastrulation / MDM2/MDM4 family protein binding / cytosolic ribosome / translation initiation factor activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / cellular response to leukemia inhibitory factor / small-subunit processome / translational initiation / protein kinase C binding / positive regulation of apoptotic signaling pathway / positive regulation of protein-containing complex assembly / placenta development / spindle / cytoplasmic ribonucleoprotein granule / modification-dependent protein catabolic process / G1/S transition of mitotic cell cycle / protein tag activity / rRNA processing / ribosomal small subunit biogenesis / rhythmic process / positive regulation of canonical Wnt signaling pathway / small ribosomal subunit rRNA binding / ribosome binding / glucose homeostasis / regulation of translation / ribosomal small subunit assembly / virus receptor activity / small ribosomal subunit / T cell differentiation in thymus / cytosolic small ribosomal subunit / cell body / cytoplasmic translation / perikaryon / tRNA binding / mitochondrial inner membrane / postsynaptic density / cell differentiation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / positive regulation of apoptotic process / positive regulation of protein phosphorylation / ribonucleoprotein complex / translation / cell division / DNA repair / GTPase activity / mRNA binding / centrosome / dendrite / ubiquitin protein ligase binding / positive regulation of cell population proliferation / synapse / negative regulation of apoptotic process / GTP binding / nucleolus / apoptotic process / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / mitochondrion / DNA binding / RNA binding / zinc ion binding / membrane / nucleus
Similarity search - Function
Elongation factor Tu-type domain / Elongation factor Tu domain 4 / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor 1A (eIF-1A), conserved site / Translation initiation factor IF-2, domain 3 superfamily / Eukaryotic initiation factor 1A signature. / eukaryotic translation initiation factor 1A / Translation initiation factor 1A (eIF-1A) ...Elongation factor Tu-type domain / Elongation factor Tu domain 4 / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor 1A (eIF-1A), conserved site / Translation initiation factor IF-2, domain 3 superfamily / 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. / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Small (40S) ribosomal subunit Asc1/RACK1 / S27a-like superfamily / 40S Ribosomal protein S10 / Ribosomal protein S10, eukaryotic/archaeal / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S30 / : / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S7e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S19e / Ribosomal protein S3Ae signature. / Ribosomal_S19e / Ribosomal protein S27e signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S19A/S15e / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / : / Ribosomal protein S6, eukaryotic / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S7e / Ribosomal protein S7e / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S27 / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S27 / Ribosomal protein S8e / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S3Ae / Ribosomal protein S28e conserved site / Ribosomal S3Ae family / Ribosomal protein S28e signature. / Ribosomal S3Ae family / Ribosomal protein S28e / Ribosomal protein S28e
Similarity search - Domain/homology
Small ribosomal subunit protein eS32 / 40S ribosomal protein S24 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein RACK1 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS1 ...Small ribosomal subunit protein eS32 / 40S ribosomal protein S24 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein RACK1 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein uS12 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein eS10 / Eukaryotic translation initiation factor 5B / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS14 / Eukaryotic translation initiation factor 1A, X-chromosomal
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit) / rabbit (rabbit) / Hepatitis C virus (isolate 1) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsBrown ZP / Abaeva IS / De S / Hellen CUT / Pestova TV / Frank J
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM55440 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM122602 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI123406 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM139453 United States
CitationJournal: EMBO J / Year: 2022
Title: Molecular architecture of 40S translation initiation complexes on the hepatitis C virus IRES.
Authors: Zuben P Brown / Irina S Abaeva / Swastik De / Christopher U T Hellen / Tatyana V Pestova / Joachim Frank /
Abstract: Hepatitis C virus mRNA contains an internal ribosome entry site (IRES) that mediates end-independent translation initiation, requiring a subset of eukaryotic initiation factors (eIFs). Biochemical ...Hepatitis C virus mRNA contains an internal ribosome entry site (IRES) that mediates end-independent translation initiation, requiring a subset of eukaryotic initiation factors (eIFs). Biochemical studies revealed that direct binding of the IRES to the 40S ribosomal subunit places the initiation codon into the P site, where it base pairs with eIF2-bound Met-tRNAiMet forming a 48S initiation complex. Subsequently, eIF5 and eIF5B mediate subunit joining, yielding an elongation-competent 80S ribosome. Initiation can also proceed without eIF2, in which case Met-tRNAiMet is recruited directly by eIF5B. However, the structures of initiation complexes assembled on the HCV IRES, the transitions between different states, and the accompanying conformational changes have remained unknown. To fill these gaps, we now obtained cryo-EM structures of IRES initiation complexes, at resolutions up to 3.5 Å, that cover all major stages from the initial ribosomal association, through eIF2-containing 48S initiation complexes, to eIF5B-containing complexes immediately prior to subunit joining. These structures provide insights into the dynamic network of 40S/IRES contacts, highlight the role of IRES domain II, and reveal conformational changes that occur during the transition from eIF2- to eIF5B-containing 48S complexes and prepare them for subunit joining.
History
DepositionNov 25, 2021-
Header (metadata) releaseJul 13, 2022-
Map releaseJul 13, 2022-
UpdateFeb 1, 2023-
Current statusFeb 1, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25543.png

Downloads & links

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Map

FileDownload / File: emd_25543.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost processed map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 400 pix.
= 380. Å		0.95 Å/pix.
x 400 pix.
= 380. Å		0.95 Å/pix.
x 400 pix.
= 380. Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
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Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.029026719 - 0.06259853
Average (Standard dev.)0.0006056475 (±0.0029703924)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 380.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_25543_msk_1.map
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Additional map: Local resolution map filtered at local resolution

Fileemd_25543_additional_1.map
AnnotationLocal resolution map filtered at local resolution
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Additional map: Local resolution values

Fileemd_25543_additional_2.map
AnnotationLocal resolution values
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Additional map: Unsharpened map

Fileemd_25543_additional_3.map
AnnotationUnsharpened map
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Half map: Half map

Fileemd_25543_half_map_1.map
AnnotationHalf map
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Half map: Half map

Fileemd_25543_half_map_2.map
AnnotationHalf map
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Sample components

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Entire : 40S ribosomal small subunit with HCV IRES

EntireName: 40S ribosomal small subunit with HCV IRES
Components
  • Complex: 40S ribosomal small subunit with HCV IRES
    • RNA: 18S rRNA
    • Protein or peptide: Eukaryotic translation initiation factor 1A, X-chromosomal
    • Protein or peptide: 40S ribosomal protein SA
    • Protein or peptide: eS1
    • Protein or peptide: 40S ribosomal protein S2
    • Protein or peptide: uS3
    • Protein or peptide: 40S ribosomal protein S4
    • Protein or peptide: uS7
    • Protein or peptide: eS6
    • Protein or peptide: 40S ribosomal protein S7
    • Protein or peptide: eS8
    • Protein or peptide: uS4
    • Protein or peptide: eS10
    • Protein or peptide: uS17
    • Protein or peptide: eS12
    • Protein or peptide: uS15
    • Protein or peptide: uS11
    • Protein or peptide: uS19
    • Protein or peptide: uS9
    • Protein or peptide: eS17
    • Protein or peptide: uS13
    • Protein or peptide: eS19
    • Protein or peptide: uS10
    • Protein or peptide: 40S ribosomal protein S21
    • Protein or peptide: uS8
    • Protein or peptide: uS12
    • Protein or peptide: 40S ribosomal protein S24
    • Protein or peptide: 40S ribosomal protein S25
    • Protein or peptide: eS27
    • Protein or peptide: eS28
    • Protein or peptide: eS29
    • Protein or peptide: eS30
    • Protein or peptide: 40S ribosomal protein S27a
    • Protein or peptide: RACK1
    • RNA: Met-tRNA-i-Met
    • Protein or peptide: 60s ribosomal protein l41
    • Protein or peptide: Eukaryotic translation initiation factor 5B
    • RNA: HCV IRES
  • Protein or peptide: 40S ribosomal protein S26
  • Ligand: ZINC ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: SODIUM ION

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Supramolecule #1: 40S ribosomal small subunit with HCV IRES

SupramoleculeName: 40S ribosomal small subunit with HCV IRES / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#28, #30-#39
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 2 MDa

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Macromolecule #1: 18S rRNA

MacromoleculeName: 18S rRNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 603.100938 KDa
SequenceString: UACCUGGUUG AUCCUGCCAG UAGCAUAUGC UUGUCUCAAA GAUUAAGCCA UGCAUGUCUA AGUACGCACG GCCGGUACAG UGAAACUGC GAAUGGCUCA UUAAAUCAGU UAUGGUUCCU UUGGUCGCUC GCUCCUCUCC UACUUGGAUA ACUGUGGUAA U UCUAGAGC ...String:
UACCUGGUUG AUCCUGCCAG UAGCAUAUGC UUGUCUCAAA GAUUAAGCCA UGCAUGUCUA AGUACGCACG GCCGGUACAG UGAAACUGC GAAUGGCUCA UUAAAUCAGU UAUGGUUCCU UUGGUCGCUC GCUCCUCUCC UACUUGGAUA ACUGUGGUAA U UCUAGAGC UAAUACAUGC CGACGGGCGC UGACCCCCUU CGCGGGGGGG AUGCGUGCAU UUAUCAGAUC AAAACCAACC CG GUCAGCC UCCCCCCGGC CCCGGCCGGG GGGGUGGGCG CCGGCGGCUU UGGUGACUCU AGAUAACCUC GGGCCGAUCG CAC GCCCUC CGUGGCGGCG ACGACCCAUU CGAACGUCUG CCCUAUCAAC UUUCGAUGGU AGUCGCCGUG CCUACCAUGG UGAC CACGG GUGACGGGGA AUCAGGGUUC GAUUCCGGAG AGGGAGCCUG AGAAACGGCU ACCACAUCCA AGGAAGGCAG CAGGC GCGC AAAUUACCCA CUCCCGACCC GGGGAGGUAG UGACGAAAAA UAACAAUACA GGACUCUUUC GAGGCCCUGU AAUUGG AAU GAGUCCACUU UAAAUCCUUU AACGAGGAUC CAUUGGAGGG CAAGUCUGGU GCCAGCAGCC GCGGUAAUUC CAGCUCC AA UAGCGUAUAU UAAAGUUGCU GCAGUUAAAA AGCUCGUAGU UGGAUCUUGG GAGCGGGCGG GCGGUCCGCC GCGAGGCG A GCCACCGCCC GUCCCCGCCC CUUGCCUCUC GGCGCCCCCU CGAUGCUCUU AGCUGAGUGU CCCGCGGGGC CCGAAGCGU UUACUUUGAA AAAAUUAGAG UGUUCAAAGC AGGCCCGAGC CGCCUGGAUA CCGCAGCUAG GAAUAAUGGA AUAGGACCGC GGUUCUAUU UUGUUGGUUU UCGGAACUGA GGCCAUGAUU AAGAGGGACG GCCGGGGGCA UUCGUAUUGC GCCGCUAGAG G UGAAAUUC UUGGACCGGC GCAAGACGGA CCAGAGCGAA AGCAUUUGCC AAGAAUGUUU UCAUUAAUCA AGAACGAAAG UC GGAGGUU CGAAGACGAU CAGAUACCGU CGUAGUUCCG ACCAUAAACG AUGCCGACCG GCGAUGCGGC GGCGUUAUUC CCA UGACCC GCCGGGCAGC UUCCGGGAAA CCAAAGUCUU UGGGUUCCGG GGGGAGUAUG GUUGCAAAGC UGAAACUUAA AGGA AUUUG GCGAAGGGCA CCACCAGGAG UGGAGCCUGC GGCUUAAUUU GACUCAACAC GGGAAACCUC ACCCGGCCCG GACAC GGAC AGGAUUGACA GAUUGAUAGC UCUUUCUCGA UUCCGUGGGU GGUGGUGCAU GGCCGUUCUU AGUUGGUGGA GCGAUU UGU CUGGUUAAUU CCGAUAACGA ACGAGACUCU GGCAUGCUAA CUAGUUACGC GACCCCCGAG CGGUCGGCGU CCCCCAA CU UCUUAGAGGG ACAAGUGGCG UUCAGCCACC CGAGAUUGAG CAAUAACAGG UCUGUGAUGC CCUUAGAUGU CCGGGGCU G CACGCGCGCU ACACUGACUG GCUCAGCGUG UGCCUACCCU ACGCCGGCAG GCGCGGGUAA CCCGUUGAAC CCCAUUCGU GAUGGGGAUC GGGGAUUGCA AUUAUUCCCC AUGAACGAGG AAUUCCCAGU AAGUGCGGGU CAUAAGCUUG CGUUGAUUAA GUCCCUGCC CUUUGUACAC ACCGCCCGUC GCUACUACCG AUUGGAUGGU UUAGUGAGGC CCUCGGAUCG GCCCCGCCGG G GUCGGCCC ACGGCCCUGG CGGAGCGCUG AGAAGACGGU CGAACUUGAC UAUCUAGAGG AAGUAAAAGU CGUAACAAGG UU UCCGUAG GUGAACCUGC GGAAGGAUCA UUA

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Macromolecule #36: Met-tRNA-i-Met

MacromoleculeName: Met-tRNA-i-Met / type: rna / ID: 36 / Number of copies: 1
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 24.23151 KDa
SequenceString:
AGCAGAGUGG CGCAGCGGAA GCGUGCUGGG CCCAUAACCC AGAGGUCGAU GGAUCGAAAC CAUCCUCUGC UACCA

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Macromolecule #39: HCV IRES

MacromoleculeName: HCV IRES / type: rna / ID: 39 / Number of copies: 1
Source (natural)Organism: Hepatitis C virus (isolate 1)
Molecular weightTheoretical: 128.746109 KDa
SequenceString: GCCAGCCCCC UGAUGGGGGC GACACUCCAC CAUGAAUCAC UCCCCUGUGA GGAACUACUG UCUUCACGCA GAAAGCGUCU AGCCAUGGC GUUAGUAUGA GUGUCGUGCA GCCUCCAGGA CCCCCCCUCC CGGGAGAGCC AUAGUGGUCU GCGGAACCGG U GAGUACAC ...String:
GCCAGCCCCC UGAUGGGGGC GACACUCCAC CAUGAAUCAC UCCCCUGUGA GGAACUACUG UCUUCACGCA GAAAGCGUCU AGCCAUGGC GUUAGUAUGA GUGUCGUGCA GCCUCCAGGA CCCCCCCUCC CGGGAGAGCC AUAGUGGUCU GCGGAACCGG U GAGUACAC CGGAAUUGCC AGGACGACCG GGUCCUUUCU UGGAUCAACC CGCUCAAUGC CUGGAGAUUU GGGCGUGCCC CC GCAAGAC UGCUAGCCGA GUAGUGUUGG GUCGCGAAAG GCCUUGUGGU ACUGCCUGAU AGGGUGCUUG CGAGUGCCCC GGG AGGUCU CGUAGACCGU GCACCAUGAG CACGAAUCCU AAACCUCAAA GAAAAACCAA ACGUAACACC AACCGUCGCC CACA

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Macromolecule #2: Eukaryotic translation initiation factor 1A, X-chromosomal

MacromoleculeName: Eukaryotic translation initiation factor 1A, X-chromosomal
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.488449 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPKNKGKGGK NRRRGKNENE SEKRELVFKE DGQEYAQVIK MLGNGRLEAM CFDGVKRLCH IRGKLRKKVW INTSDIILVG LRDYQDNKA DVILKYNADE ARSLKAYGEL PEHAKINETD TFGPGDDDEI QFDDIGDDDE DIDDI

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Macromolecule #3: 40S ribosomal protein SA

MacromoleculeName: 40S ribosomal protein SA / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 32.958016 KDa
SequenceString: MSGALDVLQM KEEDVLKFLA AGTHLGGTNL DFQMEQYIYK RKSDGIYIIN LKRTWEKLLL AARAIVAIEN PADVSVISSR NTGQRAVLK FAAATGATPI AGRFTPGTFT NQIQTAFREP RLLVVTDPRA DHQPLTEASY VNLPTIALCN TDSPLRYVDI A IPCNNKGA ...String:
MSGALDVLQM KEEDVLKFLA AGTHLGGTNL DFQMEQYIYK RKSDGIYIIN LKRTWEKLLL AARAIVAIEN PADVSVISSR NTGQRAVLK FAAATGATPI AGRFTPGTFT NQIQTAFREP RLLVVTDPRA DHQPLTEASY VNLPTIALCN TDSPLRYVDI A IPCNNKGA HSVGLMWWML AREVLRMRGT ISREHPWEVM PDLYFYRDPE EIEKEEQAAA EKAVTKEEFQ GEWTAPAPEF TA TQPEVAD WSEGVQVPSV PIQQFPTEDW SAQPATEDWS AAPTAQATEW VGTTTEWS

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Macromolecule #4: eS1

MacromoleculeName: eS1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 30.002061 KDa
SequenceString: MAVGKNKRLT KGGKKGAKKK VVDPFSKKDW YDVKAPAMFN IRNIGKTLVT RTQGTKIASD GLKGRVFEVS LADLQNDEVA FRKFKLITE DVQGKNCLTN FHGMDLTRDK MCSMVKKWQT MIEAHVDVKT TDGYLLRLFC VGFTKKRNNQ IRKTSYAQHQ Q VRQIRKKM ...String:
MAVGKNKRLT KGGKKGAKKK VVDPFSKKDW YDVKAPAMFN IRNIGKTLVT RTQGTKIASD GLKGRVFEVS LADLQNDEVA FRKFKLITE DVQGKNCLTN FHGMDLTRDK MCSMVKKWQT MIEAHVDVKT TDGYLLRLFC VGFTKKRNNQ IRKTSYAQHQ Q VRQIRKKM MEIMTREVQT NDLKEVVNKL IPDSIGKDIE KACQSIYPLH DVFVRKVKML KKPKFELGKL MELHGEGSSS GK ATGDETG AKVERADGYE PPVQESV

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Macromolecule #5: 40S ribosomal protein S2

MacromoleculeName: 40S ribosomal protein S2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 24.441846 KDa
SequenceString: KEWLPVTKLG RLVKDMKIKS LEEIYLFSLP IKESEIIDFF LGASLKDEVL KIMPVQKQTR AGQRTRFKAF VAIGDYNGHV GLGVKCSKE VATAIRGAII LAKLSIVPVR RGYWGNKIGK PHTVPCKVTG RCGSVLVRLI PAPRGTGIVS APVPKKLLMM A GIDDCYTS ...String:
KEWLPVTKLG RLVKDMKIKS LEEIYLFSLP IKESEIIDFF LGASLKDEVL KIMPVQKQTR AGQRTRFKAF VAIGDYNGHV GLGVKCSKE VATAIRGAII LAKLSIVPVR RGYWGNKIGK PHTVPCKVTG RCGSVLVRLI PAPRGTGIVS APVPKKLLMM A GIDDCYTS ARGCTATLGN FAKATFDAIS KTYSYLTPDL WKETVFTKSP YQEFTDHLVK THT

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Macromolecule #6: uS3

MacromoleculeName: uS3 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 31.146607 KDa
SequenceString: MSARRRRRRA AFRRRAEPFI PISVREPLPF LSAARGGKMA VQISKKRKFV ADGIFKAELN EFLTRELAED GYSGVEVRVT PTRTEIIIL ATRTQNVLGE KGRRIRELTA VVQKRFGFPE GSVELYAEKV ATRGLCAIAQ AESLRYKLLG GLAVRRACYG V LRFIMESG ...String:
MSARRRRRRA AFRRRAEPFI PISVREPLPF LSAARGGKMA VQISKKRKFV ADGIFKAELN EFLTRELAED GYSGVEVRVT PTRTEIIIL ATRTQNVLGE KGRRIRELTA VVQKRFGFPE GSVELYAEKV ATRGLCAIAQ AESLRYKLLG GLAVRRACYG V LRFIMESG AKGCEVVVSG KLRGQRAKSM KFVDGLMIHS GDPVNYYVDT AVRHVLLRQG VLGIKVKIML PWDPSGKIGP KK PLPDHVS IVEPKDEILP TTPISEQKGG KPEPPAMPQP VPTA

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Macromolecule #7: 40S ribosomal protein S4

MacromoleculeName: 40S ribosomal protein S4 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 29.654869 KDa
SequenceString: MARGPKKHLK RVAAPKHWML DKLTGVFAPR PSTGPHKLRE CLPLIIFLRN RLKYALTGDE VKKICMQRFI KIDGKVRTDI TYPAGFMDV ISIDKTGENF RLIYDTKGRF AVHRITPEEA KYKLCKVRKI FVGTKGIPHL VTHDARTIRY PDPLIKVNDT I QIDLETGK ...String:
MARGPKKHLK RVAAPKHWML DKLTGVFAPR PSTGPHKLRE CLPLIIFLRN RLKYALTGDE VKKICMQRFI KIDGKVRTDI TYPAGFMDV ISIDKTGENF RLIYDTKGRF AVHRITPEEA KYKLCKVRKI FVGTKGIPHL VTHDARTIRY PDPLIKVNDT I QIDLETGK ITDFIKFDTG NLCMVTGGAN LGRIGVITNR ERHPGSFDVV HVKDANGNSF ATRLSNIFVI GKGNKPWISL PR GKGIRLT IAEERDKRLA AKQSSG

+
Macromolecule #8: uS7

MacromoleculeName: uS7 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 22.913453 KDa
SequenceString: MTEWETAAPA VAETPDIKLF GKWSTDDVQI NDISLQDYIA VKEKYAKYLP HSAGRYAAKR FRKAQCPIVE RLTNSMMMHG RNNGKKLMT VRIVKHAFEI IHLLTGENPL QVLVNAIINS GPREDSTRIG RAGTVRRQAV DVSPLRRVNQ AIWLLCTGAR E AAFRNIKT ...String:
MTEWETAAPA VAETPDIKLF GKWSTDDVQI NDISLQDYIA VKEKYAKYLP HSAGRYAAKR FRKAQCPIVE RLTNSMMMHG RNNGKKLMT VRIVKHAFEI IHLLTGENPL QVLVNAIINS GPREDSTRIG RAGTVRRQAV DVSPLRRVNQ AIWLLCTGAR E AAFRNIKT IAECLADELI NAAKGSSNSY AIKKKDELER VAKSNR

+
Macromolecule #9: eS6

MacromoleculeName: eS6 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 28.751906 KDa
SequenceString: MKLNISFPAT GCQKLIEVDD ERKLRTFYEK RMATEVAADA LGEEWKGYVV RISGGNDKQG FPMKQGVLTH GRVRLLLSKG HSCYRPRRT GERKRKSVRG CIVDANLSVL NLVIVKKGEK DIPGLTDTTV PRRLGPKRAS RIRKLFNLSK EDDVRQYVVR K PLNKEGKK ...String:
MKLNISFPAT GCQKLIEVDD ERKLRTFYEK RMATEVAADA LGEEWKGYVV RISGGNDKQG FPMKQGVLTH GRVRLLLSKG HSCYRPRRT GERKRKSVRG CIVDANLSVL NLVIVKKGEK DIPGLTDTTV PRRLGPKRAS RIRKLFNLSK EDDVRQYVVR K PLNKEGKK PRTKAPKIQR LVTPRVLQHK RRRIALKKQR TKKNKEEAAE YAKLLAKRMK EAKEKRQEQI AKRRRLSSLR AS TSKSESS QK

+
Macromolecule #10: 40S ribosomal protein S7

MacromoleculeName: 40S ribosomal protein S7 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 47.356172 KDa
SequenceString: EPITNRVFQA LTSSDFKQQD GGSFSLSRTH LSGFRSRPRR TTIASAATRP PPIPSRGGSA PTGTPEGAGA SRSSRTVPRL PPQPSGPPR APRHPGFQRA LPSLIRPEPG VRAPLLASAG TRFKRPASQA VKALSARGLL QPQVQVGPRA NRVPQRREPR Q HLSGHAPG ...String:
EPITNRVFQA LTSSDFKQQD GGSFSLSRTH LSGFRSRPRR TTIASAATRP PPIPSRGGSA PTGTPEGAGA SRSSRTVPRL PPQPSGPPR APRHPGFQRA LPSLIRPEPG VRAPLLASAG TRFKRPASQA VKALSARGLL QPQVQVGPRA NRVPQRREPR Q HLSGHAPG ASEGGSASPT YWSLGITSWD ALGFPLRLGG SSGFRSSVAL FRPLSFRRGD LPRSREIWAS SSAGAQPGEA MF SSSAKIV KPNGEKPDEF ESGISQALLE LEMNSDLKAQ LRELNITAAK EIEVGGGRKA IIIFVPVPQL KSFQKIQVRL VRE LEKKFS GKHVVFIAQR RILPKPTRKS RTKNKQKRPR SRTLTAVHDA ILEDLVFPSE IVGKRIRVKL DGSRLIKVHL DKAQ QNNVE HKVETFSGVY KKLTGKDVNF EFPEFQL

+
Macromolecule #11: eS8

MacromoleculeName: eS8 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 24.263387 KDa
SequenceString: MGISRDNWHK RRKTGGKRKP YHKKRKYELG RPAANTKIGP RRIHTVRVRG GNKKYRALRL DVGNFSWGSE CCTRKTRIID VVYNASNNE LVRTKTLVKN CIVLIDSTPY RQWYESHYAL PLGRKKGAKL TPEEEEILNK KRSKKIQKKY DERKKNAKIS S LLEEQFQQ ...String:
MGISRDNWHK RRKTGGKRKP YHKKRKYELG RPAANTKIGP RRIHTVRVRG GNKKYRALRL DVGNFSWGSE CCTRKTRIID VVYNASNNE LVRTKTLVKN CIVLIDSTPY RQWYESHYAL PLGRKKGAKL TPEEEEILNK KRSKKIQKKY DERKKNAKIS S LLEEQFQQ GKLLACIASR PGQCGRADGY VLEGKELEFY LRKIKARKGK

+
Macromolecule #12: uS4

MacromoleculeName: uS4 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 22.641564 KDa
SequenceString: MPVARSWVCR KTYVTPRRPF EKSRLDQELK LIGEYGLRNK REVWRVKFTL AKIRKAAREL LTLDEKDPRR LFEGNALLRR LVRIGVLDE GKMKLDYILG LKIEDFLERR LQTQVFKLGL AKSIHHARVL IRQRHIRVRK QVVNIPSFIV RLDSQKHIDF S LRSPYGGG ...String:
MPVARSWVCR KTYVTPRRPF EKSRLDQELK LIGEYGLRNK REVWRVKFTL AKIRKAAREL LTLDEKDPRR LFEGNALLRR LVRIGVLDE GKMKLDYILG LKIEDFLERR LQTQVFKLGL AKSIHHARVL IRQRHIRVRK QVVNIPSFIV RLDSQKHIDF S LRSPYGGG RPGRVKRKNA KKGQGGAGAG DDEEED

+
Macromolecule #13: eS10

MacromoleculeName: eS10 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 17.156865 KDa
SequenceString:
MLMPKKNRIA IYELLFKEGV MVAKKDVHMP KHPELADKNV PNLHVMKAMQ SLKSRGYVKE QFAWRHFYWY LTNEGIQYLR DYLHLPPEI VPATLRRSRP ETGRPRPKGL EGERPARLTR GEADRDTYRR SAVPPGADKK AEAGAGSATE

+
Macromolecule #14: uS17

MacromoleculeName: uS17 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 18.468826 KDa
SequenceString:
MADIQTERAY QKQPTIFQNK KRVLLGETGK EKLPRYYKNI GLGFKTPKEA IEGTYIDKKC PFTGNVSIRG RILSGVVTKM KMQRTIVIR RDYLHYIRKY NRFEKRHKNM SVHLSPCFRD VQIGDIVTVG ECRPLSKTVR FNVLKVTKAA GTKKQFQKF

+
Macromolecule #15: eS12

MacromoleculeName: eS12 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 14.538987 KDa
SequenceString:
MAEEGIAAGG VMDVNTALQE VLKTALIHDG LARGIREAAK ALDKRQAHLC VLASNCDEPM YVKLVEALCA EHQINLIKVD DNKKLGEWV GLCKIDREGK PRKVVGCSCV VVKDYGKESQ AKDVIEEYFK CKK

+
Macromolecule #16: uS15

MacromoleculeName: uS15 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 17.259389 KDa
SequenceString:
MGRMHAPGKG LSQSALPYRR SVPTWLKLTS DDVKEQIYKL AKKGLTPSQI GVILRDSHGV AQVRFVTGNK ILRILKSKGL APDLPEDLY HLIKKAVAVR KHLERNRKDK DAKFRLILIE SRIHRLARYY KTKRVLPPNW KYESSTASAL VA

+
Macromolecule #17: uS11

MacromoleculeName: uS11 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 18.133984 KDa
SequenceString:
MKARALSGSG VRRRRAAMAP RKGKEKKEEQ VISLGPQVAE GENVFGVCHI FASFNDTFVH VTDLSGKETI CRVTGGMKVK ADRDESSPY AAMLAAQDVA QRCKELGITA LHIKLRATGG NRTKTPGPGA QSALRALARS GMKIGRIEDV TPIPSDSTRR K GGRRGRRL

+
Macromolecule #18: uS19

MacromoleculeName: uS19 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 17.049182 KDa
SequenceString:
MAEVEQKKKR TFRKFTYRGV DLDQLLDMSY EQLMQLYSAR QRRRLSRGLR RKQHSLLKRL RKAKKEAPPM EKPEVVKTHL RDMIILPEM VGSMVGVYNG KTFNQVEIKP EMIGHYLGEF SITYKPVKHG RPGIGATHSS RFIPLK

+
Macromolecule #19: uS9

MacromoleculeName: uS9 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 19.213465 KDa
SequenceString:
SARVAPRFPF PVVAPRGEDR HSSAAAMPSK GPLQSVQVFG RKKTATAVAH CKRGNGLIKV NGRPLEMIEP RTLQYKLLEP VLLLGKERF AGVDIRVRVK GGGHVAQIYA IRQSISKALV AYYQKYVDEA SKKEIKDILI QYDRTLLVAD PRRCESKKFG G PGARARYQ KSYR

+
Macromolecule #20: eS17

MacromoleculeName: eS17 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 15.552119 KDa
SequenceString:
MGRVRTKTVK KAARVIIEKY YTRLGNDFHT NKRVCEEIAI IPSKKLRNKI AGYVTHLMKR IQRGPVRGIS IKLQEEERER RDNYVPEVS ALDQEIIEVD PDTKEMLKLL DFGSLSNLQV TQPTVGMNFK TPRGAV

+
Macromolecule #21: uS13

MacromoleculeName: uS13 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 17.759777 KDa
SequenceString:
MSLVIPEKFQ HILRVLNTNI DGRRKIAFAI TAIKGVGRRY AHVVLRKADI DLTKRAGELT EDEVERVITI MQNPRQYKIP DWFLNRQKD VKDGKYSQVL ANGLDNKLRE DLERLKKIRA HRGLRHFWGL RVRGQHTKTT GRRGRTVGVS KKK

+
Macromolecule #22: eS19

MacromoleculeName: eS19 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 16.235796 KDa
SequenceString:
MPGVTVKDVN QQEFVRALAA FLKKSGKLKV PEWVDTVKLA KHKELAPYDE NWFYTRAAST ARHLYLRGGA GVGSMTKIYG GRQRNGVMP SHFSRGSKSV ARRVLQALEG LKMVEKDQDW GRKLTPQGQR DLDRIAGQVA AAKKKH

+
Macromolecule #23: uS10

MacromoleculeName: uS10 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 13.398763 KDa
SequenceString:
MAFKDTGKTP VEPEVAIHRI RITLTSRNVK SLEKVCADLI RGAKEKNLKV KGPVRMPTKT LRITTRKTPC GEGSKTWDRF QMRIHKRLI DLHSPSEIVK QITSISIEPG VEVEVTIADA

+
Macromolecule #24: 40S ribosomal protein S21

MacromoleculeName: 40S ribosomal protein S21 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 9.124389 KDa
SequenceString:
MQNDAGEFVD LYVPRKCSAS NRIIGAKDHA SIQMNVAEVD KVTGRFNGQF KTYAICGAIR RMGESDDSIL RLAKADGIVS KNF

+
Macromolecule #25: uS8

MacromoleculeName: uS8 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 14.865555 KDa
SequenceString:
MVRMNVLADA LKSINNAEKR GKRQVLIRPC SKVIVRFLTV MMKHGYIGEF EIIDDHRAGK IVVNLTGRLN KCGVISPRFD VQLKDLEKW QNNLLPSRQF GFIVLTTSAG IMDHEEARRK HTGGKILGFF F

+
Macromolecule #26: uS12

MacromoleculeName: uS12 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 15.844666 KDa
SequenceString:
MGKCRGLRTA RKLRSHRRDQ KWHDKQYKKA HLGTALKANP FGGASHAKGI VLEKVGVEAK QPNSAIRKCV RVQLIKNGKK ITAFVPNDG CLNFIEENDE VLVAGFGRKG HAVGDIPGVR FKVVKVANVS LLALYKGKKE RPRS

+
Macromolecule #27: 40S ribosomal protein S24

MacromoleculeName: 40S ribosomal protein S24 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 15.237104 KDa
SequenceString:
MNDTVTIRTR KFMTNRLLQR KQMVIDVLHP GKATVPKTEI REKLAKMYKT TPDVIFVFGF RTHFGGGKTT GFGMIYDSLD YAKKNEPKH RLARHGLYEK KKTSRKQRKE RKNRMKKVRG TAKANVGAGK KK

+
Macromolecule #28: 40S ribosomal protein S25

MacromoleculeName: 40S ribosomal protein S25 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 13.645028 KDa
SequenceString:
PPKDDKKKKD AGKSAKKDKD PVNKSGGKAK KKKWSKGKVR DKLNNLVLFD KATYDKLCKE VPNYKLITPA VVSERLKIRG SLARAALQE LLSKGLIKLV SKHRAQVIYT RNTKGGDAPA AGEDA

+
Macromolecule #29: 40S ribosomal protein S26

MacromoleculeName: 40S ribosomal protein S26 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 11.645794 KDa
SequenceString:
TKKRRNNGRA KKGRGHVQPI RCTNCARCVP KDKAIKKFVI RNIVEAAAVR DISEASVFDA YVLPKLYVKL HYCVSCAIHS KVVRNRSRE ARKDRTPPPR FR

+
Macromolecule #30: eS27

MacromoleculeName: eS27 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 9.480186 KDa
SequenceString:
MPLAKDLLHP SPEEEKRKHK KKRLVQSPNS YFMDVKCPGC YKITTVFSHA QTVVLCVGCS TVLCQPTGGK ARLTEGCSFR RKQH

+
Macromolecule #31: eS28

MacromoleculeName: eS28 / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 7.855052 KDa
SequenceString:
MDTSRVQPIK LARVTKVLGR TGSQGQCTQV RVEFMDDTSR SIIRNVKGPV REGDVLTLLE SEREARRLR

+
Macromolecule #32: eS29

MacromoleculeName: eS29 / type: protein_or_peptide / ID: 32 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 6.690821 KDa
SequenceString:
MGHQQLYWSH PRKFGQGSRS CRVCSNRHGL IRKYGLNMCR QCFRQYAKDI GFIKLD

+
Macromolecule #33: eS30

MacromoleculeName: eS30 / type: protein_or_peptide / ID: 33 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 14.498884 KDa
SequenceString:
MQLFVRAQEL HTLEVTGRET VAQIKAHVAS LEGIAPEDQV VLLAGTPLED EATLGQCGVE ALSTLEVAGR MLGGKVHGSL ARVGKVRGQ TLKVAKQEKK KKRTGRAKRR MQYNRRFVNV VPTFGKKKGP NANS

+
Macromolecule #34: 40S ribosomal protein S27a

MacromoleculeName: 40S ribosomal protein S27a / type: protein_or_peptide / ID: 34 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 21.431742 KDa
SequenceString:
MARHPLYQGS GIWCGRLRGG AFGGGAGKPR GPAALFLFDP PSARRWARHQ DADLRENPYG EDHHARGIPP DQQRLIFAGK QLEDGRTLS DYNIQKESTL HLVLRLRGGA KKRKKKSYTT PKKNKHKRKK VKLAVLKYYK VDENGKISRL RRECPSDECG A GVFMASHF DRHYCGKCCL TYCFNKPEDK

+
Macromolecule #35: RACK1

MacromoleculeName: RACK1 / type: protein_or_peptide / ID: 35 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 35.115652 KDa
SequenceString: MTEQMTLRGT LKGHNGWVTQ IATTPQFPDM ILSASRDKTI IMWKLTRDET NYGIPQRALR GHSHFVSDVV ISSDGQFALS GSWDGTLRL WDLTTGTTTR RFVGHTKDVL SVAFSSDNRQ IVSGSRDKTI KLWNTLGVCK YTVQDESHSE WVSCVRFSPN S SNPIIVSC ...String:
MTEQMTLRGT LKGHNGWVTQ IATTPQFPDM ILSASRDKTI IMWKLTRDET NYGIPQRALR GHSHFVSDVV ISSDGQFALS GSWDGTLRL WDLTTGTTTR RFVGHTKDVL SVAFSSDNRQ IVSGSRDKTI KLWNTLGVCK YTVQDESHSE WVSCVRFSPN S SNPIIVSC GWDKLVKVWN LANCKLKTNH IGHTGYLNTV TVSPDGSLCA SGGKDGQAML WDLNEGKHLY TLDGGDIINA LC FSPNRYW LCAATGPSIK IWDLEGKIIV DELKQEVIST SSKAEPPQCT SLAWSADGQT LFAGYTDNLV RVWQVTIGTR

+
Macromolecule #37: 60s ribosomal protein l41

MacromoleculeName: 60s ribosomal protein l41 / type: protein_or_peptide / ID: 37 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 3.473451 KDa
SequenceString:
MRAKWRKKRM RRLKRKRRKM RQRSK

+
Macromolecule #38: Eukaryotic translation initiation factor 5B

MacromoleculeName: Eukaryotic translation initiation factor 5B / type: protein_or_peptide / ID: 38 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 70.788 KDa
SequenceString: DSDDDRTKEE RAYDKAKRRI EKRRLEHSKN VNTEKLRAPV ICVLGHVDTG KTKILDKLRH THVQDGEAGG ITQQIGATNV PLEAINEQT KMIKNFDREN VRIPGMLIID TPGHESFSNL RNRGSSLCDI AILVVDIMHG LEPQTIESIN LLKSKKCPFI V ALNKIDRL ...String:
DSDDDRTKEE RAYDKAKRRI EKRRLEHSKN VNTEKLRAPV ICVLGHVDTG KTKILDKLRH THVQDGEAGG ITQQIGATNV PLEAINEQT KMIKNFDREN VRIPGMLIID TPGHESFSNL RNRGSSLCDI AILVVDIMHG LEPQTIESIN LLKSKKCPFI V ALNKIDRL YDWKKSPDSD VAATLKKQKK NTKDEFEERA KAIIVEFAQQ GLNAALFYEN KDPRTFVSLV PTSAHTGDGM GS LIYLLVE LTQTMLSKRL AHCEELRAQV MEVKALPGMG TTIDVILING RLKEGDTIIV PGVEGPIVTQ IRGLLLPPPM KEL RVKNQY EKHKEVEAAQ GVKILGKDLE KTLAGLPLLV AYKEDEIPVL KDELIHELKQ TLNAIKLEEK GVYVQASTLG SLEA LLEFL KTSEVPYAGI NIGPVHKKDV MKASVMLEHD PQYAVILAFD VRIERDAQEM ADSLGVRIFS AEIIYHLFDA FTKYR QDYK KQKQEEFKHI AVFPCKMKIL PQYIFNSRDP IVMGVTVEAG QVKQGTPMCV PSKNFVDIGI VTSIEVNHKQ VDVAKK GQE VCVKIEPIPG ESPKMFGRHF EATDILVSKI SRQSIDALKD WFRDEMQKSD WQLIVELKKV FEII

+
Macromolecule #40: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 40 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #41: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 41 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

+
Macromolecule #42: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 42 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #43: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 43 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.000075 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50.0 nm / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: OTHER / Details: H2/O2 mixture for 25 seconds at 25W power
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: 4 second blot time, force 3.

-
Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 4.0 sec. / Average electron dose: 70.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 52000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 133782
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) / Details: Relion 3
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6d9j


5flx

chain_id: z

5k0y

chain_id: N

4ujd

chain_id: BB
Output model

PDB-7syw:
Structure of the wt IRES eIF5B-containing 48S initiation complex, closed conformation. Structure 15(wt)

+
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  • 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

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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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