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- EMDB-10762: Mammalian 48S late-stage translation initiation complex with hist... -

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Basic information

Entry
Database: EMDB / ID: EMD-10762
TitleMammalian 48S late-stage translation initiation complex with histone 4 mRNA
Map data
Sample
  • Complex: LS48S IC with histone 4 mRNA
    • Complex: LS48S IC
      • Protein or peptide: x 36 types
      • RNA: x 2 types
    • Complex: histone 4 mRNA
      • RNA: x 1 types
Function / homology
Function and homology information


ribosomal subunit / translation initiation factor activity / DNA-(apurinic or apyrimidinic site) lyase / cytoplasmic stress granule / cytosolic small ribosomal subunit / small ribosomal subunit / cell differentiation / ribosome / structural constituent of ribosome / ribonucleoprotein complex ...ribosomal subunit / translation initiation factor activity / DNA-(apurinic or apyrimidinic site) lyase / cytoplasmic stress granule / cytosolic small ribosomal subunit / small ribosomal subunit / cell differentiation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / nucleolus / RNA binding / cytoplasm
Similarity search - Function
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 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S26e signature. / S1 domain profile. / Ribosomal protein S21e signature. / Ribosomal protein S3Ae, conserved site ...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 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S26e signature. / S1 domain profile. / Ribosomal protein S21e signature. / Ribosomal protein S3Ae, conserved site / Ribosomal protein S12e signature. / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S6, eukaryotic / Ribosomal protein S19e signature. / 40S Ribosomal protein S10 / Ribosomal protein S6/S6e/A/B/2, conserved site / Plectin/S10, N-terminal / Ribosomal protein S3Ae / Ribosomal S3Ae family / Plectin/S10 domain / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal S3Ae family / Ribosomal protein S17e signature. / Ribosomal protein S7e signature. / Ribosomal protein S6e / Ribosomal protein S3Ae signature. / Ribosomal protein S27e signature. / Ribosomal protein S4e signature. / Ribosomal protein S8e signature. / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S6e signature. / Ribosomal protein S28e signature. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Ribosomal protein S2 signature 2. / Ubiquitin domain signature. / Ribosomal protein S10, conserved site / Ribosomal protein L30 signature. / Ribosomal protein S10 / Ribosomal protein S3 signature. / Ribosomal protein S10 signature. / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / Type-2 KH domain profile. / Ribosomal protein S19 signature. / Ribosomal protein S7 signature. / Ribosomal protein S10p/S20e / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S17 signature. / Ribosomal protein S13 signature. / Ribosomal protein S13 family profile. / Ribosomal protein S10p/S20e / Ribosomal protein S8 signature. / Ribosomal protein S4 signature. / Ribosomal protein S15 signature. / S4 RNA-binding domain profile. / Ribosomal protein S11 signature. / Ubiquitin domain profile. / Ribosomal protein S9 signature. / Ribosomal protein S12 signature. / Ribosomal protein L23/L15e core domain superfamily / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Small ribosomal subunit protein eS32 / Small ribosomal subunit protein uS10 / 40S ribosomal protein S6 / 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 eS32 / Small ribosomal subunit protein uS10 / 40S ribosomal protein S6 / 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 eS7 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS11 / Eukaryotic translation initiation factor 2 subunit 1 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS26 / 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 eS1 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS13 / Plectin/eS10 N-terminal domain-containing protein / Small ribosomal subunit protein uS17 / 40S ribosomal protein S24 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS14
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit) / Mus musculus (house mouse) / Rabbit (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.48 Å
AuthorsBochler A / Simonetti A / Guca E / Hashem Y
Funding supportEuropean Union, France, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)759120European Union
French National Research AgencyANR-14-ACHN-0024 France
CitationJournal: Cell Rep / Year: 2020
Title: Structural Insights into the Mammalian Late-Stage Initiation Complexes.
Authors: Angelita Simonetti / Ewelina Guca / Anthony Bochler / Lauriane Kuhn / Yaser Hashem /
Abstract: In higher eukaryotes, the mRNA sequence in the direct vicinity of the start codon, called the Kozak sequence (CRCCaugG, where R is a purine), is known to influence the rate of the initiation process. ...In higher eukaryotes, the mRNA sequence in the direct vicinity of the start codon, called the Kozak sequence (CRCCaugG, where R is a purine), is known to influence the rate of the initiation process. However, the molecular basis underlying its role remains poorly understood. Here, we present the cryoelectron microscopy (cryo-EM) structures of mammalian late-stage 48S initiation complexes (LS48S ICs) in the presence of two different native mRNA sequences, β-globin and histone 4, at overall resolution of 3 and 3.5 Å, respectively. Our high-resolution structures unravel key interactions from the mRNA to eukaryotic initiation factors (eIFs): 1A, 2, 3, 18S rRNA, and several 40S ribosomal proteins. In addition, we are able to study the structural role of ABCE1 in the formation of native 48S ICs. Our results reveal a comprehensive map of ribosome/eIF-mRNA and ribosome/eIF-tRNA interactions and suggest the impact of mRNA sequence on the structure of the LS48S IC.
History
DepositionMar 12, 2020-
Header (metadata) releaseApr 8, 2020-
Map releaseApr 8, 2020-
UpdateApr 22, 2020-
Current statusApr 22, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0109
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0109
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6yan
  • Surface level: 0.0109
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10762.png

Downloads & links

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Map

FileDownload / File: emd_10762.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.0109 / Movie #1: 0.0109
Minimum - Maximum-0.06495021 - 0.11032099
Average (Standard dev.)0.00024204273 (±0.0030118984)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z422.400422.400422.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0650.1100.000

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Supplemental data

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Sample components

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Entire : LS48S IC with histone 4 mRNA

EntireName: LS48S IC with histone 4 mRNA
Components
  • Complex: LS48S IC with histone 4 mRNA
    • Complex: LS48S IC
      • Protein or peptide: 60s ribosomal protein l41
      • Protein or peptide: 40S ribosomal protein SA
      • Protein or peptide: ribosomal protein eS1
      • Protein or peptide: 40S ribosomal protein uS5
      • Protein or peptide: Ribosomal protein S3
      • Protein or peptide: 40S ribosomal protein S4
      • Protein or peptide: Ribosomal protein S5
      • Protein or peptide: 40S ribosomal protein S6
      • Protein or peptide: ribosomal protein eS7
      • Protein or peptide: 40S ribosomal protein S8
      • Protein or peptide: Ribosomal protein S9 (Predicted)Ribosome
      • Protein or peptide: 40S ribosomal protein eS10
      • Protein or peptide: Ribosomal protein S11
      • Protein or peptide: 40S ribosomal protein S12
      • Protein or peptide: ribosomal protein uS15
      • Protein or peptide: 40S ribosomal protein uS11
      • Protein or peptide: ribosomal protein uS9
      • Protein or peptide: ribosomal protein eS17
      • Protein or peptide: 40S ribosomal protein eS19
      • Protein or peptide: Ribosomal_S10 domain-containing protein
      • Protein or peptide: 40S ribosomal protein S21
      • Protein or peptide: Ribosomal protein S15aRibosome
      • Protein or peptide: 40S ribosomal protein uS12
      • Protein or peptide: 40S ribosomal protein S24
      • Protein or peptide: 40S ribosomal protein eS26
      • Protein or peptide: 40S ribosomal protein S27
      • Protein or peptide: ribosomal protein eS28
      • Protein or peptide: ribosomal protein uS14
      • Protein or peptide: ribosomal protein eS31
      • Protein or peptide: ribosomal protein RACK1
      • Protein or peptide: ribosomal protein eS25
      • Protein or peptide: 40S ribosomal protein eS30
      • RNA: 18S ribosomal RNA
      • Protein or peptide: Eukaryotic translation initiation factor 2 subunit 1
      • Protein or peptide: eukaryotic translation initiation factor 2 subunit gamma
      • Protein or peptide: 40S ribosomal protein uS13
      • Protein or peptide: Ribosomal protein S15
      • RNA: initiator methionylated tRNA
    • Complex: histone 4 mRNA
      • RNA: histone 4 (H4) mRNA

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Supramolecule #1: LS48S IC with histone 4 mRNA

SupramoleculeName: LS48S IC with histone 4 mRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#39

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Supramolecule #2: LS48S IC

SupramoleculeName: LS48S IC / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#33, #35-#39
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Supramolecule #3: histone 4 mRNA

SupramoleculeName: histone 4 mRNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #34
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: synthetic construct (others)

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Macromolecule #1: 60s ribosomal protein l41

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

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Macromolecule #2: 40S ribosomal protein SA

MacromoleculeName: 40S ribosomal protein SA / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 23.360791 KDa
SequenceString: SGALDVLQMK EEDVLKFLAA GTHLGGTNLD FQMEQYIYKR KSDGIYIINL KRTWEKLLLA ARAIVAIENP ADVSVISSRN TGQRAVLKF AAATGATPIA GRFTPGTFTN QIQAAFREPR LLVVTDPRAD HQPLTEASYV NLPTIALCNT DSPLRYVDIA I PCNNKGAH ...String:
SGALDVLQMK EEDVLKFLAA GTHLGGTNLD FQMEQYIYKR KSDGIYIINL KRTWEKLLLA ARAIVAIENP ADVSVISSRN TGQRAVLKF AAATGATPIA GRFTPGTFTN QIQAAFREPR LLVVTDPRAD HQPLTEASYV NLPTIALCNT DSPLRYVDIA I PCNNKGAH SVGLMWWMLA REVLRMRGTI SREHPWEVMP DLYFYRDPEE

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Macromolecule #3: ribosomal protein eS1

MacromoleculeName: ribosomal protein eS1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 24.944408 KDa
SequenceString: KKVVDPFSKK DWYDVKAPAM FNIRNIGKTL VTRTQGTKIA SDGLKGRVFE VSLADLQNDE VAFRKFKLIT EDVQGKNCLT NFHGMDLTR DKMCSMVKKW QTMIEAHVDV KTTDGYLLHL FCVGFTKKCN NQIRKTSYAQ HQQVRQIRKK MMEIMTREVQ T NDLKEVVN ...String:
KKVVDPFSKK DWYDVKAPAM FNIRNIGKTL VTRTQGTKIA SDGLKGRVFE VSLADLQNDE VAFRKFKLIT EDVQGKNCLT NFHGMDLTR DKMCSMVKKW QTMIEAHVDV KTTDGYLLHL FCVGFTKKCN NQIRKTSYAQ HQQVRQIRKK MMEIMTREVQ T NDLKEVVN KLIPDSIGKD IEKACQSIYP LHDVFVRKVK MLKKPKFELG KLMELHG

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Macromolecule #4: 40S ribosomal protein uS5

MacromoleculeName: 40S ribosomal protein uS5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 24.814285 KDa
SequenceString: GKAGDKEWLP VTKLGRLVKD MKIKSLEEIY LFSLPIKESE IIDFFLGAAL KDKVLKIMPV QKQTQAGQRT RFKAFVAIGD YNGHVGLGM KCSKEVATAI RGAIILAKLS IVPVRRGYWG NKIGKPHTVR CKVTGRCGSV LVRLIPAPRG TGIISAPVPK K LLLMAGID ...String:
GKAGDKEWLP VTKLGRLVKD MKIKSLEEIY LFSLPIKESE IIDFFLGAAL KDKVLKIMPV QKQTQAGQRT RFKAFVAIGD YNGHVGLGM KCSKEVATAI RGAIILAKLS IVPVRRGYWG NKIGKPHTVR CKVTGRCGSV LVRLIPAPRG TGIISAPVPK K LLLMAGID DCYTSAGGCT ATLGNFAKAT FDAISKTYSY LTPDLWKETV FTKSPYQEFT DHLVKTHT

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Macromolecule #5: Ribosomal protein S3

MacromoleculeName: Ribosomal protein S3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 25.158535 KDa
SequenceString: MAVQISKKRK FVADGIFKAE LNEFLTRELA EDGYSGVEVR VTPTRTEIII LATRTQNVLG EKGRRIRELT AVVQKRFGFP EGSVELYAE KVATRGLCAI AQAESLRYKL LGGLAVRRAC YGVLRFIMES GAKGCEVVVS GKLRGQRAKS MKFVDGLMIH S GDPVNYYV ...String:
MAVQISKKRK FVADGIFKAE LNEFLTRELA EDGYSGVEVR VTPTRTEIII LATRTQNVLG EKGRRIRELT AVVQKRFGFP EGSVELYAE KVATRGLCAI AQAESLRYKL LGGLAVRRAC YGVLRFIMES GAKGCEVVVS GKLRGQRAKS MKFVDGLMIH S GDPVNYYV DTAVRHVLLR QGVLGIKVKI MLPWDPSGKI GPKKPLPDHV SIVEPKDEIL PTTPISEQK

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Macromolecule #6: 40S ribosomal protein S4

MacromoleculeName: 40S ribosomal protein S4 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 29.65892 KDa
SequenceString: MARGPKKHLK RVAAPKHWML DKLTSVFAPR PSTGPHKLRE CLPLIIFLRN KLKYALTGDE VKKICMQRFI KIDGKVRADI TYPAGFMDV ISIDKTGENF RLIYDTKGRF AVHRITPEEA KYKLCKVRKI FVGTKGIPHL VTHDARTIRY PDPLIKMNDT I QIDLETGK ...String:
MARGPKKHLK RVAAPKHWML DKLTSVFAPR PSTGPHKLRE CLPLIIFLRN KLKYALTGDE VKKICMQRFI KIDGKVRADI TYPAGFMDV ISIDKTGENF RLIYDTKGRF AVHRITPEEA KYKLCKVRKI FVGTKGIPHL VTHDARTIRY PDPLIKMNDT I QIDLETGK ITDFIKFDTG NLCMVTGGAN LGRIGVITNR ERHPGSFDVV HVKDANGNSF ATRLSNIFVI GKGNKPWISL PR GKGIRLT IAEERDKRLA AKQSSG

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Macromolecule #7: Ribosomal protein S5

MacromoleculeName: Ribosomal protein S5 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 21.525941 KDa
SequenceString:
TPDIKLFGKW STDDVQINDI SLQDYIAVKE KYAKYLPHSA GRYAAKRFRK AQCPIVERLT NSMMMHGRNN GKKLMTVRIV KHAFEIIHL LTGENPLQVL VNAIINSGPR EDSTRIGRAG TVRRQAVDVS PLRRVNQAIW LLCTGAREAA FRNIKTIAEC L ADELINAA KGSSNSYAIK KKDELERVAK SNR

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Macromolecule #8: 40S ribosomal protein S6

MacromoleculeName: 40S ribosomal protein S6 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 27.471535 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 AKRRRLSSL

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Macromolecule #9: ribosomal protein eS7

MacromoleculeName: ribosomal protein eS7 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 21.716387 KDa
SequenceString:
SAKIVKPNGE KPDEFESGIS QALLELEMNS DLKAQLRELN ITAAKEIEVG GGRKAIIIFV PVPQLKSFQK IQVRLVRELE KKFSGKHVV FIAQRRILPK PTRKSRTKNK QKRPRSRTLT AVHDAILEDL VFPSEIVGKR IRVKLDGSRL IKVHLDKAQQ N NVEHKVET FSGVYKKLTG KDVNFEFPEF QL

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Macromolecule #10: 40S ribosomal protein S8

MacromoleculeName: 40S ribosomal protein S8 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 23.902871 KDa
SequenceString: GISRDNWHKR RKTGGKRKPY HKKRKYELGR PAANTKIGPR RIHTVGVRGG NKKYRALRLD VGNFSWGSEC CTRKTRIIDV VYNASNNEL VRTKTLVKNC IVLIDSTPYR QWYESHYALP LGRKKGAKLT PEEEEILNKK RSKKIQKKYD ERKKNAKISS L LEEQFQQG ...String:
GISRDNWHKR RKTGGKRKPY HKKRKYELGR PAANTKIGPR RIHTVGVRGG NKKYRALRLD VGNFSWGSEC CTRKTRIIDV VYNASNNEL VRTKTLVKNC IVLIDSTPYR QWYESHYALP LGRKKGAKLT PEEEEILNKK RSKKIQKKYD ERKKNAKISS L LEEQFQQG KLLACIASRP GQCGRADGYV LEGKELEFYL RKIKARKG

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Macromolecule #11: Ribosomal protein S9 (Predicted)

MacromoleculeName: Ribosomal protein S9 (Predicted) / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 21.266166 KDa
SequenceString:
WVCRKTYVTP RRPFEKSRLD QELKLIGEYG LRNKREVWRV KFTLAKIRKA ARELLTLDEK DPRRLFEGNA LLRRLVRIGV LDEGKMKLD YILGLKIEDF LERRLQTQVF KLGLAKSIHH ARVLIRQRHI RVRKQVVNIP SFIVRLDSQK HIDFSLRSPY G GGRPGRVK RKNAKKGQGG AGAG

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Macromolecule #12: 40S ribosomal protein eS10

MacromoleculeName: 40S ribosomal protein eS10 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 11.773953 KDa
SequenceString:
MLMPKKNRIA IYELLFKEGV MVAKKDVHMP KHPELADKNV PNLHVMKAMQ SLKSRGYVKE QFAWRHFYWY LTNEGIQYLR DYLHLPPEI VPATLRRSR

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Macromolecule #13: Ribosomal protein S11

MacromoleculeName: Ribosomal protein S11 / type: protein_or_peptide / ID: 13 / 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

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Macromolecule #14: 40S ribosomal protein S12

MacromoleculeName: 40S ribosomal protein S12 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 13.766122 KDa
SequenceString:
GGVMDVNTAL QEVLKTALIH DGLARGIREA AKALDKRQAH LCVLASNCDE PMYVKLVEAL CAEHQINLIK VDDNKKLGEW VGLCKIDRE GKPRKVVGCS CVVVKDYGKE SQAKDVIEEY FKCKK

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Macromolecule #15: ribosomal protein uS15

MacromoleculeName: ribosomal protein uS15 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 17.128191 KDa
SequenceString:
GRMHAPGKGL SQSALPYRRS VPTWLKLTSD DVKEQIYKLA KKGLTPSQIG VILRDSHGVA QVRFVTGNKI LRILKSKGLA PDLPEDLYH LIKKAVAVRK HLERNRKDKD AKFRLILIES RIHRLARYYK TKRVLPPNWK YESSTASALV A

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Macromolecule #16: 40S ribosomal protein uS11

MacromoleculeName: 40S ribosomal protein uS11 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 14.544659 KDa
SequenceString:
SLGPQVAEGE NVFGVCHIFA SFNDTFVHVT DLSGKETICR VTGGMKVKAD RDESSPYAAM LAAQDVAQRC KELGITALHI KLRATGGNR TKTPGPGAQS ALRALARSGM KIGRIEDVTP IPSDSTRRKG GRRGRRL

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Macromolecule #17: ribosomal protein uS9

MacromoleculeName: ribosomal protein uS9 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 15.975753 KDa
SequenceString:
PLQSVQVFGR KKTATAVAHC KRGNGLIKVN GRPLEMIEPR TLQYKLLEPV LLLGKERFAG VDIRVRVKGG GHVAQIYAIR QSISKALVA YYQKYVDEAS KKEIKDILIQ YDRTLLVADP RRCESKKFGG PGARARYQKS YR

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Macromolecule #18: ribosomal protein eS17

MacromoleculeName: ribosomal protein eS17 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 14.578988 KDa
SequenceString:
MGRVRTKTVK KAARVIIEKY YTRLGNDFHT NKRVCEEIAI IPSKKLRNKI AGYVTHLMKR IQRGPVRGIS IKLQEEERER RDNYVPEVS ALDQEIIEVD PDTKEMLKLL DFGSLSNLQV TQPTVGM

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Macromolecule #19: 40S ribosomal protein eS19

MacromoleculeName: 40S ribosomal protein eS19 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 15.812286 KDa
SequenceString:
VTVKDVNQQE FVRALAAFLK KSGKLKVPEW VDTVKLAKHK ELAPYDENWF YTRAASTARH LYLRGGAGVG SMTKIYGGRQ RNGVMPSHF SRGSKSVARR VLQALEGLKM VEKDQDWGRK LTPQGQRDLD RIAGQVAAAK KK

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Macromolecule #20: Ribosomal_S10 domain-containing protein

MacromoleculeName: Ribosomal_S10 domain-containing protein / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 11.76589 KDa
SequenceString:
AIHRIRITLT SRNVKSLEKV CADLIRGAKE KNLKVKGPVR MPTKTLRITT RKTPCGEGSK TWDRFQMRIH KRLIDLHSPS EIVKQITSI SIEPGVEVEV TIADA

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Macromolecule #21: 40S ribosomal protein S21

MacromoleculeName: 40S ribosomal protein S21 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 8.896102 KDa
SequenceString:
MQSNAGEFVD LYVPRKCSAS NRIIGAKDHA SIPMNVAEVD KVTGRFNGQS KTYAICGAIR RMGESDDSIL RLAKSHGIVS QN

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Macromolecule #22: Ribosomal protein S15a

MacromoleculeName: Ribosomal protein S15a / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 14.734357 KDa
SequenceString:
VRMNVLADAL KSINNAEKRG KRQVLIRPCS KVIVRFLTVM MKHGYIGEFE IIDDHRAGKI VVNLTGRLNK CGVISPRFDV QLKDLEKWQ NNLLPSRQFG FIVLTTSAGI MDHEEARRKH TGGKILGFFF

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Macromolecule #23: 40S ribosomal protein uS12

MacromoleculeName: 40S ribosomal protein uS12 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 15.757587 KDa
SequenceString:
MGKCRGLRTA RKLRSHRRDQ KWHDKQYKKA HLGTALKANP FGGASHAKGI VLEKVGVEAK QPNSAIRKCV RVQLIKNGKK ITAFVPNDG CLNFIEENDE VLVAGFGRKG HAVGDIPGVR FKVVKVANVS LLALYKGKKE RPR

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Macromolecule #24: 40S ribosomal protein S24

MacromoleculeName: 40S ribosomal protein S24 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 14.575199 KDa
SequenceString:
DTVTIRTRKF MTNRLLQRKQ MVIDVLHPGK ATVPKTEIQE KLAKMYKTTP DVIFVFGFRT HFGGGKTTGF GMIYDSLDYA KKNEPKHRL ARHGLYEKKK TSRKQRKERK NRMKKVRGTA KANVGAG

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Macromolecule #25: 40S ribosomal protein eS26

MacromoleculeName: 40S ribosomal protein eS26 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 11.315428 KDa
SequenceString:
TKKRRNNGRA KKGRGHVQPI RCTNCACCVP KDKAIKKFVI RNIVEAAAVR DISEVSVFDA YVLPKLYVKL HYCVSCAIHS KVVRNRSRE ARKDRTPPPR

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Macromolecule #26: 40S ribosomal protein S27

MacromoleculeName: 40S ribosomal protein S27 / type: protein_or_peptide / ID: 26 / 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

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Macromolecule #27: ribosomal protein eS28

MacromoleculeName: ribosomal protein eS28 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 7.263394 KDa
SequenceString:
RVQPIKLARV TKVLGRTGSQ GQCTQVRVEF MDDTSRSIIR NVKGPVREGD VLTLLESERE ARRL

+
Macromolecule #28: ribosomal protein uS14

MacromoleculeName: ribosomal protein uS14 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 6.364426 KDa
SequenceString:
QQLYWSHPRK FGQGSRSCRV CSNRHGLIRK YGLNMCRQCF RQYAKDIGFI KLD

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Macromolecule #29: ribosomal protein eS31

MacromoleculeName: ribosomal protein eS31 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 8.358903 KDa
SequenceString:
KKSYTTPKKN KHKRKKVKLA VLKYYKVDEN GKISRLRREC PSDECGAGVF MASHFDRHYC GKCCLTYCFN K

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Macromolecule #30: ribosomal protein RACK1

MacromoleculeName: ribosomal protein RACK1 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 34.669113 KDa
SequenceString: TEQMTLRGTL KGHNGWVTQI ATTPQFPDMI LSASRDKTII MWKLTRDETN YGIPQRALRG HSHFVSDVVI SSDGQFALSG SWDGTLRLW DLTTGTTTRR FVGHTKDVLS VAFSSDNRQI VSGSRDKTIK LWNTLGVCKY TVQDESHSEW VSCVRFSPNS S NPIIVSCG ...String:
TEQMTLRGTL KGHNGWVTQI ATTPQFPDMI LSASRDKTII MWKLTRDETN YGIPQRALRG HSHFVSDVVI SSDGQFALSG SWDGTLRLW DLTTGTTTRR FVGHTKDVLS VAFSSDNRQI VSGSRDKTIK LWNTLGVCKY TVQDESHSEW VSCVRFSPNS S NPIIVSCG WDKLVKVWNL ANCKLKTNHI GHTGYLNTVT VSPDGSLCAS GGKDGQAMLW DLNEGKHLYT LDGGDIINAL CF SPNRYWL CAATGPSIKI WDLEGKIIVD ELKQEVISTS SKAEPPQCTS LAWSADGQTL FAGYTDNLVR VWQVTI

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Macromolecule #31: ribosomal protein eS25

MacromoleculeName: ribosomal protein eS25 / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 8.526119 KDa
SequenceString:
RDKLNNLVLF DKATYDKLCK EVPNYKLITP AVVSERLKIR GSLARAALQE LLSKGLIKLV SKHRAQVIYT RNTKG

+
Macromolecule #32: 40S ribosomal protein eS30

MacromoleculeName: 40S ribosomal protein eS30 / type: protein_or_peptide / ID: 32 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 6.741048 KDa
SequenceString:
KVHGSLARVG KVRGQTLKVA KQEKKKKRTG RAKRRMQYNR RFVNVVPTFG KKKGPNANS

+
Macromolecule #35: Eukaryotic translation initiation factor 2 subunit 1

MacromoleculeName: Eukaryotic translation initiation factor 2 subunit 1 / type: protein_or_peptide / ID: 35 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 30.633297 KDa
SequenceString: CRFYQHKFPE VEDVVMVNVR SIAEMGAYVS LLEYNNIEGM ILLSELSRRR IRSINKLIRI GRNECVVVIR VDKEKGYIDL SKRRVSPEE AIKCEDKFTK SKTVYSILRH VAEVLEYTKD EQLESLFQRT AWVFDDKYKR PGYGAYDAFK HAVSDPSILD S LDLNEDER ...String:
CRFYQHKFPE VEDVVMVNVR SIAEMGAYVS LLEYNNIEGM ILLSELSRRR IRSINKLIRI GRNECVVVIR VDKEKGYIDL SKRRVSPEE AIKCEDKFTK SKTVYSILRH VAEVLEYTKD EQLESLFQRT AWVFDDKYKR PGYGAYDAFK HAVSDPSILD S LDLNEDER EVLINNINRR LTPQAVKIRA DIEVACYGYE GIDAVKEALR AGLNCSTETM PIKINLIAPP RYVMTTTTLE RT EGLSVLN QAMAVIKEKI EEKRGVFNV

+
Macromolecule #36: eukaryotic translation initiation factor 2 subunit gamma

MacromoleculeName: eukaryotic translation initiation factor 2 subunit gamma
type: protein_or_peptide / ID: 36 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 45.862441 KDa
SequenceString: QATINIGTIG HVAHGKSTVV KAISGVHTVR FKNELERNIT IKLGYANAKI YKLDDPSCPR PECYRSCGSS TPDEFPTDIP GTKGNFKLV RHVSFVDCPG HDILMATMLN GAAVMDAALL LIAGNESCPQ PQTSEHLAAI EIMKLKHILI LQNKIDLVKE S QAKEQYEQ ...String:
QATINIGTIG HVAHGKSTVV KAISGVHTVR FKNELERNIT IKLGYANAKI YKLDDPSCPR PECYRSCGSS TPDEFPTDIP GTKGNFKLV RHVSFVDCPG HDILMATMLN GAAVMDAALL LIAGNESCPQ PQTSEHLAAI EIMKLKHILI LQNKIDLVKE S QAKEQYEQ ILAFVQGTVA EGAPIIPISA QLKYNIEVVC EYIVKKIPVP PRDFTSEPRL IVIRSFDVNK PGCEVDDLKG GV AGGSILK GVLKVGQEIE VRPGIVSKDS EGKLMCKPIF SKIVSLFAEH NDLQYAAPGG LIGVGTKIDP TLCRADRMVG QVL GAVGAL PEIFTELEIS YFLLRRLLGV RTEGDKKAAK VQKLSKNEVL MVNIGSLSTG GRVSAVKADL GKIVLTNPVC TEVG EKIAL SRRVEKHWRL IGWGQIR

+
Macromolecule #37: 40S ribosomal protein uS13

MacromoleculeName: 40S ribosomal protein uS13 / type: protein_or_peptide / ID: 37 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 16.642307 KDa
SequenceString:
PEKFQHILRV LNTNIDGRRK IAFAITAIKG VGRRYAHVVL RKADIDLTKR AGELTEDEVE RVITIMQNPR QYKIPDWFLN RQKDVKDGK YSQVLANGLD NKLREDLERL KKIRAHRGLR HFWGLRVRGQ HTKTTGRRGR TVG

+
Macromolecule #38: Ribosomal protein S15

MacromoleculeName: Ribosomal protein S15 / type: protein_or_peptide / ID: 38 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 15.873732 KDa
SequenceString:
VEQKKKRTFR KFTYRGVDLD QLLDMSYEQL MQLYSARQRR RLSRGLRRKQ HSLLKRLRKA KKEAPPMEKP EVVKTHLRDM IILPEMVGS MVGVYNGKTF NQVEIKPEMI GHYLGEFSIT YKPVKHGRPG IGATHS

+
Macromolecule #33: 18S ribosomal RNA

MacromoleculeName: 18S ribosomal RNA / type: rna / ID: 33 / Details: U at position 1244 is modified / Number of copies: 1
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 601.015688 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 CGACGGCGCU GACUCCCUUU GUGUGGGAUG CGUGCAUUUA UCAGAUCAAA ACCAACCCGG UC AGCCUCC CCGCCGGCCG GGGGGGUGGG GCGGCGGCUU UGGUGACUCU AGAUAACCUC GGGCCGAUCG CAGCCCUCCG UGG CGGCGA CGACCCAUUC GAACGUCUGC CCUAUCAACU UUCGAUGGUA GUCGCCGUGC CUACCAUGGU GACCACGGGU GACG GGGAA UCAGGGUUCG AUUCCGGAGA GGGAGCCUGA GAAACGGCUA CCACAUCCAA GGAAGGCAGC AGGCGCGCAA AUUAC CCAC UCCCGACCCG GGGAGGUAGU GACGAAAAAU AACAAUACAG GACUCUUUCG AGGCCCUGUA AUUGGAAUGA GUCCAC UUU AAAUCCUUUA ACGAGGAUCC AUUGGAGGGC AAGUCUGGUC GCAGCAGCCG CGGUAAUUCC AGCUCCAAUA GCGUAUA UU AAAGUUGCUG CAGUUAAAAA GCUCGUAGUU GGAUCUUGUG GAGGGUGCGU AGCGGGCGGU CCGCCGCGAG GCGAGCCA C CGCCCGUCCC CGCCCCUUGC CUCUCGGCGC CCCCUCGAUG CUCUUAGCUG AGUGUCCCGC GGGGCCCGAA GCGUUUACU UUGAAAAAAU UAGAGUGUUC AAAGCAGGCC CGAGCCGCCU GGAUACCGCA GCUAGGAAUA AUGGAAUAGG ACCGCGGUUC UAUUUUGUU GGUUUUCGGA ACUGAGGCCA UGAUUAAGAG GGACGGCCGG GGGCAUUCGU AUUGCGCCGC UAGAGGUGAA A UUCUUGGA CCGGCGCAAG ACGGACCAGA GCGAAAGCAU UUGCCAAGAA UGUUUUCAUU AAUCAAGAAC GAAAGUCGGA GG UUCGAAG ACGAUCAGAU ACCGUCGUAG UUCCGACCAU AAACGAUGCC GACUGGCGAU GCGGCGGCGU UAUUCCCAUG ACC CGCCGG GCAGCUUCCG GGAAACCAAA GUCUUUGGGU UCCGGGGGGA GUAUGGUUGC AAAGCUGAAA CUUAAAGGAA UUGA CGGAA GGGCACCACC AGGAGUGGAG CCUGCGGCUU AAUUUGAC(C4J)C AACACGGGAA ACCUCACCCG GCCCGGACAC G GACAGGAU UGACAGAUUG AUAGCUCUUU CUCGAUUCUG UGGGUGGUGG UGCAUGGCCG UUCUUAGUUG GUGGAGCGAU UU GUCUGGU UAAUUCCGAU AACGAACGAG ACUCUGGCAU GCUAACUAGU UACGCGACCC CCGAGCGGUC GGCGUCCCCC AAC UUCUUA GAGGGACAAG UGGCGUUCAG CCACCCGAGA UUGAGCAAUA ACAGGUCUGU GAUGCCCUUA GAUGUCGGGG CUGC ACGCG CGCUACACUG ACUGGCUCAG CGUGUGCCUA CCCUACGCCG GCAGGCGCGG GUAACCCGUU GAACCCCAUU CGUGA UGGG GAUCGGGGAU UGCAAUUAUU CCCCAUGAAC GAGGAAUUCC CAGUAAGUGC GGGUCAUAAG CUUGCGUUGA UUAAGU CCC UGCCCUUUGU ACACACCGCC CGUCGCUACU ACCGAUUGGA UGGUUUAGUG AGGCCCUCGG AUCGGCCCGC CGGGGUC GG CCCACGGCCC UGGCGGAGCG CUGAGAAGAC GGUCGAACUU GACUAUCUAG AGGAAGUAAA AGUCGUAACA AGGUUUCC G UAGGUGAACC UGCGGAAGGA UCAUUA

+
Macromolecule #34: histone 4 (H4) mRNA

MacromoleculeName: histone 4 (H4) mRNA / type: rna / ID: 34 / Number of copies: 1
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.685985 KDa
SequenceString:
GGUCAUAACC AUGUCUGGAC GUGGCAAGGG UGGUAA

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Macromolecule #39: initiator methionylated tRNA

MacromoleculeName: initiator methionylated tRNA / type: rna / ID: 39
Details: adenine at position 37 is modified (threonyl-carbomoyl-adenosine (t6A))
Number of copies: 1
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 24.376625 KDa
SequenceString:
AGCAGAGUGG CGCAGCGGAA GCGUGCUGGG CCCAU(T6A)ACCC AGAGGUCGAU GGAUCGAAAC CAUCCUCUGC UACCA

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Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
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) / Detector mode: SUPER-RESOLUTION / Average electron dose: 26.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5k0y

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 372000

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-6yan:
Mammalian 48S late-stage translation initiation complex with histone 4 mRNA

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