[English] 日本語
Yorodumi
- EMDB-3770: Human 40S-eIF2D-re-initiation complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3770
TitleHuman 40S-eIF2D-re-initiation complex
Map dataThis map was used for refinement (boxed and map origin re-set to 0).
Sample
  • Complex: human translation re-initiation complex of eIFD, initiator tRNA and the small ribosomal subunit
    • Complex: eIF2D
      • Protein or peptide: x 1 types
    • Complex: small ribosomal subunit
      • RNA: x 1 types
      • Protein or peptide: x 34 types
    • Complex: HCV IRES mRNA
      • RNA: x 1 types
    • Complex: initiator Met-tRNA-i
      • RNA: x 1 types
  • Ligand: x 1 types
Function / homology
Function and homology information


IRES-dependent viral translational initiation / ribosome disassembly / formation of translation preinitiation complex / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / nucleolus organization / response to extracellular stimulus / positive regulation of endodeoxyribonuclease activity ...IRES-dependent viral translational initiation / ribosome disassembly / formation of translation preinitiation complex / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / nucleolus organization / response to extracellular stimulus / positive regulation of endodeoxyribonuclease activity / TNFR1-mediated ceramide production / negative regulation of RNA splicing / neural crest cell differentiation / rRNA modification in the nucleus and cytosol / regulation of establishment of cell polarity / positive regulation of ubiquitin-protein transferase activity / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / pigmentation / protein tyrosine kinase inhibitor activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / IRE1-RACK1-PP2A complex / ion channel inhibitor activity / positive regulation of Golgi to plasma membrane protein transport / negative regulation of DNA repair / Translation initiation complex formation / oxidized purine DNA binding / negative regulation of Wnt signaling pathway / supercoiled DNA binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / NF-kappaB complex / negative regulation of phagocytosis / fibroblast growth factor binding / ubiquitin-like protein conjugating enzyme binding / regulation of cell division / SARS-CoV-1 modulates host translation machinery / Protein hydroxylation / TOR signaling / iron-sulfur cluster binding / mTORC1-mediated signalling / protein kinase A binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Peptide chain elongation / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / monocyte chemotaxis / Formation of a pool of free 40S subunits / ubiquitin ligase inhibitor activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / Eukaryotic Translation Termination / phagocytic cup / positive regulation of mitochondrial depolarization / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of T cell receptor signaling pathway / Viral mRNA Translation / positive regulation of activated T cell proliferation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / negative regulation of respiratory burst involved in inflammatory response / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / BH3 domain binding / 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) / regulation of translational fidelity / cysteine-type endopeptidase activator activity involved in apoptotic process / ribosomal small subunit export from nucleus / Protein methylation / Nuclear events stimulated by ALK signaling in cancer / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translation regulator activity / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / positive regulation of cell cycle / stress granule assembly / translation initiation factor binding / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / maturation of SSU-rRNA / rough endoplasmic reticulum / laminin binding / Mitotic Prometaphase / gastrulation / spindle assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / EML4 and NUDC in mitotic spindle formation / positive regulation of apoptotic signaling pathway / positive regulation of JUN kinase activity / signaling adaptor activity / MDM2/MDM4 family protein binding / translational initiation / : / DNA-(apurinic or apyrimidinic site) endonuclease activity / Resolution of Sister Chromatid Cohesion
Similarity search - Function
Eukaryotic translation initiation factor 2D, SUI1 domain / : / : / Eukaryotic translation initiation factor 2D / Pre-PUA domain / Pre-PUA-like domain / SUI1 domain superfamily / Translation initiation factor SUI1 / Translation initiation factor SUI1 family profile. / SUI1 domain ...Eukaryotic translation initiation factor 2D, SUI1 domain / : / : / Eukaryotic translation initiation factor 2D / Pre-PUA domain / Pre-PUA-like domain / SUI1 domain superfamily / Translation initiation factor SUI1 / Translation initiation factor SUI1 family profile. / SUI1 domain / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / PUA domain profile. / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / PUA-like superfamily / : / Ribosomal protein S26e signature. / : / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / 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 S2, eukaryotic / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S10, eukaryotic/archaeal / 40S Ribosomal protein S10 / S27a-like superfamily / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a / : / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S8e subdomain, eukaryotes / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S7e signature. / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S27e signature. / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S19A/S15e / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S6, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal protein S7e / Ribosomal protein S7e / 40S ribosomal protein S11, N-terminal / Ribosomal protein S4, KOW domain / Ribosomal_S17 N-terminal / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S24e / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S24e / Ribosomal protein S27 / Ribosomal protein S27 / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature.
Similarity search - Domain/homology
Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein eS19 / Eukaryotic translation initiation factor 2D / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS7 ...Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein eS19 / Eukaryotic translation initiation factor 2D / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein eS4, X isoform / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS26 / Small ribosomal subunit protein eS28 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein eS32 / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein RACK1 / Ubiquitin carboxyl extension protein 80
Similarity search - Component
Biological speciesHomo sapiens (human) / Hepatitis C virus / Saccharomyces cerevisiae (brewer's yeast) / Human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsWeisser M / Schaefer T / Leibundgut M / Boehringer D / Aylett CHS / Ban N
CitationJournal: Mol Cell / Year: 2017
Title: Structural and Functional Insights into Human Re-initiation Complexes.
Authors: Melanie Weisser / Tanja Schäfer / Marc Leibundgut / Daniel Böhringer / Christopher Herbert Stanley Aylett / Nenad Ban /
Abstract: After having translated short upstream open reading frames, ribosomes can re-initiate translation on the same mRNA. This process, referred to as re-initiation, controls the translation of a large ...After having translated short upstream open reading frames, ribosomes can re-initiate translation on the same mRNA. This process, referred to as re-initiation, controls the translation of a large fraction of mammalian cellular mRNAs, many of which are important in cancer. Key ribosomal binding proteins involved in re-initiation are the eukaryotic translation initiation factor 2D (eIF2D) or the homologous complex of MCT-1/DENR. We determined the structures of these factors bound to the human 40S ribosomal subunit in complex with initiator tRNA positioned on an mRNA start codon in the P-site using a combination of cryoelectron microscopy and X-ray crystallography. The structures, supported by biochemical experiments, reveal how eIF2D emulates the function of several canonical translation initiation factors by using three independent, flexibly connected RNA binding domains to simultaneously monitor codon-anticodon interactions in the ribosomal P-site and position the initiator tRNA.
History
DepositionJun 20, 2017-
Header (metadata) releaseAug 9, 2017-
Map releaseAug 9, 2017-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5oa3
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_3770.map.gz / Format: CCP4 / Size: 28.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis map was used for refinement (boxed and map origin re-set to 0).
Voxel sizeX=Y=Z: 1.4 Å
Density
Contour LevelBy AUTHOR: 0.09 / Movie #1: 0.12
Minimum - Maximum-0.64837015 - 0.8811471
Average (Standard dev.)0.007678762 (±0.047832664)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions196196196
Spacing196196196
CellA=B=C: 274.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z196196196
origin x/y/z0.0000.0000.000
length x/y/z274.400274.400274.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS196196196
D min/max/mean-0.6480.8810.008

-
Supplemental data

-
Additional map: This map was low-pass filtered to 8 Angstroem...

Fileemd_3770_additional.map
AnnotationThis map was low-pass filtered to 8 Angstroem and used for the visualization of secondary structure elements (boxed and map origin re-set to 0).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: unboxed, unfiltered half-map; origin not re-set.

Fileemd_3770_half_map_1.map
Annotationunboxed, unfiltered half-map; origin not re-set.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: unboxed, unfiltered half-map; origin not re-set.

Fileemd_3770_half_map_2.map
Annotationunboxed, unfiltered half-map; origin not re-set.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

+
Entire : human translation re-initiation complex of eIFD, initiator tRNA a...

EntireName: human translation re-initiation complex of eIFD, initiator tRNA and the small ribosomal subunit
Components
  • Complex: human translation re-initiation complex of eIFD, initiator tRNA and the small ribosomal subunit
    • Complex: eIF2D
      • Protein or peptide: Eukaryotic translation initiation factor 2D
    • Complex: small ribosomal subunit
      • RNA: 18S ribosomal RNA
      • Protein or peptide: 40S ribosomal protein SA
      • Protein or peptide: 40S ribosomal protein S3a
      • Protein or peptide: 40S ribosomal protein S2
      • Protein or peptide: 40S ribosomal protein S3
      • Protein or peptide: 40S ribosomal protein S4, X isoformRibosome
      • Protein or peptide: 40S ribosomal protein S5
      • Protein or peptide: 40S ribosomal protein S6
      • Protein or peptide: 40S ribosomal protein S7
      • Protein or peptide: 40S ribosomal protein S8
      • Protein or peptide: 40S ribosomal protein S9
      • Protein or peptide: 40S ribosomal protein S10
      • Protein or peptide: 40S ribosomal protein S11
      • Protein or peptide: 40S ribosomal protein S12
      • Protein or peptide: 40S ribosomal protein S13
      • Protein or peptide: 40S ribosomal protein S14
      • Protein or peptide: 40S ribosomal protein S15
      • Protein or peptide: 40S ribosomal protein S16
      • Protein or peptide: 40S ribosomal protein S17
      • Protein or peptide: 40S ribosomal protein S18
      • Protein or peptide: 40S ribosomal protein S19
      • Protein or peptide: 40S ribosomal protein S20
      • Protein or peptide: 40S ribosomal protein S21
      • Protein or peptide: 40S ribosomal protein S15a
      • Protein or peptide: 40S ribosomal protein S23
      • Protein or peptide: 40S ribosomal protein S24
      • Protein or peptide: 40S ribosomal protein S25
      • Protein or peptide: 40S ribosomal protein S26
      • Protein or peptide: 40S ribosomal protein S27
      • Protein or peptide: 40S ribosomal protein S28
      • Protein or peptide: 40S ribosomal protein S29
      • Protein or peptide: 40S ribosomal protein S30
      • Protein or peptide: Ribosomal protein S27aRibosome
      • Protein or peptide: Receptor of activated protein C kinase 1
      • Protein or peptide: RIBOSOMAL PROTEIN EL41
    • Complex: HCV IRES mRNA
      • RNA: IRES mRNA
    • Complex: initiator Met-tRNA-i
      • RNA: initiator Met-tRNA-i
  • Ligand: ZINC ION

+
Supramolecule #1: human translation re-initiation complex of eIFD, initiator tRNA a...

SupramoleculeName: human translation re-initiation complex of eIFD, initiator tRNA and the small ribosomal subunit
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#38
Molecular weightTheoretical: 1.4 MDa

+
Supramolecule #2: eIF2D

SupramoleculeName: eIF2D / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

+
Supramolecule #3: small ribosomal subunit

SupramoleculeName: small ribosomal subunit / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3, #5-#38
Source (natural)Organism: Homo sapiens (human)

+
Supramolecule #4: HCV IRES mRNA

SupramoleculeName: HCV IRES mRNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Hepatitis C virus
Recombinant expressionOrganism: Synthetic construct (others)

+
Supramolecule #5: initiator Met-tRNA-i

SupramoleculeName: initiator Met-tRNA-i / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

+
Macromolecule #1: Eukaryotic translation initiation factor 2D

MacromoleculeName: Eukaryotic translation initiation factor 2D / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 64.788301 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MFAKAFRVKS NTAIKGSDRR KLRADVTTAF PTLGTDQVSE LVPGKEELNI VKLYAHKGDA VTVYVSGGNP ILFELEKNLY PTVYTLWSY PDLLPTFTTW PLVLEKLVGG ADLMLPGLVM PPAGLPQVQK GDLCAISLVG NRAPVAIGVA AMSTAEMLTS G LKGRGFSV ...String:
MFAKAFRVKS NTAIKGSDRR KLRADVTTAF PTLGTDQVSE LVPGKEELNI VKLYAHKGDA VTVYVSGGNP ILFELEKNLY PTVYTLWSY PDLLPTFTTW PLVLEKLVGG ADLMLPGLVM PPAGLPQVQK GDLCAISLVG NRAPVAIGVA AMSTAEMLTS G LKGRGFSV LHTYQDHLWR SGNKSSPPSI APLALDSADL SEEKGSVQMD STLQGDMRHM TLEGEEENGE VHQAREDKSL SE APEDTST RGLNQDSTDS KTLQEQMDEL LQQCFLHALK CRVKKADLPL LTSTFLGSHM FSCCPEGRQL DIKKSSYKKL SKF LQQMQQ EQIIQVKELS KGVESIVAVD WKHPRITSFV IPEPSPTSQT IQEGSREQPY HPPDIKPLYC VPASMTLLFQ ESGH KKGSF LEGSEVRTIV INYAKKNDLV DADNKNLVRL DPILCDCILE KNEQHTVMKL PWDSLLTRCL EKLQPAYQVT LPGQE PIVK KGRICPIDIT LAQRASNKKV TVVRNLEAYG LDPYSVAAIL QQRCQASTTV NPAPGAKDSL QVQIQGNQVH HLGWLL LEE YQLPRKHIQG LEKALKPGKK K

+
Macromolecule #5: 40S ribosomal protein SA

MacromoleculeName: 40S ribosomal protein SA / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 32.883938 KDa
SequenceString: MSGALDVLQM KEEDVLKFLA AGTHLGGTNL DFQMEQYIYK RKSDGIYIIN LKRTWEKLLL AARAIVAIEN PADVSVISSR NTGQRAVLK FAAATGATPI AGRFTPGTFT NQIQAAFREP RLLVVTDPRA DHQPLTEASY VNLPTIALCN TDSPLRYVDI A IPCNNKGA ...String:
MSGALDVLQM KEEDVLKFLA AGTHLGGTNL DFQMEQYIYK RKSDGIYIIN LKRTWEKLLL AARAIVAIEN PADVSVISSR NTGQRAVLK FAAATGATPI AGRFTPGTFT NQIQAAFREP RLLVVTDPRA DHQPLTEASY VNLPTIALCN TDSPLRYVDI A IPCNNKGA HSVGLMWWML AREVLRMRGT ISREHPWEVM PDLYFYRDPE EIEKEEQAAA EKAVTKEEFQ GEWTAPAPEF TA TQPEVAD WSEGVQVPSV PIQQFPTEDW SAQPATEDWS AAPTAQATEW VGATTDWS

+
Macromolecule #6: 40S ribosomal protein S3a

MacromoleculeName: 40S ribosomal protein S3a / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
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

+
Macromolecule #7: 40S ribosomal protein S2

MacromoleculeName: 40S ribosomal protein S2 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 31.376516 KDa
SequenceString: MADDAGAAGG PGGPGGPGMG NRGGFRGGFG SGIRGRGRGR GRGRGRGRGA RGGKAEDKEW MPVTKLGRLV KDMKIKSLEE IYLFSLPIK ESEIIDFFLG ASLKDEVLKI MPVQKQTRAG QRTRFKAFVA IGDYNGHVGL GVKCSKEVAT AIRGAIILAK L SIVPVRRG ...String:
MADDAGAAGG PGGPGGPGMG NRGGFRGGFG SGIRGRGRGR GRGRGRGRGA RGGKAEDKEW MPVTKLGRLV KDMKIKSLEE IYLFSLPIK ESEIIDFFLG ASLKDEVLKI MPVQKQTRAG QRTRFKAFVA IGDYNGHVGL GVKCSKEVAT AIRGAIILAK L SIVPVRRG YWGNKIGKPH TVPCKVTGRC GSVLVRLIPA PRGTGIVSAP VPKKLLMMAG IDDCYTSARG CTATLGNFAK AT FDAISKT YSYLTPDLWK ETVFTKSPYQ EFTDHLVKTH TRVSVQRTQA PAVATT

+
Macromolecule #8: 40S ribosomal protein S3

MacromoleculeName: 40S ribosomal protein S3 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-(apurinic or apyrimidinic site) lyase
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 26.729369 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 MLPWDPTGKI GPKKPLPDHV SIVEPKDEIL PTTPISEQKG GKPEPPAMPQ PV PTA

+
Macromolecule #9: 40S ribosomal protein S4, X isoform

MacromoleculeName: 40S ribosomal protein S4, X isoform / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
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 #10: 40S ribosomal protein S5

MacromoleculeName: 40S ribosomal protein S5 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
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 #11: 40S ribosomal protein S6

MacromoleculeName: 40S ribosomal protein S6 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
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 #12: 40S ribosomal protein S7

MacromoleculeName: 40S ribosomal protein S7 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 22.168914 KDa
SequenceString: MFSSSAKIVK PNGEKPDEFE SGISQALLEL EMNSDLKAQL RELNITAAKE IEVGGGRKAI IIFVPVPQLK SFQKIQVRLV RELEKKFSG KHVVFIAQRR ILPKPTRKSR TKNKQKRPRS RTLTAVHDAI LEDLVFPSEI VGKRIRVKLD GSRLIKVHLD K AQQNNVEH ...String:
MFSSSAKIVK PNGEKPDEFE SGISQALLEL EMNSDLKAQL RELNITAAKE IEVGGGRKAI IIFVPVPQLK SFQKIQVRLV RELEKKFSG KHVVFIAQRR ILPKPTRKSR TKNKQKRPRS RTLTAVHDAI LEDLVFPSEI VGKRIRVKLD GSRLIKVHLD K AQQNNVEH KVETFSGVYK KLTGKDVNFE FPEFQL

+
Macromolecule #13: 40S ribosomal protein S8

MacromoleculeName: 40S ribosomal protein S8 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
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 #14: 40S ribosomal protein S9

MacromoleculeName: 40S ribosomal protein S9 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
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 #15: 40S ribosomal protein S10

MacromoleculeName: 40S ribosomal protein S10 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 18.933846 KDa
SequenceString:
MLMPKKNRIA IYELLFKEGV MVAKKDVHMP KHPELADKNV PNLHVMKAMQ SLKSRGYVKE QFAWRHFYWY LTNEGIQYLR DYLHLPPEI VPATLRRSRP ETGRPRPKGL EGERPARLTR GEADRDTYRR SAVPPGADKK AEAGAGSATE FQFRGGFGRG R GQPPQ

+
Macromolecule #16: 40S ribosomal protein S11

MacromoleculeName: 40S ribosomal protein S11 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 18.468826 KDa
SequenceString:
MADIQTERAY QKQPTIFQNK KRVLLGETGK EKLPRYYKNI GLGFKTPKEA IEGTYIDKKC PFTGNVSIRG RILSGVVTKM KMQRTIVIR RDYLHYIRKY NRFEKRHKNM SVHLSPCFRD VQIGDIVTVG ECRPLSKTVR FNVLKVTKAA GTKKQFQKF

+
Macromolecule #17: 40S ribosomal protein S12

MacromoleculeName: 40S ribosomal protein S12 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 14.538987 KDa
SequenceString:
MAEEGIAAGG VMDVNTALQE VLKTALIHDG LARGIREAAK ALDKRQAHLC VLASNCDEPM YVKLVEALCA EHQINLIKVD DNKKLGEWV GLCKIDREGK PRKVVGCSCV VVKDYGKESQ AKDVIEEYFK CKK

+
Macromolecule #18: 40S ribosomal protein S13

MacromoleculeName: 40S ribosomal protein S13 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 17.259389 KDa
SequenceString:
MGRMHAPGKG LSQSALPYRR SVPTWLKLTS DDVKEQIYKL AKKGLTPSQI GVILRDSHGV AQVRFVTGNK ILRILKSKGL APDLPEDLY HLIKKAVAVR KHLERNRKDK DAKFRLILIE SRIHRLARYY KTKRVLPPNW KYESSTASAL VA

+
Macromolecule #19: 40S ribosomal protein S14

MacromoleculeName: 40S ribosomal protein S14 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 16.302772 KDa
SequenceString:
MAPRKGKEKK EEQVISLGPQ VAEGENVFGV CHIFASFNDT FVHVTDLSGK ETICRVTGGM KVKADRDESS PYAAMLAAQD VAQRCKELG ITALHIKLRA TGGNRTKTPG PGAQSALRAL ARSGMKIGRI EDVTPIPSDS TRRKGGRRGR RL

+
Macromolecule #20: 40S ribosomal protein S15

MacromoleculeName: 40S ribosomal protein S15 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 17.076207 KDa
SequenceString:
MAEVEQKKKR TFRKFTYRGV DLDQLLDMSY EQLMQLYSAR QRRRLNRGLR RKQHSLLKRL RKAKKEAPPM EKPEVVKTHL RDMIILPEM VGSMVGVYNG KTFNQVEIKP EMIGHYLGEF SITYKPVKHG RPGIGATHSS RFIPLK

+
Macromolecule #21: 40S ribosomal protein S16

MacromoleculeName: 40S ribosomal protein S16 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 16.477377 KDa
SequenceString:
MPSKGPLQSV QVFGRKKTAT AVAHCKRGNG LIKVNGRPLE MIEPRTLQYK LLEPVLLLGK ERFAGVDIRV RVKGGGHVAQ IYAIRQSIS KALVAYYQKY VDEASKKEIK DILIQYDRTL LVADPRRCES KKFGGPGARA RYQKSYR

+
Macromolecule #22: 40S ribosomal protein S17

MacromoleculeName: 40S ribosomal protein S17 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 15.578156 KDa
SequenceString:
MGRVRTKTVK KAARVIIEKY YTRLGNDFHT NKRVCEEIAI IPSKKLRNKI AGYVTHLMKR IQRGPVRGIS IKLQEEERER RDNYVPEVS ALDQEIIEVD PDTKEMLKLL DFGSLSNLQV TQPTVGMNFK TPRGPV

+
Macromolecule #23: 40S ribosomal protein S18

MacromoleculeName: 40S ribosomal protein S18 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 17.759777 KDa
SequenceString:
MSLVIPEKFQ HILRVLNTNI DGRRKIAFAI TAIKGVGRRY AHVVLRKADI DLTKRAGELT EDEVERVITI MQNPRQYKIP DWFLNRQKD VKDGKYSQVL ANGLDNKLRE DLERLKKIRA HRGLRHFWGL RVRGQHTKTT GRRGRTVGVS KKK

+
Macromolecule #24: 40S ribosomal protein S19

MacromoleculeName: 40S ribosomal protein S19 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 16.091562 KDa
SequenceString:
MPGVTVKDVN QQEFVRALAA FLKKSGKLKV PEWVDTVKLA KHKELAPYDE NWFYTRAAST ARHLYLRGGA GVGSMTKIYG GRQRNGVMP SHFSRGSKSV ARRVLQALEG LKMVEKDQDG GRKLTPQGQR DLDRIAGQVA AANKKH

+
Macromolecule #25: 40S ribosomal protein S20

MacromoleculeName: 40S ribosomal protein S20 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 13.398763 KDa
SequenceString:
MAFKDTGKTP VEPEVAIHRI RITLTSRNVK SLEKVCADLI RGAKEKNLKV KGPVRMPTKT LRITTRKTPC GEGSKTWDRF QMRIHKRLI DLHSPSEIVK QITSISIEPG VEVEVTIADA

+
Macromolecule #26: 40S ribosomal protein S21

MacromoleculeName: 40S ribosomal protein S21 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 9.124389 KDa
SequenceString:
MQNDAGEFVD LYVPRKCSAS NRIIGAKDHA SIQMNVAEVD KVTGRFNGQF KTYAICGAIR RMGESDDSIL RLAKADGIVS KNF

+
Macromolecule #27: 40S ribosomal protein S15a

MacromoleculeName: 40S ribosomal protein S15a / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 14.865555 KDa
SequenceString:
MVRMNVLADA LKSINNAEKR GKRQVLIRPC SKVIVRFLTV MMKHGYIGEF EIIDDHRAGK IVVNLTGRLN KCGVISPRFD VQLKDLEKW QNNLLPSRQF GFIVLTTSAG IMDHEEARRK HTGGKILGFF F

+
Macromolecule #28: 40S ribosomal protein S23

MacromoleculeName: 40S ribosomal protein S23 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 15.844666 KDa
SequenceString:
MGKCRGLRTA RKLRSHRRDQ KWHDKQYKKA HLGTALKANP FGGASHAKGI VLEKVGVEAK QPNSAIRKCV RVQLIKNGKK ITAFVPNDG CLNFIEENDE VLVAGFGRKG HAVGDIPGVR FKVVKVANVS LLALYKGKKE RPRS

+
Macromolecule #29: 40S ribosomal protein S24

MacromoleculeName: 40S ribosomal protein S24 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 15.107924 KDa
SequenceString:
MNDTVTIRTR KFMTNRLLQR KQMVIDVLHP GKATVPKTEI REKLAKMYKT TPDVIFVFGF RTHFGGGKTT GFGMIYDSLD YAKKNEPKH RLARHGLYEK KKTSRKQRKE RKNRMKKVRG TAKANVGAGK K

+
Macromolecule #30: 40S ribosomal protein S25

MacromoleculeName: 40S ribosomal protein S25 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 13.776224 KDa
SequenceString:
MPPKDDKKKK DAGKSAKKDK DPVNKSGGKA KKKKWSKGKV RDKLNNLVLF DKATYDKLCK EVPNYKLITP AVVSERLKIR GSLARAALQ ELLSKGLIKL VSKHRAQVIY TRNTKGGDAP AAGEDA

+
Macromolecule #31: 40S ribosomal protein S26

MacromoleculeName: 40S ribosomal protein S26 / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 11.645794 KDa
SequenceString:
TKKRRNNGRA KKGRGHVQPI RCTNCARCVP KDKAIKKFVI RNIVEAAAVR DISEASVFDA YVLPKLYVKL HYCVSCAIHS KVVRNRSRE ARKDRTPPPR FR

+
Macromolecule #32: 40S ribosomal protein S27

MacromoleculeName: 40S ribosomal protein S27 / type: protein_or_peptide / ID: 32 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 9.210843 KDa
SequenceString:
PLAKDLLHPS PEEEKRKHKK KRLVQSPNSY FMDVKCPGCY KITTVFSHAQ TVVLCVGCST VLCQPTGGKA RLTEGCSFRR KQ

+
Macromolecule #33: 40S ribosomal protein S28

MacromoleculeName: 40S ribosomal protein S28 / type: protein_or_peptide / ID: 33 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 6.87894 KDa
SequenceString:
PIKLARVTKV LGRTGSQGQC TQVRVEFMDD TSRSIIRNVK GPVREGDVLT LLESEREARR L

+
Macromolecule #34: 40S ribosomal protein S29

MacromoleculeName: 40S ribosomal protein S29 / type: protein_or_peptide / ID: 34 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 6.559625 KDa
SequenceString:
GHQQLYWSHP RKFGQGSRSC RVCSNRHGLI RKYGLNMCRQ CFRQYAKDIG FIKLD

+
Macromolecule #35: 40S ribosomal protein S30

MacromoleculeName: 40S ribosomal protein S30 / type: protein_or_peptide / ID: 35 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 6.30248 KDa
SequenceString:
GSLARAGKVR GQTPKVAKQE KKKKKTGRAK RRMQYNRRFV NVVPTFGKKK GPNANS

+
Macromolecule #36: Ribosomal protein S27a

MacromoleculeName: Ribosomal protein S27a / type: protein_or_peptide / ID: 36 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 8.45315 KDa
SequenceString:
KKRKKKSCTT PKKNKHKRKK VKLAVLKYYK VDENGKISRL RRECPSDECG AGVFMASHFD RHYCGKCCLT YC

+
Macromolecule #37: Receptor of activated protein C kinase 1

MacromoleculeName: Receptor of activated protein C kinase 1 / type: protein_or_peptide / ID: 37 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 34.857355 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 RVWQVTIG

+
Macromolecule #38: RIBOSOMAL PROTEIN EL41

MacromoleculeName: RIBOSOMAL PROTEIN EL41 / type: protein_or_peptide / ID: 38 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 3.342255 KDa
SequenceString:
RAKWRKKRMR RLKRKRRKMR QRSK

+
Macromolecule #2: initiator Met-tRNA-i

MacromoleculeName: initiator Met-tRNA-i / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 24.2385 KDa
SequenceString:
AGCGCCGUGG CGCAGUGGAA GCGCGCAGGG CUCAUAACCC UGAUGUCCUC GGAUCGAAAC CGAGCGGCGC UACCA

+
Macromolecule #3: 18S ribosomal RNA

MacromoleculeName: 18S ribosomal RNA / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 602.472688 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 CCUCUCCGGC CCCGGCCGGG GGGCGGGCCG CGGCGGCUUU GGUGACUCUA GAUAACCUCG GGCCGAUCGC ACG CCCCCC GUGGCGGCGA CGACCCAUUC GAACGUCUGC CCUAUCAACU UUCGAUGGUA GUCGCCGUGC CUACCAUGGU GACC ACGGG UGACGGGGAA UCAGGGUUCG AUUCCGGAGA GGGAGCCUGA GAAACGGCUA CCACAUCCAA GGAAGGCAGC AGGCG CGCA AAUUACCCAC UCCCGACCCG GGGAGGUAGU GACGAAAAAU AACAAUACAG GACUCUUUCG AGGCCCUGUA AUUGGA AUG AGUCCACUUU AAAUCCUUUA ACGAGGAUCC AUUGGAGGGC AAGUCUGGUG CCAGCAGCCG CGGUAAUUCC AGCUCCA AU AGCGUAUAUU AAAGUUGCUG CAGUUAAAAA GCUCGUAGUU GGAUCUUGGG AGCGGGCGGG CGGUCCGCCG CGAGGCGA G CCACCGCCCG UCCCCGCCCC UUGCCUCUCG GCGCCCCCUC GAUGCUCUUA GCUGAGUGUC CCGCGGGGCC CGAAGCGUU UACUUUGAAA AAAUUAGAGU GUUCAAAGCA GGCCCGAGCC GCCUGGAUAC CGCAGCUAGG AAUAAUGGAA UAGGACCGCG GUUCUAUUU UGUUGGUUUU CGGAACUGAG GCCAUGAUUA AGAGGGACGG CCGGGGGCAU UCGUAUUGCG CCGCUAGAGG U GAAAUUCU UGGACCGGCG CAAGACGGAC CAGAGCGAAA GCAUUUGCCA AGAAUGUUUU CAUUAAUCAA GAACGAAAGU CG GAGGUUC GAAGACGAUC AGAUACCGUC GUAGUUCCGA CCAUAAACGA UGCCGACCGG CGAUGCGGCG GCGUUAUUCC CAU GACCCG CCGGGCAGCU UCCGGGAAAC CAAAGUCUUU GGGUUCCGGG GGGAGUAUGG UUGCAAAGCU GAAACUUAAA GGAA UUGAC GGAAGGGCAC CACCAGGAGU GGAGCCUGCG GCUUAAUUUG ACUCAACACG GGAAACCUCA CCCGGCCCGG ACACG GACA GGAUUGACAG AUUGAUAGCU CUUUCUCGAU UCCGUGGGUG GUGGUGCAUG GCCGUUCUUA GUUGGUGGAG CGAUUU GUC UGGUUAAUUC CGAUAACGAA CGAGACUCUG GCAUGCUAAC UAGUUACGCG ACCCCCGAGC GGUCGGCGUC CCCCAAC UU CUUAGAGGGA CAAGUGGCGU UCAGCCACCC GAGAUUGAGC AAUAACAGGU CUGUGAUGCC CUUAGAUGUC CGGGGCUG C ACGCGCGCUA CACUGACUGG CUCAGCGUGU GCCUACCCUA CGCCGGCAGG CGCGGGUAAC CCGUUGAACC CCAUUCGUG AUGGGGAUCG GGGAUUGCAA UUAUUCCCCA UGAACGAGGA AUUCCCAGUA AGUGCGGGUC AUAAGCUUGC GUUGAUUAAG UCCCUGCCC UUUGUACACA CCGCCCGUCG CUACUACCGA UUGGAUGGUU UAGUGAGGCC CUCGGAUCGG CCCCGCCGGG G UCGGCCCA CGGCCUGGCG GAGCGCUGAG AAGACGGUCG AACUUGACUA UCUAGAGGAA GUAAAAGUCG UAACAAGGUU UC CGUAGGU GAACCUGCGG AAGGAUCAUU A

+
Macromolecule #4: IRES mRNA

MacromoleculeName: IRES mRNA / type: rna / ID: 4
Details: HCV IRES mRNA (delta domain II mutant, in which domain II of the IRES is replaced with a small stem loop)
Number of copies: 1
Source (natural)Organism: Hepatitis C virus
Molecular weightTheoretical: 88.648414 KDa
SequenceString: CUCCCCUGCU UCGGCAGGAC CCCCCCUCCC GGGAGAGCCA UAGUGGUCUG CGGAACCGGU GAGUACACCG GAAUUGCCAG GACGACCGG GUCCUUUCUU GGAUAAACCC GCUCAAUGCC UGGAGAUUUG GGCGUGCCCC CGCAAGACUG CUAGCCGAGU A GUGUUGGG ...String:
CUCCCCUGCU UCGGCAGGAC CCCCCCUCCC GGGAGAGCCA UAGUGGUCUG CGGAACCGGU GAGUACACCG GAAUUGCCAG GACGACCGG GUCCUUUCUU GGAUAAACCC GCUCAAUGCC UGGAGAUUUG GGCGUGCCCC CGCAAGACUG CUAGCCGAGU A GUGUUGGG UCGCGAAAGG CCUUGUGGUA CUGCCUGAUA GGGUGCUUGC GAGUGCCCCG GGAGGUCUCG UAGACCGUGC AC CAUGAGC ACGAAUCCUA AACCUCAAAG AAAAAGAU

+
Macromolecule #39: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 39 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.11 mg/mL
BufferpH: 7.6
Component:
ConcentrationNameFormula
25.0 mMHEPES-KOH
75.0 mMPotassium chlorideKCl
2.5 mMMagnesium acetate
2.0 mMDTT
GridModel: Quantifoil R2/2 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE

-
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: FEI FALCON II (4k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

CTF correctionSoftware - Name: RELION (ver. 1.4) / Software - details: CTFFIND4
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 62177
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