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- PDB-5flx: Mammalian 40S HCV-IRES complex -

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Basic information

Entry
Database: PDB / ID: 5flx
TitleMammalian 40S HCV-IRES complex
Components
  • (40S RIBOSOMAL PROTEIN ...) x 31
  • 18S RRNA18S ribosomal RNA
  • GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-2-LIKE 1
  • HCV-IRES
  • UBIQUITIN-40S RIBOSOMAL PROTEIN S27A
KeywordsRIBOSOME / TRANSLATION INITIATION / HEPATITIS C VIRUS INTERNAL RIBOSOME ENTRY SITE
Function / homology
Function and homology information


positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein tyrosine kinase inhibitor activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / IRE1-RACK1-PP2A complex ...positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein tyrosine kinase inhibitor activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / IRE1-RACK1-PP2A complex / nucleolus organization / : / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of RNA splicing / negative regulation of DNA repair / laminin receptor activity / oxidized purine DNA binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / supercoiled DNA binding / neural crest cell differentiation / rRNA modification in the nucleus and cytosol / negative regulation of phagocytosis / NF-kappaB complex / ubiquitin-like protein conjugating enzyme binding / 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 / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / pigmentation / protein kinase A binding / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / Translation initiation complex formation / phagocytic cup / positive regulation of mitochondrial depolarization / negative regulation of Wnt signaling pathway / positive regulation of T cell receptor signaling pathway / positive regulation of activated T cell proliferation / fibroblast growth factor binding / regulation of cell division / SARS-CoV-1 modulates host translation machinery / Protein hydroxylation / iron-sulfur cluster binding / TOR signaling / BH3 domain binding / mTORC1-mediated signalling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Peptide chain elongation / Selenocysteine synthesis / monocyte chemotaxis / cysteine-type endopeptidase activator activity involved in apoptotic process / Formation of a pool of free 40S subunits / ribosomal small subunit export from nucleus / positive regulation of cyclic-nucleotide phosphodiesterase activity / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / translation regulator activity / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of respiratory burst involved in inflammatory response / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / gastrulation / 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) / rough endoplasmic reticulum / spindle assembly / regulation of translational fidelity / MDM2/MDM4 family protein binding / laminin binding / Protein methylation / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Nuclear events stimulated by ALK signaling in cancer / negative regulation of smoothened signaling pathway / rescue of stalled ribosome / signaling adaptor activity / positive regulation of cell cycle / negative regulation of peptidyl-serine phosphorylation / translation initiation factor binding / stress granule assembly / maturation of SSU-rRNA / positive regulation of intrinsic apoptotic signaling pathway / Mitotic Prometaphase / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / EML4 and NUDC in mitotic spindle formation / positive regulation of apoptotic signaling pathway / Maturation of protein E / negative regulation of ubiquitin-dependent protein catabolic process / positive regulation of microtubule polymerization
Similarity search - Function
N-terminal domain of TfIIb - #150 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2650 / Ribosomal protein S17 / Ribosomal protein S26 / Ribosomal protein S8e, subdomain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #1000 / Ribosomal protein S4, central domain / Phosducin; domain 2 / Ribosomal protein S21 / Alpha-Beta Plaits - #3370 ...N-terminal domain of TfIIb - #150 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2650 / Ribosomal protein S17 / Ribosomal protein S26 / Ribosomal protein S8e, subdomain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #1000 / Ribosomal protein S4, central domain / Phosducin; domain 2 / Ribosomal protein S21 / Alpha-Beta Plaits - #3370 / Hypothetical Cytosolic Protein; Chain: A; / Ribosomal protein S27 / first zn-finger domain of poly(adp-ribose) polymerase-1 / Diphtheria Toxin Repressor; domain 2 / N-terminal domain of TfIIb / Ribosomal protein S3, C-terminal domain / Ribosomal Protein S14/S29 / 30s Ribosomal Protein S14; Chain N / Ribosomal Protein S8; Chain: A, domain 1 - #30 / RNA-binding S4 domain / Ribosomal Protein S7 / Ribosomal protein S7/S5 / Ribosomal protein S3 C-terminal domain / Dna Ligase; domain 1 - #10 / Ribosomal protein S11/S14 / Ribosomal protein S10 / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / S15/NS1, RNA-binding / SH3 type barrels. - #30 / K homology (KH) domain / Ubiquitin-like protein FUBI / Ribosomal protein L30/S12 / 40S ribosomal protein SA / Double Stranded RNA Binding Domain - #20 / 40S ribosomal protein SA, C-terminal domain / Helicase, Ruva Protein; domain 3 - #50 / 40S ribosomal protein SA C-terminus / Glucose-6-phosphate isomerase like protein; domain 1 / Ribosomal Protein S8; Chain: A, domain 1 / Other non-globular / Ribosomal Protein S5; domain 2 - #10 / N-terminal domain of TfIIb / : / Ribosomal protein S12e / : / Small (40S) ribosomal subunit Asc1/RACK1 / GMP Synthetase; Chain A, domain 3 / Ribosomal protein S21e, conserved site / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S19e, conserved site / S27a-like superfamily / Ribosomal protein S26e / Ribosomal Protein S5; domain 2 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / Ribosomal protein S26e signature. / Ribosomal protein S17e, conserved site / : / Ribosomal protein S2, eukaryotic / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / S25 ribosomal protein / Ribosomal protein S19A/S15e / Ribosomal protein S21e signature. / Ribosomal protein S30 / Ribosomal protein S3Ae, conserved site / Ribosomal protein S12e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S5, eukaryotic/archaeal / Double Stranded RNA Binding Domain / Ribosomal protein S8e, conserved site / 40S ribosomal protein S11, N-terminal / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S6, eukaryotic / Ribosomal protein S7e / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal S17 / Ribosomal protein S19e signature. / Ribosomal protein S19e / Ribosomal protein S27, zinc-binding domain superfamily / 40S Ribosomal protein S10 / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S27 / Ribosomal protein S28e conserved site / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S28e
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein eS4, Y isoform 1 / Small ribosomal subunit protein uS3 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein eS4, Y isoform 1 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein eS19 / 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 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 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein RACK1
Similarity search - Component
Biological speciesHEPATITIS C VIRUS
ORYCTOLAGUS CUNICULUS (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsYamamoto, H. / Collier, M. / Loerke, J. / Ismer, J. / Schmidt, A. / Hilal, T. / Sprink, T. / Yamamoto, K. / Mielke, T. / Burger, J. ...Yamamoto, H. / Collier, M. / Loerke, J. / Ismer, J. / Schmidt, A. / Hilal, T. / Sprink, T. / Yamamoto, K. / Mielke, T. / Burger, J. / Shaikh, T.R. / Dabrowski, M. / Hildebrand, P.W. / Scheerer, P. / Spahn, C.M.T.
CitationJournal: EMBO J / Year: 2015
Title: Molecular architecture of the ribosome-bound Hepatitis C Virus internal ribosomal entry site RNA.
Authors: Hiroshi Yamamoto / Marianne Collier / Justus Loerke / Jochen Ismer / Andrea Schmidt / Tarek Hilal / Thiemo Sprink / Kaori Yamamoto / Thorsten Mielke / Jörg Bürger / Tanvir R Shaikh / ...Authors: Hiroshi Yamamoto / Marianne Collier / Justus Loerke / Jochen Ismer / Andrea Schmidt / Tarek Hilal / Thiemo Sprink / Kaori Yamamoto / Thorsten Mielke / Jörg Bürger / Tanvir R Shaikh / Marylena Dabrowski / Peter W Hildebrand / Patrick Scheerer / Christian M T Spahn /
Abstract: Internal ribosomal entry sites (IRESs) are structured cis-acting RNAs that drive an alternative, cap-independent translation initiation pathway. They are used by many viruses to hijack the ...Internal ribosomal entry sites (IRESs) are structured cis-acting RNAs that drive an alternative, cap-independent translation initiation pathway. They are used by many viruses to hijack the translational machinery of the host cell. IRESs facilitate translation initiation by recruiting and actively manipulating the eukaryotic ribosome using only a subset of canonical initiation factor and IRES transacting factors. Here we present cryo-EM reconstructions of the ribosome 80S- and 40S-bound Hepatitis C Virus (HCV) IRES. The presence of four subpopulations for the 80S•HCV IRES complex reveals dynamic conformational modes of the complex. At a global resolution of 3.9 Å for the most stable complex, a derived atomic model reveals a complex fold of the IRES RNA and molecular details of its interaction with the ribosome. The comparison of obtained structures explains how a modular architecture facilitates mRNA loading and tRNA binding to the P-site. This information provides the structural foundation for understanding the mechanism of HCV IRES RNA-driven translation initiation.
History
DepositionOct 28, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Aug 30, 2017Group: Data collection / Derived calculations / Category: em_image_scans / em_software / struct_conn
Item: _em_software.fitting_id / _em_software.image_processing_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "LA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "LA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "XA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
1: 18S RRNA
A: 40S RIBOSOMAL PROTEIN SA
B: 40S RIBOSOMAL PROTEIN S3A
C: 40S RIBOSOMAL PROTEIN S2
D: 40S RIBOSOMAL PROTEIN S3
E: 40S RIBOSOMAL PROTEIN S4, Y ISOFORM 1
F: 40S RIBOSOMAL PROTEIN S5
G: 40S RIBOSOMAL PROTEIN S6
H: 40S RIBOSOMAL PROTEIN S7
I: 40S RIBOSOMAL PROTEIN S8
J: 40S RIBOSOMAL PROTEIN S9
K: 40S RIBOSOMAL PROTEIN S10
L: 40S RIBOSOMAL PROTEIN S11
M: 40S RIBOSOMAL PROTEIN S12
N: 40S RIBOSOMAL PROTEIN S13
O: 40S RIBOSOMAL PROTEIN S14
P: 40S RIBOSOMAL PROTEIN S15
Q: 40S RIBOSOMAL PROTEIN S16
R: 40S RIBOSOMAL PROTEIN S17
S: 40S RIBOSOMAL PROTEIN S18
T: 40S RIBOSOMAL PROTEIN S19
U: 40S RIBOSOMAL PROTEIN S20
V: 40S RIBOSOMAL PROTEIN S21
W: 40S RIBOSOMAL PROTEIN S15A
X: 40S RIBOSOMAL PROTEIN S23
Y: 40S RIBOSOMAL PROTEIN S24
Z: 40S RIBOSOMAL PROTEIN S25
a: 40S RIBOSOMAL PROTEIN S26
b: 40S RIBOSOMAL PROTEIN S27
c: 40S RIBOSOMAL PROTEIN S28
d: 40S RIBOSOMAL PROTEIN S29
e: 40S RIBOSOMAL PROTEIN S30
f: UBIQUITIN-40S RIBOSOMAL PROTEIN S27A
g: GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-2-LIKE 1
z: HCV-IRES
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,385,962111
Polymers1,384,03335
Non-polymers1,92976
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

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RNA chain , 2 types, 2 molecules 1z

#1: RNA chain 18S RRNA / 18S ribosomal RNA


Mass: 602776.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: GenBank: 36162
#35: RNA chain HCV-IRES


Mass: 162190.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HEPATITIS C VIRUS / Production host: ORYCTOLAGUS CUNICULUS (rabbit)

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40S RIBOSOMAL PROTEIN ... , 31 types, 31 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZabcde

#2: Protein 40S RIBOSOMAL PROTEIN SA / / 37 KDA LAMININ RECEPTOR PRECURSOR / 37LRP / 37/67 KDA LAMININ RECEPTOR / LRP/LR / 67 KDA LAMININ ...37 KDA LAMININ RECEPTOR PRECURSOR / 37LRP / 37/67 KDA LAMININ RECEPTOR / LRP/LR / 67 KDA LAMININ RECEPTOR / 67LR / COLON CARCINOMA LAMININ-BINDING PROTEIN / LAMININ RECEPTOR 1 / LAMR / LAMININ-BINDING PROTEIN PRECURSOR P40 / LBP/P40 / MULTIDRUG RESISTANCE-ASSOCIATED PROTEIN MGR1-AG / NEM/1CHD4 / 40S RIBOSOMAL PROTEIN US2


Mass: 32883.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: P08865
#3: Protein 40S RIBOSOMAL PROTEIN S3A / / V-FOS TRANSFORMATION EFFECTOR PROTEIN / FTE-1 / 40S RIBOSOMAL PROTEIN ES1


Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: P61247
#4: Protein 40S RIBOSOMAL PROTEIN S2 / / 40S RIBOSOMAL PROTEIN S4 / PROTEIN LLREP3 / 40S RIBOSOMAL PROTEIN US5


Mass: 31376.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: P15880
#5: Protein 40S RIBOSOMAL PROTEIN S3 / / 40S RIBOSOMAL PROTEIN US3


Mass: 26729.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
References: UniProt: P23396, DNA-(apurinic or apyrimidinic site) lyase
#6: Protein 40S RIBOSOMAL PROTEIN S4, Y ISOFORM 1 / Ribosome / 40S RIBOSOMAL PROTEIN ES4


Mass: 29512.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: P22090
#7: Protein 40S RIBOSOMAL PROTEIN S5 / / 40S RIBOSOMAL PROTEIN US7


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: P46782
#8: Protein 40S RIBOSOMAL PROTEIN S6 / / PHOSPHOPROTEIN NP33 / 40S RIBOSOMAL PROTEIN ES6


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: P62753
#9: Protein 40S RIBOSOMAL PROTEIN S7 / / 40S RIBOSOMAL PROTEIN ES7


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: P62081
#10: Protein 40S RIBOSOMAL PROTEIN S8 / / 40S RIBOSOMAL PROTEIN ES8


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: P62241
#11: Protein 40S RIBOSOMAL PROTEIN S9 / / 40S RIBOSOMAL PROTEIN US4


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: P46781
#12: Protein 40S RIBOSOMAL PROTEIN S10 / / 40S RIBOSOMAL PROTEIN ES10


Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: P46783
#13: Protein 40S RIBOSOMAL PROTEIN S11 / / 40S RIBOSOMAL PROTEIN US17


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: P62280
#14: Protein 40S RIBOSOMAL PROTEIN S12 / / 40S RIBOSOMAL PROTEIN ES12


Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: P25398
#15: Protein 40S RIBOSOMAL PROTEIN S13 / / 40S RIBOSOMAL PROTEIN US15


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: P62277
#16: Protein 40S RIBOSOMAL PROTEIN S14 / / 40S RIBOSOMAL PROTEIN US11


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: P62263
#17: Protein 40S RIBOSOMAL PROTEIN S15 / / RIG PROTEIN / 40S RIBOSOMAL PROTEIN US19


Mass: 17076.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: P62841
#18: Protein 40S RIBOSOMAL PROTEIN S16 / / 40S RIBOSOMAL PROTEIN US9


Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: P62249
#19: Protein 40S RIBOSOMAL PROTEIN S17 / / 40S RIBOSOMAL PROTEIN ES17


Mass: 15578.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: P08708
#20: Protein 40S RIBOSOMAL PROTEIN S18 / / KE-3 / KE3 / 40S RIBOSOMAL PROTEIN US13


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: P62269
#21: Protein 40S RIBOSOMAL PROTEIN S19 / / 40S RIBOSOMAL PROTEIN ES19


Mass: 16091.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: P39019
#22: Protein 40S RIBOSOMAL PROTEIN S20 / / 40S RIBOSOMAL PROTEIN US10


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: P60866
#23: Protein 40S RIBOSOMAL PROTEIN S21 / / 40S RIBOSOMAL PROTEIN ES21


Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: P63220
#24: Protein 40S RIBOSOMAL PROTEIN S15A / / 40S RIBOSOMAL PROTEIN US8


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: P62244
#25: Protein 40S RIBOSOMAL PROTEIN S23 / / 40S RIBOSOMAL PROTEIN US12


Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: P62266
#26: Protein 40S RIBOSOMAL PROTEIN S24 / / 40S RIBOSOMAL PROTEIN ES24


Mass: 15463.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: P62847
#27: Protein 40S RIBOSOMAL PROTEIN S25 / / 40S RIBOSOMAL PROTEIN ES25


Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: P62851
#28: Protein 40S RIBOSOMAL PROTEIN S26 / / 40S RIBOSOMAL PROTEIN ES26


Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: P62854
#29: Protein 40S RIBOSOMAL PROTEIN S27 / / METALLOPAN-STIMULIN 1 / MPS-1 / 40S RIBOSOMAL PROTEIN ES27


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: P42677
#30: Protein 40S RIBOSOMAL PROTEIN S28 / / 40S RIBOSOMAL PROTEIN ES28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: P62857
#31: Protein 40S RIBOSOMAL PROTEIN S29 / / 40S RIBOSOMAL PROTEIN US14


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: P62273
#32: Protein 40S RIBOSOMAL PROTEIN S30 / / 40S RIBOSOMAL PROTEIN ES30


Mass: 6668.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: P62861

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Protein , 2 types, 2 molecules fg

#33: Protein UBIQUITIN-40S RIBOSOMAL PROTEIN S27A / UBIQUITIN CARBOXYL EXTENSION PROTEIN 80 / 40S RIBOSOMAL PROTEIN ES31


Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: P62979
#34: Protein GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-2-LIKE 1 / CELL PROLIFERATION-INDUCING GENE 21 PROTEIN / GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-LIKE ...CELL PROLIFERATION-INDUCING GENE 21 PROTEIN / GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-LIKE PROTEIN 12.3 / HUMAN LUNG CANCER ONCOGENE 7 PROTEIN / HLC-7 / RECEPTOR FOR ACTIVATED C KINASE / RECEPTOR OF ACTIVATED PROTEIN KINASE C 1 / RACK1 / 40S RIBOSOMAL PROTEIN RACK1


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: P63244

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Non-polymers , 2 types, 76 molecules

#36: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 74 / Source method: obtained synthetically / Formula: Mg
#37: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: MAMMALIAN 80S HCV-IRES COMPLEX, CLASSICAL / Type: RIBOSOME
Buffer solutionName: 20MM TRIS-HCL, 7.5MM MGCL2, 100MM KCL, 0.2MM SPERMIDINE, 2MM DTT
pH: 7.6
Details: 20MM TRIS-HCL, 7.5MM MGCL2, 100MM KCL, 0.2MM SPERMIDINE, 2MM DTT
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 93, INSTRUMENT- FEI VITROBOT MARK I, METHOD- BLOT FOR 2-4 SECONDS BEFORE PLUNGING,

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Oct 16, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 X / Calibrated magnification: 130293 X / Nominal defocus max: 4500 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameCategory
1UCSF Chimeramodel fitting
2SPARX3D reconstruction
3SPIDER3D reconstruction
CTF correctionDetails: CTFFIND3
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.9 Å / Num. of particles: 171820 / Nominal pixel size: 1.07 Å / Actual pixel size: 1.07 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3221. (DEPOSITION ID: 13955).
Symmetry type: POINT
Atomic model buildingSpace: REAL
RefinementHighest resolution: 3.9 Å
Refinement stepCycle: LAST / Highest resolution: 3.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38423 42093 76 0 80592

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