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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 RRNA
  • 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


negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / protein tyrosine kinase inhibitor activity / positive regulation of ubiquitin-protein transferase activity / IRE1-RACK1-PP2A complex ...negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / protein tyrosine kinase inhibitor activity / positive regulation of ubiquitin-protein transferase activity / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / nucleolus organization / positive regulation of DNA-templated transcription initiation / TNFR1-mediated ceramide production / negative regulation of RNA splicing / neural crest cell differentiation / ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA / supercoiled DNA binding / negative regulation of DNA repair / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / cysteine-type endopeptidase activator activity involved in apoptotic process / oxidized purine DNA binding / NF-kappaB complex / cytoplasmic translational initiation / rRNA modification in the nucleus and cytosol / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / erythrocyte homeostasis / regulation of establishment of cell polarity / negative regulation of phagocytosis / negative regulation of bicellular tight junction assembly / ubiquitin-like protein conjugating enzyme binding / cytoplasmic side of rough endoplasmic reticulum membrane / Formation of the ternary complex, and subsequently, the 43S complex / pigmentation / ion channel inhibitor activity / protein kinase A binding / laminin receptor activity / Ribosomal scanning and start codon recognition / positive regulation of mitochondrial depolarization / Translation initiation complex formation / negative regulation of Wnt signaling pathway / fibroblast growth factor binding / Protein hydroxylation / BH3 domain binding / negative regulation of translational frameshifting / TOR signaling / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / monocyte chemotaxis / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / regulation of cell division / iron-sulfur cluster binding / positive regulation of GTPase activity / cellular response to ethanol / Peptide chain elongation / Selenocysteine synthesis / negative regulation of protein binding / Formation of a pool of free 40S subunits / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Eukaryotic Translation Termination / protein serine/threonine kinase inhibitor activity / negative regulation of respiratory burst involved in inflammatory response / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / ubiquitin ligase inhibitor activity / Viral mRNA Translation / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / positive regulation of signal transduction by p53 class mediator / negative regulation of ubiquitin-dependent protein catabolic process / 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 / regulation of translational fidelity / positive regulation of microtubule polymerization / phagocytic cup / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / spindle assembly / cellular response to leukemia inhibitory factor / positive regulation of intrinsic apoptotic signaling pathway / Protein methylation / 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) / translation regulator activity / Nuclear events stimulated by ALK signaling in cancer / gastrulation / rough endoplasmic reticulum / ribosomal small subunit export from nucleus / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / laminin binding / DNA-(apurinic or apyrimidinic site) endonuclease activity / positive regulation of cell cycle / rescue of stalled cytosolic ribosome / signaling adaptor activity / Maturation of protein E / negative regulation of protein ubiquitination / Maturation of protein E / MDM2/MDM4 family protein binding / ER Quality Control Compartment (ERQC) / Mitotic Prometaphase / Myoclonic epilepsy of Lafora
Similarity search - Function
N-terminal domain of TfIIb - #150 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2650 / Ribosomal protein S26 / Ribosomal protein S8e, subdomain / Ribosomal protein S17 / Ribosomal protein S4, central domain / Phosducin; domain 2 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #1000 / Ribosomal protein S21 / Hypothetical Cytosolic Protein; Chain: A; ...N-terminal domain of TfIIb - #150 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2650 / Ribosomal protein S26 / Ribosomal protein S8e, subdomain / Ribosomal protein S17 / Ribosomal protein S4, central domain / Phosducin; domain 2 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #1000 / Ribosomal protein S21 / Hypothetical Cytosolic Protein; Chain: A; / Ribosomal protein S27 / first zn-finger domain of poly(adp-ribose) polymerase-1 / Alpha-Beta Plaits - #3370 / 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 / Ribosomal protein S3 C-terminal domain / Dna Ligase; domain 1 - #10 / Ribosomal protein S11/S14 / Ribosomal protein S10 / S15/NS1, RNA-binding / Ribosomal Protein S7 / Ribosomal protein S7/S5 / RNA-binding S4 domain / SH3 type barrels. - #30 / Ribosomal protein L30/S12 / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / K homology (KH) domain / Helicase, Ruva Protein; domain 3 - #50 / Double Stranded RNA Binding Domain - #20 / Glucose-6-phosphate isomerase like protein; domain 1 / Ribosomal Protein S8; Chain: A, domain 1 / Other non-globular / N-terminal domain of TfIIb / Ribosomal Protein S5; domain 2 - #10 / GMP Synthetase; Chain A, domain 3 / 40S ribosomal protein SA / Ribosomal Protein S5; domain 2 / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / Double Stranded RNA Binding Domain / 60s Ribosomal Protein L30; Chain: A; / : / Ribosomal protein S26e signature. / Single Sheet / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / : / Ribosomal protein S12e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S12e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / 40S Ribosomal protein S10 / Helicase, Ruva Protein; domain 3 / Nucleic acid-binding proteins / S27a-like superfamily / Plectin/S10, N-terminal / Plectin/S10 domain / Dna Ligase; domain 1 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S8e subdomain, eukaryotes / : / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S7e signature. / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S27e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S19A/S15e / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S4e, N-terminal, conserved site
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
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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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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
Water00
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


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 / 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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Details

Has protein modificationY

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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 FIELD / 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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