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- PDB-5a2q: Structure of the HCV IRES bound to the human ribosome -

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Basic information

Entry
Database: PDB / ID: 5a2q
TitleStructure of the HCV IRES bound to the human ribosome
Components
  • (RIBOSOMAL PROTEIN ...) x 36
  • 18S RRNA
  • HCV IRES
KeywordsRIBOSOME / HUMAN RIBOSOME / HEPATITIS-C / IRES / TRANSLATION INITIATION
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 / negative regulation of peptidyl-serine phosphorylation / positive regulation of respiratory burst involved in inflammatory response / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / protein tyrosine kinase inhibitor activity ...negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / negative regulation of peptidyl-serine phosphorylation / positive regulation of respiratory burst involved in inflammatory response / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / protein tyrosine kinase inhibitor activity / IRE1-RACK1-PP2A complex / positive regulation of endodeoxyribonuclease activity / nucleolus organization / positive regulation of Golgi to plasma membrane protein transport / translation at postsynapse / TNFR1-mediated ceramide production / negative regulation of DNA repair / negative regulation of RNA splicing / mammalian oogenesis stage / supercoiled DNA binding / activation-induced cell death of T cells / neural crest cell differentiation / NF-kappaB complex / oxidized purine DNA binding / cysteine-type endopeptidase activator activity involved in apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / exit from mitosis / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / translation at presynapse / positive regulation of ubiquitin-protein transferase activity / Formation of the ternary complex, and subsequently, the 43S complex / negative regulation of phagocytosis / erythrocyte homeostasis / rRNA modification in the nucleus and cytosol / optic nerve development / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / protein kinase A binding / retinal ganglion cell axon guidance / negative regulation of ubiquitin protein ligase activity / pigmentation / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / Translation initiation complex formation / positive regulation of mitochondrial depolarization / positive regulation of T cell receptor signaling pathway / positive regulation of activated T cell proliferation / fibroblast growth factor binding / negative regulation of Wnt signaling pathway / monocyte chemotaxis / negative regulation of translational frameshifting / Protein hydroxylation / BH3 domain binding / TOR signaling / SARS-CoV-1 modulates host translation machinery / regulation of cell division / mTORC1-mediated signalling / T cell proliferation involved in immune response / Peptide chain elongation / iron-sulfur cluster binding / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / negative regulation of ubiquitin-dependent protein catabolic process / Viral mRNA Translation / negative regulation of respiratory burst involved in inflammatory response / phagocytic cup / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / erythrocyte development / Major pathway of rRNA processing in the nucleolus and cytosol / regulation of translational fidelity / 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) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Protein methylation / spindle assembly / Nuclear events stimulated by ALK signaling in cancer / ribosomal small subunit export from nucleus / positive regulation of intrinsic apoptotic signaling pathway / rough endoplasmic reticulum / laminin binding / translation regulator activity / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / positive regulation of cell cycle / translation initiation factor binding / signaling adaptor activity / gastrulation / Maturation of protein E / Maturation of protein E / MDM2/MDM4 family protein binding / positive regulation of microtubule polymerization / cytosolic ribosome
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1270 / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1270 / 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 / 40S ribosomal protein SA / N-terminal domain of TfIIb / Ribosomal Protein S5; domain 2 - #10 / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / GMP Synthetase; Chain A, domain 3 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Ribosomal Protein S5; domain 2 / metallochaperone-like domain / TRASH domain / : / Ribosomal protein S26e signature. / Double Stranded RNA Binding Domain / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / S27a-like superfamily / 40S Ribosomal protein S10 / : / Ribosomal protein S7e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L19, eukaryotic / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a / Ribosomal protein S17e, conserved site / Ribosomal protein S27a / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S2, eukaryotic/archaeal / : / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S27e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus
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 uS3 / Small ribosomal subunit protein eS12 ...: / 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 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 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 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL19 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein eS1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
HEPATITIS C VIRUS
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsQuade, N. / Leiundgut, M. / Boehringer, D. / Heuvel, J.v.d. / Ban, N.
CitationJournal: Nat Commun / Year: 2015
Title: Cryo-EM structure of Hepatitis C virus IRES bound to the human ribosome at 3.9-Å resolution.
Authors: Nick Quade / Daniel Boehringer / Marc Leibundgut / Joop van den Heuvel / Nenad Ban /
Abstract: Hepatitis C virus (HCV), a widespread human pathogen, is dependent on a highly structured 5'-untranslated region of its mRNA, referred to as internal ribosome entry site (IRES), for the translation ...Hepatitis C virus (HCV), a widespread human pathogen, is dependent on a highly structured 5'-untranslated region of its mRNA, referred to as internal ribosome entry site (IRES), for the translation of all of its proteins. The HCV IRES initiates translation by directly binding to the small ribosomal subunit (40S), circumventing the need for many eukaryotic translation initiation factors required for mRNA scanning. Here we present the cryo-EM structure of the human 40S ribosomal subunit in complex with the HCV IRES at 3.9 Å resolution, determined by focused refinement of an 80S ribosome-HCV IRES complex. The structure reveals the molecular details of the interactions between the IRES and the 40S, showing that expansion segment 7 (ES7) of the 18S rRNA acts as a central anchor point for the HCV IRES. The structural data rationalizes previous biochemical and genetic evidence regarding the initiation mechanism of the HCV and other related IRESs.
History
DepositionMay 21, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 2.0Aug 2, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / em_3d_fitting ...atom_site / em_3d_fitting / em_image_scans / em_software / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _em_3d_fitting.target_criteria / _em_software.fitting_id / _em_software.image_processing_id / _em_software.name / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_validate_close_contact.auth_atom_id_1
Revision 2.1Dec 18, 2019Group: Derived calculations / Other / Category: atom_sites / struct_conn
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_conn_type.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 "IC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "IC" 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 "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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Assembly

Deposited unit
2: 18S RRNA
3: HCV IRES
A: RIBOSOMAL PROTEIN US2
B: RIBOSOMAL PROTEIN ES1
C: RIBOSOMAL PROTEIN US5
D: RIBOSOMAL PROTEIN US3
E: RIBOSOMAL PROTEIN ES4
F: RIBOSOMAL PROTEIN US7
G: RIBOSOMAL PROTEIN ES6
H: RIBOSOMAL PROTEIN ES7
I: RIBOSOMAL PROTEIN ES8
J: RIBOSOMAL PROTEIN US4
K: RIBOSOMAL PROTEIN ES10
L: RIBOSOMAL PROTEIN US17
M: RIBOSOMAL PROTEIN ES12
N: RIBOSOMAL PROTEIN US15
O: RIBOSOMAL PROTEIN US11
P: RIBOSOMAL PROTEIN US19
Q: RIBOSOMAL PROTEIN US9
R: RIBOSOMAL PROTEIN ES17
S: RIBOSOMAL PROTEIN US13
T: RIBOSOMAL PROTEIN ES19
U: RIBOSOMAL PROTEIN US10
V: RIBOSOMAL PROTEIN ES21
W: RIBOSOMAL PROTEIN US8
X: RIBOSOMAL PROTEIN US12
Y: RIBOSOMAL PROTEIN ES24
Z: RIBOSOMAL PROTEIN ES25
a: RIBOSOMAL PROTEIN ES26
b: RIBOSOMAL PROTEIN ES27
c: RIBOSOMAL PROTEIN ES28
d: RIBOSOMAL PROTEIN US14
e: RIBOSOMAL PROTEIN ES30
f: RIBOSOMAL PROTEIN ES31
g: RIBOSOMAL PROTEIN RACK1
h: RIBOSOMAL PROTEIN EL41
r: RIBOSOMAL PROTEIN EL19
w: RIBOSOMAL PROTEIN EL24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,305,500139
Polymers1,302,92238
Non-polymers2,578101
Water2,594144
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 23

#1: RNA chain 18S RRNA


Mass: 602432.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: GenBank: 337376
#2: RNA chain HCV IRES


Mass: 82914.953 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HEPATITIS C VIRUS

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RIBOSOMAL PROTEIN ... , 36 types, 36 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZabcd...

#3: Protein RIBOSOMAL PROTEIN US2


Mass: 32883.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: P08865
#4: Protein RIBOSOMAL PROTEIN ES1


Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: Q6NXR8, UniProt: P61247*PLUS
#5: Protein RIBOSOMAL PROTEIN US5


Mass: 31376.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: P15880
#6: Protein RIBOSOMAL PROTEIN US3


Mass: 26729.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: P23396
#7: Protein RIBOSOMAL PROTEIN ES4


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: P62701
#8: Protein RIBOSOMAL PROTEIN US7


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: P46782
#9: Protein RIBOSOMAL PROTEIN ES6


Mass: 28779.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: P62753
#10: Protein RIBOSOMAL PROTEIN ES7


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: P62081
#11: Protein RIBOSOMAL PROTEIN ES8


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: P62241
#12: Protein RIBOSOMAL PROTEIN US4


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: P46781
#13: Protein RIBOSOMAL PROTEIN ES10


Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: P46783
#14: Protein RIBOSOMAL PROTEIN US17


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: P62280
#15: Protein RIBOSOMAL PROTEIN ES12


Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: P25398
#16: Protein RIBOSOMAL PROTEIN US15


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: P62277
#17: Protein RIBOSOMAL PROTEIN US11


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: P62263
#18: Protein RIBOSOMAL PROTEIN US19


Mass: 17076.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: P62841
#19: Protein RIBOSOMAL PROTEIN US9


Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: P62249
#20: Protein RIBOSOMAL PROTEIN ES17


Mass: 15578.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: P08708
#21: Protein RIBOSOMAL PROTEIN US13


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: P62269
#22: Protein RIBOSOMAL PROTEIN ES19


Mass: 16178.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: P39019
#23: Protein RIBOSOMAL PROTEIN US10


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: P60866
#24: Protein RIBOSOMAL PROTEIN ES21


Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: P63220
#25: Protein RIBOSOMAL PROTEIN US8


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: P62244
#26: Protein RIBOSOMAL PROTEIN US12


Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: P62266
#27: Protein RIBOSOMAL PROTEIN ES24


Mass: 15107.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: P62847
#28: Protein RIBOSOMAL PROTEIN ES25


Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: P62851
#29: Protein RIBOSOMAL PROTEIN ES26


Mass: 11673.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: P62854
#30: Protein RIBOSOMAL PROTEIN ES27


Mass: 9210.843 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: P42677
#31: Protein RIBOSOMAL PROTEIN ES28


Mass: 6878.940 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: P62857
#32: Protein RIBOSOMAL PROTEIN US14


Mass: 6559.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: P62273
#33: Protein RIBOSOMAL PROTEIN ES30


Mass: 6302.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: P62861
#34: Protein RIBOSOMAL PROTEIN ES31


Mass: 8453.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: Q5RKT7, UniProt: P62979*PLUS
#35: Protein RIBOSOMAL PROTEIN RACK1


Mass: 34857.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: P63244
#36: Protein/peptide RIBOSOMAL PROTEIN EL41


Mass: 3342.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: P62945
#37: Protein/peptide RIBOSOMAL PROTEIN EL19


Mass: 1709.011 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: P84098
#38: Protein RIBOSOMAL PROTEIN EL24


Mass: 6481.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: UniProt: P83731

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Non-polymers , 3 types, 245 molecules

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


Mass: 24.305 Da / Num. of mol.: 98 / Source method: obtained synthetically / Formula: Mg
#40: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#41: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsGENBANK REFERENCE FOR CHAIN A CAA54808.1 GENBANK REFERENCE FOR CHAIN G AAH27620.1

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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: HCV IRES BOUND TO HUMAN 80S RIBOSOME / Type: RIBOSOME
Buffer solutionName: 20MM HEPES, 100 MM KCL, 5 MM MGCL2 / pH: 7.6 / Details: 20MM HEPES, 100 MM KCL, 5 MM MGCL2
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE-PROPANE
Details: FROZEN ON 200 MESH QUANTIFOIL R 2 2 HOLEY CARBON GRIDS WITH A THIN CONTINUOUS CARBON SUPPORT FILM APPLIED IN ETHANE PROPANE MIX

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Nov 20, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 100719 X / Nominal defocus max: 3400 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1UCSF Chimeramodel fitting
2RELION3D reconstruction
CTF correctionDetails: INDIVIDUAL FRAMES
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: MAXIMUM LIKELIHOOD BASED REFINEMENT / Resolution: 3.9 Å / Num. of particles: 404357 / Nominal pixel size: 1.39 Å / Symmetry type: POINT
Atomic model buildingB value: 119.1 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: R-factor
Details: METHOD--RIGID BODY REFINEMENT FOLLOWED BY MANUAL MODEL BUILDING REFINEMENT PROTOCOL--CRYO-EM
Atomic model buildingPDB-ID: 4W23

4w23
PDB Unreleased entry


Accession code: 4W23 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.9 Å
Refinement stepCycle: LAST / Highest resolution: 3.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39467 41037 101 144 80749

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