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- PDB-7sym: Structure of the HCV IRES bound to the 40S ribosomal subunit, hea... -

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Basic information

Entry
Database: PDB / ID: 7sym
TitleStructure of the HCV IRES bound to the 40S ribosomal subunit, head opening. Structure 7(delta dII)
Components
  • (40S ribosomal protein ...) x 9
  • 18S rRNA18S ribosomal RNA
  • 60s ribosomal protein l41
  • HCV IRESHepatitis C virus internal ribosome entry site
  • RACK1Receptor for activated C kinase 1
  • eS10
  • eS12
  • eS17
  • eS19
  • eS26 (S26)
  • eS27
  • eS28
  • eS29
  • eS30
  • eS6
  • eS8
  • uS10
  • uS11
  • uS12
  • uS13
  • uS15
  • uS17
  • uS19
  • uS3
  • uS4
  • uS7
  • uS8
  • uS9
KeywordsRIBOSOME / HCV / IRES / 40S
Function / homology
Function and homology information


ribosomal subunit / DNA-(apurinic or apyrimidinic site) lyase / cytosolic small ribosomal subunit / structural constituent of ribosome / translation / nucleolus / RNA binding
Similarity search - Function
Ribosomal protein S21e signature. / Ribosomal protein S12e signature. / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e signature. / 40S Ribosomal protein S10 / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S17e signature. / Ribosomal protein S7e signature. / Ribosomal protein S3Ae signature. ...Ribosomal protein S21e signature. / Ribosomal protein S12e signature. / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e signature. / 40S Ribosomal protein S10 / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S17e signature. / Ribosomal protein S7e signature. / Ribosomal protein S3Ae signature. / Ribosomal protein S27e signature. / Ribosomal protein S4e signature. / Ribosomal protein S8e signature. / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S6e signature. / Ribosomal protein S28e signature. / Ribosomal protein S2 signature 2. / Ubiquitin domain signature. / Ribosomal protein S3 signature. / Ribosomal protein S10 signature. / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / Type-2 KH domain profile. / Ribosomal protein S19 signature. / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S7 signature. / Ribosomal protein S5 / Ribosomal protein S5, N-terminal / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, C-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S17 signature. / Ribosomal protein S5, C-terminal domain / Ribosomal protein S13 signature. / Ribosomal protein S13 family profile. / Ribosomal protein S8 signature. / Ribosomal protein S4 signature. / Ribosomal protein S15 signature. / S4 RNA-binding domain profile. / Ribosomal protein S11 signature. / Ribosomal protein S9 signature. / Ubiquitin domain profile. / Ribosomal protein S12 signature. / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / 40S ribosomal protein S24 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein uS9 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / 40S ribosomal protein S24 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein RACK1 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein uS12 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS13 / Plectin/eS10 N-terminal domain-containing protein / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS5
Similarity search - Component
Biological speciesHepatitis C virus
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsBrown, Z.P. / Abaeva, I.S. / De, S. / Hellen, C.U.T. / Pestova, T.V. / Frank, J.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM139453 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM122602 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI123406 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM55440 United States
CitationJournal: To Be Published
Title: Comprehensive structural overview of the HCV IRES-mediated translation initiation pathway
Authors: Brown, Z.P. / Abaeva, I.S. / De, S. / Hellen, C.U.T. / Pestova, T.V. / Frank, J.
History
DepositionNov 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
2: 18S rRNA
B: 40S ribosomal protein SA
C: 40S ribosomal protein S3a
D: 40S ribosomal protein S2
E: uS3
F: 40S ribosomal protein S4
G: uS7
H: eS6
I: 40S ribosomal protein S7
J: eS8
K: uS4
L: eS10
M: uS17
N: eS12
O: uS15
P: uS11
Q: uS19
R: uS9
S: eS17
T: uS13
U: eS19
V: uS10
W: 40S ribosomal protein S21
X: uS8
Y: uS12
Z: 40S ribosomal protein S24
a: 40S ribosomal protein S25
b: eS26 (S26)
c: eS27
d: eS28
e: eS29
f: eS30
g: 40S ribosomal protein S27a
h: RACK1
n: 60s ribosomal protein l41
z: HCV IRES
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,389,78338
Polymers1,389,65236
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 2 types, 2 molecules 2z

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


Mass: 603100.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#36: RNA chain HCV IRES / Hepatitis C virus internal ribosome entry site


Mass: 128746.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus (isolate 1) / Production host: Escherichia coli (E. coli) / References: GenBank: 149384897

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40S ribosomal protein ... , 9 types, 9 molecules BCDFIWZag

#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 / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40


Mass: 32958.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TLT8
#3: Protein 40S ribosomal protein S3a /


Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SS70
#4: Protein 40S ribosomal protein S2 /


Mass: 24441.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: O18789
#6: Protein 40S ribosomal protein S4 /


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TK17
#9: Protein 40S ribosomal protein S7 /


Mass: 47356.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVB0
#23: Protein 40S ribosomal protein S21 /


Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM82
#26: Protein 40S ribosomal protein S24 /


Mass: 15237.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A5F9CNN4
#27: Protein 40S ribosomal protein S25 /


Mass: 13645.028 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDB3
#33: Protein 40S ribosomal protein S27a / / Ubiquitin carboxyl extension protein 80 / Ubiquitin-40S ribosomal protein S27a


Mass: 21431.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SK22

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Protein , 24 types, 24 molecules EGHJKLMNOPQRSTUVXYbcdefh

#5: Protein uS3 / Ribosomal protein S3


Mass: 31146.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TNM3
#7: Protein uS7 / 40S ribosomal protein S5


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFM5
#8: Protein eS6 / 40S ribosomal protein S6


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM55
#10: Protein eS8 / 40S ribosomal protein S8


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TJW1
#11: Protein uS4 / Ribosomal protein S9


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZS8
#12: Protein eS10


Mass: 17156.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPV3
#13: Protein uS17 / 40S ribosomal protein S11


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TRM4
#14: Protein eS12 / 40S ribosomal protein S12


Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SFR8
#15: Protein uS15 / Ribosomal protein S13


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SP51
#16: Protein uS11


Mass: 18133.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U472
#17: Protein uS19


Mass: 17049.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U0Q2
#18: Protein uS9 / Ribosomal protein S16


Mass: 19213.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGX4
#19: Protein eS17


Mass: 15552.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TU13
#20: Protein uS13


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPG3
#21: Protein eS19


Mass: 16235.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TN62
#22: Protein uS10


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIZ2
#24: Protein uS8 / Ribosomal protein S15a


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TG89
#25: Protein uS12


Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ47
#28: Protein eS26 (S26)


Mass: 11645.794 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#29: Protein eS27 / 40S ribosomal protein S27


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TZ76
#30: Protein eS28 / Ribosomal protein S28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TIB4
#31: Protein eS29


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7M4
#32: Protein eS30 / 40S ribosomal protein S30


Mass: 14498.884 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T8A2
#34: Protein RACK1 / Receptor for activated C kinase 1


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SJB4

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Protein/peptide / Non-polymers , 2 types, 3 molecules n

#35: Protein/peptide 60s ribosomal protein l41 /


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A087WNH4
#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 ligand of interestN

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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: 40S ribosomal small subunit with HCV IRES / Type: RIBOSOME / Entity ID: #1-#27, #29-#36 / Source: MULTIPLE SOURCES
Molecular weightValue: 2 MDa / Experimental value: NO
Buffer solutionpH: 7.5
SpecimenConc.: 7.5E-5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: H2/O2 mixture for 25 seconds at 25W power / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: 4 second blot time, force 3

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 52000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.26 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 4 sec. / Electron dose: 70.9 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.1_4122: / Classification: refinement
EM software
IDNameVersionCategory
2Leginonimage acquisition
4CTFFINDCTF correction
7UCSF Chimera1.15model fitting
8Coot0.9.3model fitting
10PHENIX1.19.1-4122model refinement
11RELION3.1initial Euler assignment
14RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 59660 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-ID
16D9J

6d9j

6D9J1
25FLX

5flx

z5FLX2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00384105
ELECTRON MICROSCOPYf_angle_d0.817122449
ELECTRON MICROSCOPYf_dihedral_angle_d15.69127708
ELECTRON MICROSCOPYf_chiral_restr0.04215194
ELECTRON MICROSCOPYf_plane_restr0.0068634

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