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- PDB-1jgq: The Path of Messenger RNA Through the Ribosome. THIS FILE, 1JGQ, ... -

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Entry
Database: PDB / ID: 1jgq
TitleThe Path of Messenger RNA Through the Ribosome. THIS FILE, 1JGQ, CONTAINS THE 30S RIBOSOME SUBUNIT, THREE TRNA, AND MRNA MOLECULES. 50S RIBOSOME SUBUNIT IS IN THE FILE 1GIY
Components
  • (30S RIBOSOMAL PROTEIN ...) x 20
  • (tRNA(Phe)) x 2
  • 30S 16S ribosomal RNA
  • MESSENGER RNA MF36
KeywordsRIBOSOME / ribosome assembly / protein synthesis / life
Function / homology
Function and homology information


ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation ...ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein S14, type Z / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S14/S29 / Ribosomal protein S6 signature. ...30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein S14, type Z / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S14/S29 / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / : / K homology domain superfamily, prokaryotic type / Ribosomal protein S5 / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S5, C-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / Ribosomal protein S8 signature. / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4, conserved site / Ribosomal protein S15 signature. / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / K homology domain-like, alpha/beta / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / Ribosomal protein S10p/S20e / Ribosomal protein S13-like, H2TH / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e
Similarity search - Domain/homology
: / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 ...: / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / 30S ribosomal protein Thx / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS19 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S8 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 5 Å
AuthorsYusupova, G.Z. / Yusupov, M.M. / Cate, J.H.D. / Noller, H.F.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2001
Title: The path of messenger RNA through the ribosome.
Authors: Yusupova, G.Z. / Yusupov, M.M. / Cate, J.H. / Noller, H.F.
History
DepositionJun 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 30S 16S ribosomal RNA
B: tRNA(Phe)
C: tRNA(Phe)
D: tRNA(Phe)
1: MESSENGER RNA MF36
E: 30S RIBOSOMAL PROTEIN S2
F: 30S RIBOSOMAL PROTEIN S3
G: 30S RIBOSOMAL PROTEIN S4
H: 30S RIBOSOMAL PROTEIN S5
I: 30S RIBOSOMAL PROTEIN S6
J: 30S RIBOSOMAL PROTEIN S7
K: 30S RIBOSOMAL PROTEIN S8
L: 30S RIBOSOMAL PROTEIN S9
M: 30S RIBOSOMAL PROTEIN S10
N: 30S RIBOSOMAL PROTEIN S11
O: 30S RIBOSOMAL PROTEIN S12
P: 30S RIBOSOMAL PROTEIN S13
Q: 30S RIBOSOMAL PROTEIN S14
R: 30S RIBOSOMAL PROTEIN S15
S: 30S RIBOSOMAL PROTEIN S16
T: 30S RIBOSOMAL PROTEIN S17
U: 30S RIBOSOMAL PROTEIN S18
V: 30S RIBOSOMAL PROTEIN S19
W: 30S RIBOSOMAL PROTEIN S20
X: 30S RIBOSOMAL PROTEIN THX


Theoretical massNumber of molelcules
Total (without water)869,01325
Polymers869,01325
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)507.20, 507.20, 803.66
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number97
Cell settingtetragonal
Space group name H-MI422

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Components

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RNA chain , 4 types, 5 molecules ABCD1

#1: RNA chain 30S 16S ribosomal RNA / Coordinate model: P atoms only


Mass: 493958.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 155076
#2: RNA chain tRNA(Phe)


Mass: 24890.121 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: sequence naturally occurs in Saccharomyces cerevisiae
References: GenBank: 176479
#3: RNA chain tRNA(Phe)


Mass: 23728.123 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: sequence naturally occurs in Saccharomyces cerevisiae
#4: RNA chain MESSENGER RNA MF36


Mass: 11568.915 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: 36 nt long mRNA fragment. The actual sequence GGCAAGGAGGUAAAA AUG UUUAAACGUAAAUCUACU modeled as GGCAAGGAGGUAAAA UUU UUUAAACGUAAAUCUACU

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30S RIBOSOMAL PROTEIN ... , 20 types, 20 molecules EFGHIJKLMNOPQRSTUVWX

#5: Protein 30S RIBOSOMAL PROTEIN S2 / Coordinate model: Cα atoms only


Mass: 29317.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80371
#6: Protein 30S RIBOSOMAL PROTEIN S3 / Coordinate model: Cα atoms only


Mass: 26751.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80372*PLUS
#7: Protein 30S RIBOSOMAL PROTEIN S4 / Coordinate model: Cα atoms only


Mass: 24373.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80373
#8: Protein 30S RIBOSOMAL PROTEIN S5 / Coordinate model: Cα atoms only


Mass: 17583.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SHQ5
#9: Protein 30S RIBOSOMAL PROTEIN S6 / Coordinate model: Cα atoms only


Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SLP8
#10: Protein 30S RIBOSOMAL PROTEIN S7 / Coordinate model: Cα atoms only


Mass: 18050.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P17291
#11: Protein 30S RIBOSOMAL PROTEIN S8 / Coordinate model: Cα atoms only


Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SHQ2, UniProt: P0DOY9*PLUS
#12: Protein 30S RIBOSOMAL PROTEIN S9 / Coordinate model: Cα atoms only


Mass: 14429.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80374
#13: Protein 30S RIBOSOMAL PROTEIN S10 / Coordinate model: Cα atoms only


Mass: 11954.968 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SHN7
#14: Protein 30S RIBOSOMAL PROTEIN S11 / Coordinate model: Cα atoms only


Mass: 13737.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80376
#15: Protein 30S RIBOSOMAL PROTEIN S12 / Coordinate model: Cα atoms only


Mass: 14920.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SHN3
#16: Protein 30S RIBOSOMAL PROTEIN S13 / Coordinate model: Cα atoms only


Mass: 14338.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80377
#17: Protein 30S RIBOSOMAL PROTEIN S14 / Coordinate model: Cα atoms only


Mass: 7158.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SHQ1, UniProt: P0DOY6*PLUS
#18: Protein 30S RIBOSOMAL PROTEIN S15 / Coordinate model: Cα atoms only


Mass: 10578.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SJ76
#19: Protein 30S RIBOSOMAL PROTEIN S16 / Coordinate model: Cα atoms only


Mass: 10808.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 12056104, UniProt: Q5SJH3*PLUS
#20: Protein 30S RIBOSOMAL PROTEIN S17 / Coordinate model: Cα atoms only


Mass: 12324.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P0DOY7*PLUS
#21: Protein 30S RIBOSOMAL PROTEIN S18 / Coordinate model: Cα atoms only


Mass: 10244.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 6739549, UniProt: Q5SLQ0*PLUS
#22: Protein 30S RIBOSOMAL PROTEIN S19 / Coordinate model: Cα atoms only


Mass: 10605.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80381, UniProt: Q5SHP2*PLUS
#23: Protein 30S RIBOSOMAL PROTEIN S20 / Coordinate model: Cα atoms only


Mass: 11722.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 11125386, UniProt: P80380*PLUS
#24: Protein/peptide 30S RIBOSOMAL PROTEIN THX / Coordinate model: Cα atoms only


Mass: 3218.835 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P32193, UniProt: Q5SIH3*PLUS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal growMethod: vapor diffusion / pH: 7.4
Details: 20 mM MgCl2, 100 mM KCl, 20 mM tris HCl, pH 7.4, VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1MgCl211
2KCl11
3tris HCl11
4MgCl212
5KCl12
6tris HCl12
Crystal grow
*PLUS
Method: vapor diffusion, hanging, sitting drop / Details: Cate, J.H., (1999) Science, 285, 2095.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mM1dropMgCl2
2100 mM1dropKCl
320 mMTris-HCl1drop
41
51
61

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 5→250 Å / Num. obs: 209044 / % possible obs: 95.3 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rsym value: 0.094
Reflection
*PLUS
Lowest resolution: 250 Å / Rmerge(I) obs: 0.094

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Processing

Software
NameClassification
CCP4model building
Omodel building
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 5→250 Å / σ(I): 0
Details: THE MODEL WAS BUILT BY MANUAL FITTING OF INDIVIDUAL MOLECULES INTO THE EXPERIMENTAL ELECTRON DENSITY USING THE GRAPHIC PROGRAM O.
Num. reflection% reflection
all209044 -
obs209044 95.3 %
Refinement stepCycle: LAST / Resolution: 5→250 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2396 6486 0 0 8882
Refinement
*PLUS
σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS

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