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- PDB-2rdo: 50S subunit with EF-G(GDPNP) and RRF bound -

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Entry
Database: PDB / ID: 2rdo
Title50S subunit with EF-G(GDPNP) and RRF bound
Components
  • (50S ribosomal protein ...) x 30
  • 23S RIBOSOMAL RNA
  • 5S RIBOSOMAL RNA
  • Elongation factor GEF-G
  • Ribosome recycling factor
KeywordsRIBOSOME / elongation factor G / EF-G / RRF / ribosome recycling factor / GDPNP / 50S subunit / cryo-EM / Real-space refinement / Ribonucleoprotein / Ribosomal protein / RNA-binding / rRNA-binding / Methylation / Antibiotic resistance / Repressor / Transcription / Transcription regulation / Transcription termination / Translation regulation / tRNA-binding / Phosphoprotein / Metal-binding / GTP-binding / Nucleotide-binding / Protein biosynthesis
Function / homologyElongation Factor G, domain II / Ribosomal protein L13 superfamily / Ribosomal protein L36 superfamily / Ribosomal protein L29/L35 superfamily / L21-like superfamily / RRF superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L17 superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L11, C-terminal domain superfamily ...Elongation Factor G, domain II / Ribosomal protein L13 superfamily / Ribosomal protein L36 superfamily / Ribosomal protein L29/L35 superfamily / L21-like superfamily / RRF superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L17 superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / EF-G domain III/V-like / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L35 superfamily / Ribosomal protein L33 superfamily / Ribosomal protein L19 superfamily / Elongation factor Tu GTP binding domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L22p/L17e / Ribosomal protein L14p/L23e / Ribosomal protein L16p/L10e / Ribosomal protein L23 / Ribosomal protein L5 / EFG, domain V / Ribosomal protein L20, C-terminal / Ribosomal protein L11, RNA binding domain / Ribosomal protein L2, conserved site / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L11, C-terminal / Ribosomal protein L11, N-terminal / Ribosomal protein L11, conserved site / Ribosomal protein L16, conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L5, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L18e/L15P / Ribosomal protein L35 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal / Ribosomal protein L5 domain superfamily / L28p-like / Ribosomal protein L4 domain superfamily / Ribosome recycling factor domain / Ribosomal protein L1, conserved site / Ribosomal protein L1-like / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein L31 type A / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L21-like / Ribosomal protein L25 / Ribosomal protein L15 / Tr-type G domain, conserved site / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / Ribosomal protein L3 / Ribosomal protein L30p/L7e / Ribosomal protein L9, N-terminal / Ribosomal protein L9 signature. / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Ribosomal protein L5 signature. / Ribosomal protein L11 signature. / Ribosomal protein L22 signature. / Ribosomal protein L2 signature. / Ribosomal protein L3 signature. / Ribosomal protein L15 signature. / Ribosomal protein L6 signature 1. / Ribosomal protein L29 signature. / Ribosomal protein L33 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L30 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L14 signature. / Ribosomal protein L13 signature. / Ribosomal protein L34 signature. / Ribosomal protein L36 signature. / Ribosomal protein L27 signature. / Ribosomal protein L35 signature. / Ribosomal protein L20 signature. / Ribosomal protein L19 signature. / Ribosomal protein L24 signature. / Ribosomal protein L31 signature. / Ribosomal protein L17 signature. / Ribosomal protein L21 signature. / Ribosomal protein L1 signature. / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein L23 signature. / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L6 / Ribosomal L29 protein / Ribosomal protein L36 / Ribosomal protein L20 / KOW motif / Ribosomal protein L34 / Ribosomal protein L33 / Ribosomal protein L13
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 9.1 Å resolution
AuthorsGao, N. / Zavialov, A.V. / Ehrenberg, M. / Frank, J.
Citation
Journal: J. Mol. Biol. / Year: 2007
Title: Specific interaction between EF-G and RRF and its implication for GTP-dependent ribosome splitting into subunits.
Authors: Ning Gao / Andrey V Zavialov / Måns Ehrenberg / Joachim Frank
#1: Journal: J.Mol.Biol. / Year: 2005
Title: Structural insights into fusidic acid resistance and sensitivity in EF-G.
Authors: Hansson, S. / Singh, R. / Gudkov, A.T. / Liljas, A. / Logan, D.T.
#2: Journal: Science / Year: 2005
Title: Structures of the bacterial ribosome at 3.5 A resolution.
Authors: Schuwirth, B.S. / Borovinskaya, M.A. / Hau, C.W. / Zhang, W. / Vila-Sanjurjo, A. / Holton, J.M. / Cate, J.H.
#3: Journal: Embo J. / Year: 2000
Title: Crystal structure of the ribosome recycling factor from Escherichia coli.
Authors: Kim, K.K. / Min, K. / Suh, S.W.
#4: Journal: Nat.Struct.Mol.Biol. / Year: 2003
Title: Structure of the L1 protuberance in the ribosome.
Authors: Nikulin, A. / Eliseikina, I. / Tishchenko, S. / Nevskaya, N. / Davydova, N. / Platonova, O. / Piendl, W. / Selmer, M. / Liljas, A. / Drygin, D. / Zimmermann, R. / Garber, M. / Nikonov, S.
#5: Journal: Mol.Cell / Year: 2005
Title: Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies.
Authors: Gao, N. / Zavialov, A.V. / Li, W. / Sengupta, J. / Valle, M. / Gursky, R.P. / Ehrenberg, M. / Frank, J.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 24, 2007 / Release: Mar 4, 2008
RevisionDateData content typeGroupProviderType
1.0Mar 4, 2008Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance

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Assembly

Deposited unit
A: 5S RIBOSOMAL RNA
B: 23S RIBOSOMAL RNA
V: 50S ribosomal protein L25
C: 50S ribosomal protein L2
D: 50S ribosomal protein L3
E: 50S ribosomal protein L4
F: 50S ribosomal protein L5
G: 50S ribosomal protein L6
J: 50S ribosomal protein L13
K: 50S ribosomal protein L14
L: 50S ribosomal protein L15
M: 50S ribosomal protein L16
N: 50S ribosomal protein L17
O: 50S ribosomal protein L18
P: 50S ribosomal protein L19
Q: 50S ribosomal protein L20
R: 50S ribosomal protein L21
S: 50S ribosomal protein L22
T: 50S ribosomal protein L23
U: 50S ribosomal protein L24
W: 50S ribosomal protein L27
X: 50S ribosomal protein L29
Y: 50S ribosomal protein L30
Z: 50S ribosomal protein L31
0: 50S ribosomal protein L32
1: 50S ribosomal protein L33
2: 50S ribosomal protein L34
3: 50S ribosomal protein L35
4: 50S ribosomal protein L36
I: 50S ribosomal protein L11
H: 50S ribosomal protein L9
9: 50S ribosomal protein L1
7: Elongation factor G
8: Ribosome recycling factor


Theoretical massNumber of molelcules
Total (without water)1,477,82434
Polyers1,477,82434
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 2 types, 2 molecules AB

#1: RNA chain 5S RIBOSOMAL RNA / / Coordinate model: P atoms only


Mass: 38790.090 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: GenBank: 33357928
#2: RNA chain 23S RIBOSOMAL RNA / / Coordinate model: P atoms only


Mass: 941612.375 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: GenBank: 33357927

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50S ribosomal protein ... , 30 types, 30 molecules VCDEFGJKLMNOPQRSTUWXYZ01234IH9

#3: Protein/peptide 50S ribosomal protein L25 / / Coordinate model: Cα atoms only


Mass: 10713.465 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P68919
#4: Protein/peptide 50S ribosomal protein L2 / / Coordinate model: Cα atoms only


Mass: 29792.424 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P60422
#5: Protein/peptide 50S ribosomal protein L3 / / Coordinate model: Cα atoms only


Mass: 22277.535 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P60438
#6: Protein/peptide 50S ribosomal protein L4 / / Coordinate model: Cα atoms only


Mass: 22121.566 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P60723
#7: Protein/peptide 50S ribosomal protein L5 / / Coordinate model: Cα atoms only


Mass: 20202.416 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P62399
#8: Protein/peptide 50S ribosomal protein L6 / / Coordinate model: Cα atoms only


Mass: 18801.598 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P0AG55
#9: Protein/peptide 50S ribosomal protein L13 / / Coordinate model: Cα atoms only


Mass: 16050.606 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P0AA10
#10: Protein/peptide 50S ribosomal protein L14 / / Coordinate model: Cα atoms only


Mass: 13565.067 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P0ADY3
#11: Protein/peptide 50S ribosomal protein L15 / / Coordinate model: Cα atoms only


Mass: 15008.471 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P02413
#12: Protein/peptide 50S ribosomal protein L16 / / Coordinate model: Cα atoms only


Mass: 15312.269 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P0ADY7
#13: Protein/peptide 50S ribosomal protein L17 / / Coordinate model: Cα atoms only


Mass: 14393.657 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P0AG44
#14: Protein/peptide 50S ribosomal protein L18 / / Coordinate model: Cα atoms only


Mass: 12794.668 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P0C018
#15: Protein/peptide 50S ribosomal protein L19 / / Coordinate model: Cα atoms only


Mass: 13028.082 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P0A7K6
#16: Protein/peptide 50S ribosomal protein L20 / / Coordinate model: Cα atoms only


Mass: 13396.828 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P0A7L3
#17: Protein/peptide 50S ribosomal protein L21 / / Coordinate model: Cα atoms only


Mass: 11586.374 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P0AG48
#18: Protein/peptide 50S ribosomal protein L22 / / Coordinate model: Cα atoms only


Mass: 12253.359 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P61175
#19: Protein/peptide 50S ribosomal protein L23 / / Coordinate model: Cα atoms only


Mass: 11222.160 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P0ADZ0
#20: Protein/peptide 50S ribosomal protein L24 / / Coordinate model: Cα atoms only


Mass: 11208.054 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P60624
#21: Protein/peptide 50S ribosomal protein L27 / / Coordinate model: Cα atoms only


Mass: 9015.344 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P0A7L8
#22: Protein/peptide 50S ribosomal protein L29 / / Coordinate model: Cα atoms only


Mass: 7286.464 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P0A7M6
#23: Protein/peptide 50S ribosomal protein L30 / / Coordinate model: Cα atoms only


Mass: 6423.625 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P0AG51
#24: Protein/peptide 50S ribosomal protein L31 / / Coordinate model: Cα atoms only


Mass: 7887.117 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P0A7M9
#25: Protein/peptide 50S ribosomal protein L32 / / Coordinate model: Cα atoms only


Mass: 6332.249 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P0A7N4
#26: Protein/peptide 50S ribosomal protein L33 / / Coordinate model: Cα atoms only


Mass: 6257.436 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P0A7N9
#27: Protein/peptide 50S ribosomal protein L34 / / Coordinate model: Cα atoms only


Mass: 5397.463 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P0A7P5
#28: Protein/peptide 50S ribosomal protein L35 / / Coordinate model: Cα atoms only


Mass: 7181.835 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P0A7Q1
#29: Protein/peptide 50S ribosomal protein L36 / / Ribosomal protein B / Coordinate model: Cα atoms only


Mass: 4377.390 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P0A7Q6
#30: Protein/peptide 50S ribosomal protein L11 / / Coordinate model: Cα atoms only


Mass: 14763.165 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P0A7J7
#31: Protein/peptide 50S ribosomal protein L9 / / Coordinate model: Cα atoms only


Mass: 15789.020 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P0A7R1
#32: Protein/peptide 50S ribosomal protein L1 / / Coordinate model: Cα atoms only


Mass: 24634.465 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P0A7L0

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Protein/peptide , 2 types, 2 molecules 78

#33: Protein/peptide Elongation factor G / EF-G / EF-G / Coordinate model: Cα atoms only


Mass: 77676.227 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P0A6M8
#34: Protein/peptide Ribosome recycling factor / / Ribosome-releasing factor / RRF / Coordinate model: Cα atoms only


Mass: 20671.621 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P0A805

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: E. coli 50S complex / Type: RIBOSOME
Buffer solutionName: PolyMix / Details: PolyMix / pH: 7.5
SpecimenConc.: 32 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil holey carbon film grids
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: Rapid-freezing in liquid ethane by Vitrobot

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F20 / Date: Jan 1, 2005
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 / Calibrated magnification: 49700 / Nominal defocus max: 4900 nm / Nominal defocus min: 1100 nm / Cs: 2 mm
Specimen holderTemperature: 93 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategoryDetails
1RSRefmodel fittingTNT and Real-space refinement procedure
2SPIDER3D reconstruction
CTF correctionDetails: CTF correction of 3D maps by Wiener filtration
SymmetryPoint symmetry: C1
3D reconstructionMethod: 3D projection matching / Resolution: 9.1 Å / Number of particles: 113355 / Nominal pixel size: 2.82 / Details: Spider Package / Symmetry type: POINT
Atomic model buildingDetails: REFINEMENT PROTOCOL--Real-space refinement / Ref protocol: OTHER / Ref space: REAL
Atomic model building
IDPDB-ID 3D fitting ID
12AW41
21EK81
Number of atoms included #LASTProtein: 4470 / Nucleic acid: 2958 / Ligand: 0 / Solvent: 0 / Total: 7428

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