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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
Descriptor50S RIBOSOMAL SUBUNIT
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
Specimen sourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
MethodElectron microscopy (9.1 Å resolution / Particle / Single particle)
AuthorsGao, N. / Zavialov, A.V. / Ehrenberg, M. / Frank, J.
CitationJ. Mol. Biol., 2007, 374, 1345-1358

primary. J. Mol. Biol., 2007, 374, 1345-1358 StrPapers
Specific interaction between EF-G and RRF and its implication for GTP-dependent ribosome splitting into subunits.
Ning Gao / Andrey V Zavialov / Måns Ehrenberg / Joachim Frank

#1. J.Mol.Biol., 2005, 348, 939-949
Structural insights into fusidic acid resistance and sensitivity in EF-G.
Hansson, S. / Singh, R. / Gudkov, A.T. / Liljas, A. / Logan, D.T.

#2. Science, 2005, 310, 827-834
Structures of the bacterial ribosome at 3.5 A resolution.
Schuwirth, B.S. / Borovinskaya, M.A. / Hau, C.W. / Zhang, W. / Vila-Sanjurjo, A. / Holton, J.M. / Cate, J.H.

#3. Embo J., 2000, 19, 2362-2370
Crystal structure of the ribosome recycling factor from Escherichia coli.
Kim, K.K. / Min, K. / Suh, S.W.

#4. Nat.Struct.Mol.Biol., 2003, 10, 104-108
Structure of the L1 protuberance in the ribosome.
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. Mol.Cell, 2005, 18, 663-674
Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies.
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 chain5S RIBOSOMAL RNA / Coordinate model: P atoms only


Mass: 38790.090 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: GenBank: 33357928
#2: RNA chain23S RIBOSOMAL RNA / Coordinate model: P atoms only


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

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

#3: Polypeptide(L)50S ribosomal protein L25 / Coordinate model: Cα atoms only


Mass: 10713.465 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P68919

Cellular component

Molecular function

Biological process

#4: Polypeptide(L)50S ribosomal protein L2 / Coordinate model: Cα atoms only


Mass: 29792.424 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P60422

Cellular component

Molecular function

Biological process

#5: Polypeptide(L)50S ribosomal protein L3 / Coordinate model: Cα atoms only


Mass: 22277.535 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P60438

Cellular component

Molecular function

Biological process

#6: Polypeptide(L)50S ribosomal protein L4 / Coordinate model: Cα atoms only


Mass: 22121.566 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P60723

Cellular component

Molecular function

Biological process

#7: Polypeptide(L)50S ribosomal protein L5 / Coordinate model: Cα atoms only


Mass: 20202.416 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P62399

Cellular component

Molecular function

Biological process

#8: Polypeptide(L)50S ribosomal protein L6 / Coordinate model: Cα atoms only


Mass: 18801.598 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0AG55

Cellular component

Molecular function

Biological process

#9: Polypeptide(L)50S ribosomal protein L13 / Coordinate model: Cα atoms only


Mass: 16050.606 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0AA10

Cellular component

Molecular function

Biological process

#10: Polypeptide(L)50S ribosomal protein L14 / Coordinate model: Cα atoms only


Mass: 13565.067 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0ADY3

Cellular component

Molecular function

Biological process

#11: Polypeptide(L)50S ribosomal protein L15 / Coordinate model: Cα atoms only


Mass: 15008.471 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P02413

Cellular component

Molecular function

Biological process

#12: Polypeptide(L)50S ribosomal protein L16 / Coordinate model: Cα atoms only


Mass: 15312.269 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0ADY7

Cellular component

Molecular function

Biological process

#13: Polypeptide(L)50S ribosomal protein L17 / Coordinate model: Cα atoms only


Mass: 14393.657 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0AG44

Cellular component

Molecular function

Biological process

#14: Polypeptide(L)50S ribosomal protein L18 / Coordinate model: Cα atoms only


Mass: 12794.668 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0C018

Cellular component

Molecular function

Biological process

#15: Polypeptide(L)50S ribosomal protein L19 / Coordinate model: Cα atoms only


Mass: 13028.082 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7K6

Cellular component

Molecular function

Biological process

#16: Polypeptide(L)50S ribosomal protein L20 / Coordinate model: Cα atoms only


Mass: 13396.828 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7L3

Cellular component

Molecular function

Biological process

#17: Polypeptide(L)50S ribosomal protein L21 / Coordinate model: Cα atoms only


Mass: 11586.374 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0AG48

Cellular component

Molecular function

Biological process

#18: Polypeptide(L)50S ribosomal protein L22 / Coordinate model: Cα atoms only


Mass: 12253.359 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P61175

Cellular component

Molecular function

Biological process

#19: Polypeptide(L)50S ribosomal protein L23 / Coordinate model: Cα atoms only


Mass: 11222.160 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0ADZ0

Cellular component

Molecular function

Biological process

#20: Polypeptide(L)50S ribosomal protein L24 / Coordinate model: Cα atoms only


Mass: 11208.054 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P60624

Cellular component

Molecular function

Biological process

#21: Polypeptide(L)50S ribosomal protein L27 / Coordinate model: Cα atoms only


Mass: 9015.344 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7L8

Cellular component

Molecular function

Biological process

#22: Polypeptide(L)50S ribosomal protein L29 / Coordinate model: Cα atoms only


Mass: 7286.464 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7M6

Cellular component

Molecular function

Biological process

#23: Polypeptide(L)50S ribosomal protein L30 / Coordinate model: Cα atoms only


Mass: 6423.625 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0AG51

Cellular component

Molecular function

Biological process

#24: Polypeptide(L)50S ribosomal protein L31 / Coordinate model: Cα atoms only


Mass: 7887.117 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7M9

Cellular component

Molecular function

Biological process

#25: Polypeptide(L)50S ribosomal protein L32 / Coordinate model: Cα atoms only


Mass: 6332.249 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7N4

Cellular component

Molecular function

Biological process

#26: Polypeptide(L)50S ribosomal protein L33 / Coordinate model: Cα atoms only


Mass: 6257.436 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7N9

Cellular component

Molecular function

Biological process

#27: Polypeptide(L)50S ribosomal protein L34 / Coordinate model: Cα atoms only


Mass: 5397.463 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7P5

Cellular component

Molecular function

Biological process

#28: Polypeptide(L)50S ribosomal protein L35 / Coordinate model: Cα atoms only


Mass: 7181.835 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7Q1

Cellular component

Molecular function

Biological process

#29: Polypeptide(L)50S ribosomal protein L36 / Ribosomal protein B / Coordinate model: Cα atoms only


Mass: 4377.390 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7Q6

Cellular component

Molecular function

Biological process

#30: Polypeptide(L)50S ribosomal protein L11 / Coordinate model: Cα atoms only


Mass: 14763.165 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7J7

Cellular component

Molecular function

Biological process

#31: Polypeptide(L)50S ribosomal protein L9 / Coordinate model: Cα atoms only


Mass: 15789.020 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7R1

Cellular component

Molecular function

Biological process

#32: Polypeptide(L)50S ribosomal protein L1 / Coordinate model: Cα atoms only


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

Cellular component

Molecular function

Biological process

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Polypeptide(L) , 2 types, 2 molecules 78

#33: Polypeptide(L)Elongation factor G / EF-G / Coordinate model: Cα atoms only


Mass: 77676.227 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A6M8

Cellular component

Molecular function

#34: Polypeptide(L)Ribosome recycling factor / Ribosome-releasing factor / RRF / Coordinate model: Cα atoms only


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

Cellular component

Molecular function

Biological process

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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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 FIELD / 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
2SPIDERRECONSTRUCTION
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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