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- PDB-3j5l: Structure of the E. coli 50S subunit with ErmBL nascent chain -

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Basic information

Entry
Database: PDB / ID: 3j5l
TitleStructure of the E. coli 50S subunit with ErmBL nascent chain
DescriptorErythromycin resistance leader peptide
(50S ribosomal protein ...) x 28
KeywordsRIBOSOME/ANTIBIOTIC / erythromycin / stalling / RIBOSOME-ANTIBIOTIC complex
Specimen sourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Streptococcus sanguinis / bacteria / ストレプトコッカス・サングイニス
MethodElectron microscopy (6.6 Å resolution / Particle / Single particle)
AuthorsArenz, S. / Ramu, H. / Gupta, P. / Berninghausen, O. / Beckmann, R. / Vazquez-Laslop, N. / Mankin, A.S. / Wilson, D.N.
CitationNat Commun, 2014, 5, 3501-3501

Nat Commun, 2014, 5, 3501-3501 Yorodumi Papers
Molecular basis for erythromycin-dependent ribosome stalling during translation of the ErmBL leader peptide.
Stefan Arenz / Haripriya Ramu / Pulkit Gupta / Otto Berninghausen / Roland Beckmann / Nora Vázquez-Laslop / Alexander S Mankin / Daniel N Wilson

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 23, 2013 / Release: Mar 26, 2014
RevisionDateData content typeGroupProviderType
1.0Mar 26, 2014Structure modelrepositoryInitial release
1.1Apr 2, 2014Structure modelDatabase references

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Assembly

Deposited unit
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
5: 5'-R(*CP*(MA6))-3'
6: Erythromycin resistance leader peptide
7: 5'-R(*CP*CP*A)-3'
A: 23S ribsomal RNA
B: 5S ribosomal RNA
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
H: 50S ribosomal protein L9
I: 50S ribosomal protein L11
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
V: 50S ribosomal protein L25
W: 50S ribosomal protein L27
X: 50S ribosomal protein L28
Y: 50S ribosomal protein L29
Z: 50S ribosomal protein L30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,345,99636
Polyers1,345,26234
Non-polymers7342
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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50S ribosomal protein ... , 29 types, 29 molecules 01234CDEFG...

#1: Polypeptide(L)50S ribosomal protein L32


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

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)50S ribosomal protein L33


Mass: 5814.842 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7N9

Cellular component

Molecular function

Biological process

#3: Polypeptide(L)50S ribosomal protein L34


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

Cellular component

Molecular function

Biological process

#4: Polypeptide(L)50S ribosomal protein L35


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

Cellular component

Molecular function

Biological process

#5: Polypeptide(L)50S ribosomal protein L36


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

Cellular component

Molecular function

Biological process

#11: Polypeptide(L)50S ribosomal protein L2


Mass: 29663.244 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P60422

Cellular component

Molecular function

Biological process

#12: Polypeptide(L)50S ribosomal protein L3


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

Cellular component

Molecular function

Biological process

#13: Polypeptide(L)50S ribosomal protein L4


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

Cellular component

Molecular function

Biological process

#14: Polypeptide(L)50S ribosomal protein L5


Mass: 20073.234 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P62399

Cellular component

Molecular function

Biological process

#15: Polypeptide(L)50S ribosomal protein L6


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

Cellular component

Molecular function

Biological process

#16: Polypeptide(L)50S ribosomal protein L9


Mass: 6138.101 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source: (natural) Escherichia coli / References: UniProt: P0A7R1

Cellular component

Molecular function

Biological process

#17: Polypeptide(L)50S ribosomal protein L11


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

Cellular component

Molecular function

Biological process

#18: Polypeptide(L)50S ribosomal protein L13


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

Cellular component

Molecular function

Biological process

#19: Polypeptide(L)50S ribosomal protein L14


Mass: 13451.910 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0ADY3

Cellular component

Molecular function

Biological process

#20: Polypeptide(L)50S ribosomal protein L15


Mass: 14877.273 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P02413

Cellular component

Molecular function

Biological process

#21: Polypeptide(L)50S ribosomal protein L16


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

Cellular component

Molecular function

Biological process

#22: Polypeptide(L)50S ribosomal protein L17


Mass: 13721.938 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0AG44

Cellular component

Molecular function

Biological process

#23: Polypeptide(L)50S ribosomal protein L18


Mass: 12663.471 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0C018

Cellular component

Molecular function

Biological process

#24: Polypeptide(L)50S ribosomal protein L19


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

Cellular component

Molecular function

Biological process

#25: Polypeptide(L)50S ribosomal protein L20


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

Cellular component

Molecular function

Biological process

#26: Polypeptide(L)50S ribosomal protein L21


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

Cellular component

Molecular function

Biological process

#27: Polypeptide(L)50S ribosomal protein L22


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

Cellular component

Molecular function

Biological process

#28: Polypeptide(L)50S ribosomal protein L23


Mass: 10546.472 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0ADZ0

Cellular component

Molecular function

Biological process

#29: Polypeptide(L)50S ribosomal protein L24


Mass: 11078.874 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P60624

Cellular component

Molecular function

Biological process

#30: Polypeptide(L)50S ribosomal protein L25


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

Cellular component

Molecular function

Biological process

#31: Polypeptide(L)50S ribosomal protein L27


Mass: 8476.680 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7L8

Cellular component

Molecular function

Biological process

#32: Polypeptide(L)50S ribosomal protein L28


Mass: 8896.354 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7M2

Cellular component

Molecular function

Biological process

#33: Polypeptide(L)50S ribosomal protein L29


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

Cellular component

Molecular function

Biological process

#34: Polypeptide(L)50S ribosomal protein L30


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

Cellular component

Molecular function

Biological process

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RNA chain , 4 types, 4 molecules 57AB

#6: RNA chain5'-R(*CP*(MA6))-3'


Mass: 617.483 Da / Num. of mol.: 1 / Details: 3'-end of A-site tRNA
#8: RNA chain5'-R(*CP*CP*A)-3'


Mass: 894.612 Da / Num. of mol.: 1 / Details: 3'-end of P-site tRNA
#9: RNA chain23S ribsomal RNA


Mass: 941612.375 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: GenBank: 33357927
#10: RNA chain5S ribosomal RNA


Mass: 38177.762 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: GenBank: CP000948.1

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Polypeptide(L) , 1 types, 1 molecules 6

#7: Polypeptide(L)Erythromycin resistance leader peptide / ErmBL / Coordinate model: Cα atoms only


Mass: 1253.513 Da / Num. of mol.: 1 / Fragment: nascent chain / Source: (natural) Streptococcus sanguinis

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Non-polymers , 2 types, 2 molecules

#35: ChemicalChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1
#36: ChemicalChemComp-ERY / ERYTHROMYCIN A


Mass: 733.927 Da / Num. of mol.: 1 / Formula: C37H67NO13

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Details

Sequence detailsFULL-LENGTH PROTEIN L9 IS PRESENT IN THE RIBOSOME, BUT ONLY RESIDUES 1-56 ARE MODELED.

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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: ErmBL-stalled E. coli 70S ribosome / Type: RIBOSOME
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: Plunged into liquid ethane (FEI VITROBOT MARK IV)

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS / Date: Mar 14, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 148721 / Calibrated magnification: 148721 / Nominal defocus max: 4500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Camera length: 0 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 20 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k)
Image scansNumber digital images: 17906
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
IDNameCategory
1UCSF ChimeraMODEL FITTING
2SPIDERRECONSTRUCTION
CTF correctionDetails: Defocus groups
SymmetryPoint symmetry: C1
3D reconstructionResolution: 6.6 Å / Resolution method: FSC 0.5 CUT-OFF / Number of particles: 349744 / Nominal pixel size: 1.0605 / Actual pixel size: 1.0605 / Details: (Single particle--Applied symmetry: C1) / Symmetry type: POINT
Atomic model buildingDetails: REFINEMENT PROTOCOL--rigid body / Ref protocol: RIGID BODY FIT / Ref space: REAL
Atomic model buildingPDB-ID: 3OFR
Number of atoms included #LASTProtein: 25470 / Nucleic acid: 63857 / Ligand: 55 / Solvent: 0 / Total: 89382

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