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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
Components
  • (50S ribosomal protein ...) x 29
  • 23S ribsomal RNA
  • 5'-R(*CP*(MA6))-3'
  • 5'-R(*CP*CP*A)-3'
  • 5S ribosomal RNA
  • Erythromycin resistance leader peptide
KeywordsRIBOSOME/ANTIBIOTIC / erythromycin / stalling / RIBOSOME-ANTIBIOTIC complex
Function / homologyRibosomal protein L13, conserved site / Ribosomal protein L5, N-terminal / Ribosomal protein L5 domain superfamily / Ribosomal protein L22 signature. / Ribosomal protein L4 domain superfamily / Ribosomal protein L28/L24 / Ribosomal protein L21-like / Ribosomal protein L25 / Ribosomal protein L15 / Ribosomal protein L5, C-terminal ...Ribosomal protein L13, conserved site / Ribosomal protein L5, N-terminal / Ribosomal protein L5 domain superfamily / Ribosomal protein L22 signature. / Ribosomal protein L4 domain superfamily / Ribosomal protein L28/L24 / Ribosomal protein L21-like / Ribosomal protein L25 / Ribosomal protein L15 / Ribosomal protein L5, C-terminal / L28p-like / Ribosomal protein L2, C-terminal / Ribosomal protein L20, C-terminal / Ribosomal protein L36 superfamily / Ribosomal protein L29/L35 superfamily / L21-like 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 L2, conserved site / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L9, C-terminal / Ribosomal protein L35, conserved site / Ribosomal protein L6, bacterial-type / Ribosomal protein L3, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L14P, conserved site / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L25, short-form / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L9, N-terminal / Ribosomal protein L35 / 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 L9, C-terminal domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L27, conserved site / Ribosomal protein L19 / ribosomal L5P family C-terminus / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal prokaryotic L21 protein / Ribosomal L28 family / Ribosomal L29 protein / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal L27 protein / Ribosomal protein L17 / Ribosomal protein L9, N-terminal domain / Ribosomal protein L13 / Ribosomal L25p family / Ribosomal protein L35 / Ribosomal L32p protein family / Ribosomal protein L11, N-terminal domain / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L9, C-terminal domain / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L14 signature. / Ribosomal protein L23 signature. / Ribosomal protein L4/L1 family / Ribosomal protein L33 / Ribosomal protein L13 superfamily / Ribosomal protein L14p/L23e / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L28/L24 superfamily / Ribosomal protein L35 superfamily / Ribosomal protein L33 superfamily / Ribosomal protein L19 superfamily / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L22p/L17e / Ribosomal protein L16p/L10e / Ribosomal protein L34 / Ribosomal protein L23 / Ribosomal protein L5 / Ribosomal protein L3 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L30p/L7e / Ribosomal protein L6 / Ribosomal protein L36 / Ribosomal protein L20 / KOW motif / Ribosomal protein L33, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L3 / Ribosomal protein L16 / Ribosomal protein L14P / Ribosomal protein L9 / Ribosomal protein L34 / Ribosomal protein L17
Function and homology information
Specimen sourceEscherichia coli (E. coli)
Streptococcus sanguinis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 6.6 Å resolution
AuthorsArenz, S. / Ramu, H. / Gupta, P. / Berninghausen, O. / Beckmann, R. / Vazquez-Laslop, N. / Mankin, A.S. / Wilson, D.N.
CitationJournal: Nat Commun / Year: 2014
Title: Molecular basis for erythromycin-dependent ribosome stalling during translation of the ErmBL leader peptide.
Authors: 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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Structure visualization

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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 01234CDEFGHIJKLMNOPQRSTUVWXYZ

#1: Protein/peptide 50S ribosomal protein L32 /


Mass: 6332.249 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7N4
#2: Protein/peptide 50S ribosomal protein L33 /


Mass: 5814.842 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7N9
#3: Protein/peptide 50S ribosomal protein L34 /


Mass: 5397.463 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7P5
#4: Protein/peptide 50S ribosomal protein L35 /


Mass: 7181.835 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7Q1
#5: Protein/peptide 50S ribosomal protein L36 /


Mass: 4377.390 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7Q6
#11: Protein/peptide 50S ribosomal protein L2 /


Mass: 29663.244 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P60422
#12: Protein/peptide 50S ribosomal protein L3 /


Mass: 22277.535 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P60438
#13: Protein/peptide 50S ribosomal protein L4 /


Mass: 22121.566 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P60723
#14: Protein/peptide 50S ribosomal protein L5 /


Mass: 20073.234 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P62399
#15: Protein/peptide 50S ribosomal protein L6 /


Mass: 18801.598 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0AG55
#16: Protein/peptide 50S ribosomal protein L9 /


Mass: 6138.101 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7R1
#17: Protein/peptide 50S ribosomal protein L11 /


Mass: 14763.165 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7J7
#18: Protein/peptide 50S ribosomal protein L13 /


Mass: 16050.606 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0AA10
#19: Protein/peptide 50S ribosomal protein L14 /


Mass: 13451.910 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0ADY3
#20: Protein/peptide 50S ribosomal protein L15 /


Mass: 14877.273 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P02413
#21: Protein/peptide 50S ribosomal protein L16 /


Mass: 15312.269 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0ADY7
#22: Protein/peptide 50S ribosomal protein L17 /


Mass: 13721.938 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0AG44
#23: Protein/peptide 50S ribosomal protein L18 /


Mass: 12663.471 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0C018
#24: Protein/peptide 50S ribosomal protein L19 /


Mass: 13028.082 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7K6
#25: Protein/peptide 50S ribosomal protein L20 /


Mass: 13396.828 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7L3
#26: Protein/peptide 50S ribosomal protein L21 /


Mass: 11586.374 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0AG48
#27: Protein/peptide 50S ribosomal protein L22 /


Mass: 12253.359 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P61175
#28: Protein/peptide 50S ribosomal protein L23 /


Mass: 10546.472 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0ADZ0
#29: Protein/peptide 50S ribosomal protein L24 /


Mass: 11078.874 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P60624
#30: Protein/peptide 50S ribosomal protein L25 /


Mass: 10713.465 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P68919
#31: Protein/peptide 50S ribosomal protein L27 /


Mass: 8476.680 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7L8
#32: Protein/peptide 50S ribosomal protein L28 /


Mass: 8896.354 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7M2
#33: Protein/peptide 50S ribosomal protein L29 /


Mass: 7286.464 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0A7M6
#34: Protein/peptide 50S ribosomal protein L30 /


Mass: 6423.625 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: UniProt: P0AG51

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RNA chain , 4 types, 4 molecules 57AB

#6: RNA chain 5'-R(*CP*(MA6))-3'


Mass: 617.483 Da / Num. of mol.: 1 / Details: 3'-end of A-site tRNA
#8: RNA chain 5'-R(*CP*CP*A)-3'


Mass: 894.612 Da / Num. of mol.: 1 / Details: 3'-end of P-site tRNA
#9: RNA chain 23S ribsomal RNA


Mass: 941612.375 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: GenBank: 33357927
#10: RNA chain 5S ribosomal RNA /


Mass: 38177.762 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: K-12 / References: GenBank: CP000948.1

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Protein/peptide , 1 types, 1 molecules 6

#7: Protein/peptide 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 (bacteria)

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Non-polymers , 2 types, 2 molecules

#35: Chemical ChemComp-UNL / UNKNOWN LIGAND


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


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

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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 reconstruction

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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 FIELDBright-field microscopy / 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
2SPIDER3D reconstruction
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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