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- PDB-4uy8: Molecular basis for the ribosome functioning as a L-tryptophan se... -

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Entry
Database: PDB / ID: 4uy8
TitleMolecular basis for the ribosome functioning as a L-tryptophan sensor - Cryo-EM structure of a TnaC stalled E.coli ribosome
Components
  • (50S RIBOSOMAL PROTEIN ...) x 29
  • RIBOSOMAL L7 PROTEIN
  • RIBOSOMAL PROTEIN L9
  • RNA
  • RRNA-23S RIBOSOMAL RNA
  • RRNA-5S RIBOSOMAL RNA
  • TRYPTOPHANASE
KeywordsRIBOSOME / TNAC / TRANSLATION REGULATION
Function / homologyRibosomal L18e/L15P superfamily / Ribosomal protein L5, C-terminal / Ribosomal protein L2, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein L10 / Ribosomal protein L13, conserved site / Ribosomal protein L4 domain superfamily / Ribosomal protein L28/L24 / Ribosomal protein L21-like / Ribosomal protein L25 ...Ribosomal L18e/L15P superfamily / Ribosomal protein L5, C-terminal / Ribosomal protein L2, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein L10 / Ribosomal protein L13, conserved site / Ribosomal protein L4 domain superfamily / Ribosomal protein L28/L24 / Ribosomal protein L21-like / Ribosomal protein L25 / Ribosomal protein L15 / Ribosomal protein L5, N-terminal / Ribosomal Proteins L2, RNA binding domain / L28p-like / Ribosomal protein L20, C-terminal / Ribosomal protein L36 superfamily / Ribosomal protein L29/L35 superfamily / L21-like superfamily / Ribosomal protein L11 signature. / Ribosomal protein L7/L12, oligomerisation domain superfamily / Ribosomal protein L17 superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L2, C-terminal / Ribosomal protein L35 / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L25, short-form / Ribosomal protein L22/L17, conserved site / Ribosomal protein L27, conserved site / Ribosomal protein L33, conserved site / 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/Gln-tRNA synthetase, N-terminal / Ribosomal protein L18e/L15P / Ribosomal protein L9, C-terminal / Ribosomal protein L9, N-terminal / 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 L6, alpha-beta domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L19, conserved site / Ribosomal protein L19 / Ribosomal protein L4/L1 family / 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 L7/L12 C-terminal domain / 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 / Tryptophanase operon leader peptide / Ribosomal protein L7/L12 dimerisation domain / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L14 signature. / Ribosomal protein L13 / Ribosomal protein L33 / Ribosomal protein L14 superfamily / Ribosomal protein L14p/L23e / Ribosomal protein L13 superfamily / 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 / Ribosomal protein L10 / KOW motif / Ribosomal protein L21, conserved site
Function and homology information
Specimen sourceESCHERICHIA COLI (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.8 Å resolution
AuthorsBischoff, L. / Berninghausen, O. / Beckmann, R.
CitationJournal: Cell Rep / Year: 2014
Title: Molecular basis for the ribosome functioning as an L-tryptophan sensor.
Authors: Lukas Bischoff / Otto Berninghausen / Roland Beckmann
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 29, 2014 / Release: Oct 29, 2014
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 29, 2014Structure modelrepositoryInitial release
1.1Nov 19, 2014Structure modelDatabase references
1.2Aug 30, 2017Structure modelData collection / Source and taxonomy / Structure summaryem_image_scans / entity / entity_src_nat_entity.src_method / _entity_src_nat.strain

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Structure visualization

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  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-2773
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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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: 50S RIBOSOMAL PROTEIN L10
6: RIBOSOMAL L7 PROTEIN
7: TRYPTOPHANASE
8: 50S RIBOSOMAL PROTEIN L25
A: RRNA-23S RIBOSOMAL RNA
B: RRNA-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: 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: RNA
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)1,376,256181
Polyers1,372,30635
Non-polymers3,949146
Water7,909439
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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50S RIBOSOMAL PROTEIN ... , 29 types, 29 molecules 0123458CDEFGIJKLMNOPQRSTUWXYZ

#1: Protein/peptide 50S RIBOSOMAL PROTEIN L32 /


Mass: 6332.249 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: U5SG25, UniProt: P0A7N4*PLUS
#2: Protein/peptide 50S RIBOSOMAL PROTEIN L33 /


Mass: 5814.842 Da / Num. of mol.: 1 / Fragment: RESIDUES 4-53 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: U5SML7, UniProt: P0A7N9*PLUS
#3: Protein/peptide 50S RIBOSOMAL PROTEIN L34 /


Mass: 5397.463 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / 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: KC6 / References: UniProt: W0KX84, UniProt: P0A7Q1*PLUS
#5: Protein/peptide 50S RIBOSOMAL PROTEIN L36 /


Mass: 4377.390 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: X7QRM8, UniProt: P0A7Q6*PLUS
#6: Protein/peptide 50S RIBOSOMAL PROTEIN L10 /


Mass: 15981.518 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: E1IXH4, UniProt: P0A7J3*PLUS
#9: Protein/peptide 50S RIBOSOMAL PROTEIN L25 /


Mass: 10713.465 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: E3PCX7, UniProt: P68919*PLUS
#12: Protein/peptide 50S RIBOSOMAL PROTEIN L2 /


Mass: 29663.244 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: X7QS81, UniProt: P60422*PLUS
#13: Protein/peptide 50S RIBOSOMAL PROTEIN L3 /


Mass: 22277.535 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: D6IEL8, UniProt: P60438*PLUS
#14: Protein/peptide 50S RIBOSOMAL PROTEIN L4 /


Mass: 22121.566 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: X7QRP4, UniProt: P60723*PLUS
#15: Protein/peptide 50S RIBOSOMAL PROTEIN L5 /


Mass: 20073.234 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: X7QU92, UniProt: P62399*PLUS
#16: Protein/peptide 50S RIBOSOMAL PROTEIN L6 /


Mass: 18801.598 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: X7QBP9, UniProt: P0AG55*PLUS
#18: Protein/peptide 50S RIBOSOMAL PROTEIN L11 /


Mass: 14763.165 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: E7HV64, UniProt: P0A7J7*PLUS
#19: Protein/peptide 50S RIBOSOMAL PROTEIN L13 /


Mass: 16050.606 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: X7QR95, UniProt: P0AA10*PLUS
#20: Protein/peptide 50S RIBOSOMAL PROTEIN L14 /


Mass: 13451.910 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: E1PGS6, UniProt: P0ADY3*PLUS
#21: Protein/peptide 50S RIBOSOMAL PROTEIN L15 /


Mass: 14877.273 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: P02413
#22: Protein/peptide 50S RIBOSOMAL PROTEIN L16 /


Mass: 15312.269 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: D7XL00, UniProt: P0ADY7*PLUS
#23: Protein/peptide 50S RIBOSOMAL PROTEIN L17 /


Mass: 13721.938 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: X7QRM3, UniProt: P0AG44*PLUS
#24: Protein/peptide 50S RIBOSOMAL PROTEIN L18 /


Mass: 12663.471 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: X7QRN2, UniProt: P0C018*PLUS
#25: Protein/peptide 50S RIBOSOMAL PROTEIN L19 /


Mass: 13028.082 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: X7R0V6, UniProt: P0A7K6*PLUS
#26: Protein/peptide 50S RIBOSOMAL PROTEIN L20 /


Mass: 13396.828 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: X7QXR5, UniProt: P0A7L3*PLUS
#27: Protein/peptide 50S RIBOSOMAL PROTEIN L21 /


Mass: 11586.374 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: W0L2B9, UniProt: P0AG48*PLUS
#28: Protein/peptide 50S RIBOSOMAL PROTEIN L22 /


Mass: 12253.359 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: E1JB10, UniProt: P61175*PLUS
#29: Protein/peptide 50S RIBOSOMAL PROTEIN L23 /


Mass: 10546.472 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: C6EGE8, UniProt: P0ADZ0*PLUS
#30: Protein/peptide 50S RIBOSOMAL PROTEIN L24 /


Mass: 11078.874 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: W0L2N0, UniProt: P60624*PLUS
#32: Protein/peptide 50S RIBOSOMAL PROTEIN L27 /


Mass: 8476.680 Da / Num. of mol.: 1 / Fragment: RESIDUES 7-85 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: W0KYJ4, UniProt: P0A7L8*PLUS
#33: Protein/peptide 50S RIBOSOMAL PROTEIN L28 /


Mass: 8896.354 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: C3SME2, UniProt: P0A7M2*PLUS
#34: Protein/peptide 50S RIBOSOMAL PROTEIN L29 /


Mass: 7286.464 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: D7X2Z3, UniProt: P0A7M6*PLUS
#35: Protein/peptide 50S RIBOSOMAL PROTEIN L30 /


Mass: 6423.625 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: W0L301, UniProt: P0AG51*PLUS

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Protein/peptide , 3 types, 3 molecules 67H

#7: Protein/peptide RIBOSOMAL L7 PROTEIN


Mass: 3300.856 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: V5UZV4, UniProt: P0A7K2*PLUS
#8: Protein/peptide TRYPTOPHANASE /


Mass: 2427.801 Da / Num. of mol.: 1 / Fragment: RESIDUES 5-24 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: A4GWE7, UniProt: P0AD89*PLUS
#17: Protein/peptide RIBOSOMAL PROTEIN L9 /


Mass: 5467.367 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: D8BKG3, UniProt: P0A7R1*PLUS

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RNA chain , 3 types, 3 molecules ABV

#10: RNA chain RRNA-23S RIBOSOMAL RNA


Mass: 925492.125 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: GenBank: 64682453
#11: RNA chain RRNA-5S RIBOSOMAL RNA


Mass: 38177.762 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: GenBank: 64693170
#31: RNA chain RNA /


Mass: 24890.803 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: GenBank: 66001753

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Non-polymers , 4 types, 585 molecules

#36: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 143 / Formula: Mg / Magnesium
#37: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Formula: Zn / Zinc
#38: Chemical ChemComp-TRP / TRYPTOPHAN


Mass: 204.225 Da / Num. of mol.: 2 / Formula: C11H12N2O2 / Tryptophan
#39: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / Formula: H2O / Water

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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: TNAC STALLED E.COLI RIBOSOME / Type: RIBOSOME
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE
Details: VITRIFICATION 1 --CRYOGEN- ETHANE,INSTRUMENT- 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: Jan 27, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON II (4k x 4k)
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: SPIDER / Category: 3D reconstruction
CTF correctionDetails: MICROGRAPH
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.8 Å / Number of particles: 72468
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2773. (DEPOSITION ID: 12802).
Symmetry type: POINT
Least-squares processHighest resolution: 3.8 Å
Refine hist #LASTHighest resolution: 3.8 Å
Number of atoms included #LASTProtein: 26922 / Nucleic acid: 65452 / Ligand: 174 / Solvent: 439 / Total: 92987

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