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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
DescriptorTRYPTOPHANASE
(50S RIBOSOMAL PROTEIN ...) x 27
(RIBOSOMAL ...) x 2
KeywordsRIBOSOME / TNAC / TRANSLATION REGULATION
Specimen sourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
MethodElectron microscopy (3.8 Å resolution / Particle / Single particle)
AuthorsBischoff, L. / Berninghausen, O. / Beckmann, R.
CitationCell Rep, 2014, 9, 469-475

Cell Rep, 2014, 9, 469-475 StrPapers
Molecular basis for the ribosome functioning as an L-tryptophan sensor.
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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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 0123458CDE...

#1: Polypeptide(L)50S RIBOSOMAL PROTEIN L32


Mass: 6332.249 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI / References: UniProt: U5SG25

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)50S RIBOSOMAL PROTEIN L33


Mass: 5814.842 Da / Num. of mol.: 1 / Fragment: RESIDUES 4-53 / Source: (natural) ESCHERICHIA COLI / References: UniProt: U5SML7

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: W0KX84

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: X7QRM8

Cellular component

Molecular function

Biological process

#6: Polypeptide(L)50S RIBOSOMAL PROTEIN L10


Mass: 15981.518 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI / References: UniProt: E1IXH4

Cellular component

Molecular function

Biological process

#9: Polypeptide(L)50S RIBOSOMAL PROTEIN L25


Mass: 10713.465 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI / References: UniProt: E3PCX7

Cellular component

Molecular function

Biological process

#12: Polypeptide(L)50S RIBOSOMAL PROTEIN L2


Mass: 29663.244 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI / References: UniProt: X7QS81

Cellular component

Molecular function

Biological process

#13: Polypeptide(L)50S RIBOSOMAL PROTEIN L3


Mass: 22277.535 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI / References: UniProt: D6IEL8

Cellular component

Molecular function

Biological process

#14: Polypeptide(L)50S RIBOSOMAL PROTEIN L4


Mass: 22121.566 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI / References: UniProt: X7QRP4

Cellular component

Molecular function

Biological process

#15: Polypeptide(L)50S RIBOSOMAL PROTEIN L5


Mass: 20073.234 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI / References: UniProt: X7QU92

Cellular component

Molecular function

Biological process

#16: Polypeptide(L)50S RIBOSOMAL PROTEIN L6


Mass: 18801.598 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI / References: UniProt: X7QBP9

Cellular component

Molecular function

Biological process

#18: Polypeptide(L)50S RIBOSOMAL PROTEIN L11


Mass: 14763.165 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI / References: UniProt: E7HV64

Cellular component

Molecular function

Biological process

#19: Polypeptide(L)50S RIBOSOMAL PROTEIN L13


Mass: 16050.606 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI / References: UniProt: X7QR95

Cellular component

Molecular function

Biological process

#20: Polypeptide(L)50S RIBOSOMAL PROTEIN L14


Mass: 13451.910 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI / References: UniProt: E1PGS6

Cellular component

Molecular function

Biological process

#21: 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

#22: Polypeptide(L)50S RIBOSOMAL PROTEIN L16


Mass: 15312.269 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI / References: UniProt: D7XL00

Cellular component

Molecular function

Biological process

#23: Polypeptide(L)50S RIBOSOMAL PROTEIN L17


Mass: 13721.938 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI / References: UniProt: X7QRM3

Cellular component

Molecular function

Biological process

#24: Polypeptide(L)50S RIBOSOMAL PROTEIN L18


Mass: 12663.471 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI / References: UniProt: X7QRN2

Cellular component

Molecular function

Biological process

#25: Polypeptide(L)50S RIBOSOMAL PROTEIN L19


Mass: 13028.082 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI / References: UniProt: X7R0V6

Cellular component

Molecular function

Biological process

#26: Polypeptide(L)50S RIBOSOMAL PROTEIN L20


Mass: 13396.828 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI / References: UniProt: X7QXR5

Cellular component

Molecular function

Biological process

#27: Polypeptide(L)50S RIBOSOMAL PROTEIN L21


Mass: 11586.374 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI / References: UniProt: W0L2B9

Cellular component

Molecular function

Biological process

#28: Polypeptide(L)50S RIBOSOMAL PROTEIN L22


Mass: 12253.359 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI / References: UniProt: E1JB10

Cellular component

Molecular function

Biological process

#29: Polypeptide(L)50S RIBOSOMAL PROTEIN L23


Mass: 10546.472 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI / References: UniProt: C6EGE8

Cellular component

Molecular function

Biological process

#30: Polypeptide(L)50S RIBOSOMAL PROTEIN L24


Mass: 11078.874 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI / References: UniProt: W0L2N0

Cellular component

Molecular function

Biological process

#32: Polypeptide(L)50S RIBOSOMAL PROTEIN L27


Mass: 8476.680 Da / Num. of mol.: 1 / Fragment: RESIDUES 7-85 / Source: (natural) ESCHERICHIA COLI / References: UniProt: W0KYJ4

Cellular component

Molecular function

Biological process

#33: Polypeptide(L)50S RIBOSOMAL PROTEIN L28


Mass: 8896.354 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI / References: UniProt: C3SME2

Cellular component

Molecular function

Biological process

#34: Polypeptide(L)50S RIBOSOMAL PROTEIN L29


Mass: 7286.464 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI / References: UniProt: D7X2Z3

Cellular component

Molecular function

Biological process

#35: Polypeptide(L)50S RIBOSOMAL PROTEIN L30


Mass: 6423.625 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI / References: UniProt: W0L301

Cellular component

Molecular function

Biological process

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RIBOSOMAL ... , 2 types, 2 molecules 6H

#7: Polypeptide(L)RIBOSOMAL L7 PROTEIN


Mass: 3300.856 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI / References: UniProt: V5UZV4

Cellular component

Molecular function

Biological process

#17: Polypeptide(L)RIBOSOMAL PROTEIN L9


Mass: 5467.367 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI / References: UniProt: D8BKG3

Cellular component

Molecular function

Biological process

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Polypeptide(L) , 1 types, 1 molecules 7

#8: Polypeptide(L)TRYPTOPHANASE


Mass: 2427.801 Da / Num. of mol.: 1 / Fragment: RESIDUES 5-24 / Source: (natural) ESCHERICHIA COLI / References: UniProt: A4GWE7

Biological process

  • positive regulation of tryptophan metabolic process (GO: 0090358)
  • transcriptional attenuation by ribosome (GO: 0031556)

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RNA chain , 3 types, 3 molecules ABV

#10: RNA chainRRNA-23S RIBOSOMAL RNA


Mass: 925492.125 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI / References: GenBank: 64682453
#11: RNA chainRRNA-5S RIBOSOMAL RNA


Mass: 38177.762 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI / References: GenBank: 64693170
#31: RNA chainRNA


Mass: 24890.803 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI / 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
#37: ChemicalChemComp-ZN / ZINC ION


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


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


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

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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: 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 FIELD
Image recordingFilm or detector model: FEI FALCON II (4k x 4k)
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: SPIDER / Category: 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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