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- PDB-3deg: Complex of elongating Escherichia coli 70S ribosome and EF4(LepA)... -

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Basic information

Entry
Database: PDB / ID: 3deg
TitleComplex of elongating Escherichia coli 70S ribosome and EF4(LepA)-GMPPNP
DescriptorRNA binding protein/RNA Complex
KeywordsRIBOSOME / ribosome / translation / LepA / EF4 / GTP-binding / Membrane / Nucleotide-binding / Antibiotic resistance / Ribonucleoprotein / Ribosomal protein / RNA-binding / rRNA-binding / tRNA-binding / Methylation
Specimen sourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
MethodElectron microscopy (10.9 A resolution)
AuthorsConnell, S.R. / Topf, M. / Qin, Y. / Wilson, D.N. / Mielke, T. / Fucini, P. / Nierhaus, K.H. / Spahn, C.M.T.
CitationNat. Struct. Mol. Biol., 2008, 15, 910-915

Nat. Struct. Mol. Biol., 2008, 15, 910-915 StrPapers
A new tRNA intermediate revealed on the ribosome during EF4-mediated back-translocation.
Sean R Connell / Maya Topf / Yan Qin / Daniel N Wilson / Thorsten Mielke / Paola Fucini / Knud H Nierhaus / Christian M T Spahn

DateDeposition: Jun 10, 2008 / Release: Aug 19, 2008 / Last modification: Apr 16, 2014

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Assembly

Deposited unit
A: A/L-tRNA
B: P-tRNA
E: 30S RNA helix 8
F: 30S RNA helix 14
G: 50S RNA helix 42-44
I: 50S RNA helix 95
J: 50S RNA helix 71
K: 50S RNA helix 92
C: GTP-binding protein lepA
D: 30S ribosomal protein S12
H: 50S ribosomal protein L11


Theoretical massNumber of molelcules
Total (without water)190,06011
Polyers190,06011
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 8 types, 8 molecules ABEFGIJK

#1: RNA chainA/L-tRNA


Mass: 24890.293 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli
#2: RNA chainP-tRNA


Mass: 24816.971 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli
#3: RNA chain30S RNA helix 8


Mass: 5161.180 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli
#4: RNA chain30S RNA helix 14


Mass: 3827.362 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli
#5: RNA chain50S RNA helix 42-44


Mass: 22580.658 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli
#6: RNA chain50S RNA helix 95


Mass: 9394.705 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli
#7: RNA chain50S RNA helix 71


Mass: 5765.491 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli
#8: RNA chain50S RNA helix 92


Mass: 4745.866 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli

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Polypeptide(L) , 3 types, 3 molecules CDH

#9: Polypeptide(L)GTP-binding protein lepA


Mass: 60477.324 Da / Num. of mol.: 1 / Fragment: EF4 / Source: (gene. exp.) Escherichia coli / References: UniProt: P60785

Cellular component

Molecular function

Biological process

#10: Polypeptide(L)30S ribosomal protein S12


Mass: 13637.070 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7S3

Cellular component

Molecular function

Biological process

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


Mass: 14763.286 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7J7

Cellular component

Molecular function

Biological process

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY

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Electron microscopy imaging

CameraType: KODAK SO163 FILM
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Image selectionSoftware name: Situs, Mod-EM, Flex-EM
3D reconstructionResolution: 10.9 A
Atomic model buildingSoftware name: Situs, Mod-EM, Flex-EM / Ref protocol: rigid body and flexible fitting
Atomic model buildingPDB-ID: 2i2p, 2i2t, 3cb4, 1gix, 2j01
Number of atoms included #LASTProtein: 6229 / Nucleic acid: 6721 / Ligand: 0 / Solvent: 0 / Total: 12950

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