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- PDB-5u4j: Structural Basis of Co-translational Quality Control by ArfA and ... -

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Basic information

Entry
Database: PDB / ID: 5u4j
TitleStructural Basis of Co-translational Quality Control by ArfA and RF2 Bound to Ribosome
DescriptorRibosome
KeywordsRIBOSOME / Ribosome / ArfA / RF2 / nonstop translation
Specimen sourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
MethodElectron microscopy (3.7 A resolution / Single particle)
AuthorsZeng, F. / Chen, Y. / Remis, J. / Shekhar, M. / Phillips, J.C. / Tajkhorshid, E. / Jin, H.
CitationNature, 2017

Nature, 2017
Structural Basis of Co-translational Quality Control by ArfA and RF2 Binding to Ribosome
Zeng, F. / Chen, Y. / Remis, J. / Shekhar, M. / Phillips, J.C. / Tajkhorshid, E. / Jin, H.

DateDeposition: Dec 4, 2016 / Release: Jan 11, 2017

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Assembly

Deposited unit
a: 16S rRNA
A: 23S rRNA
c: 30S ribosomal protein S3
d: 30S ribosomal protein S4
e: 30S ribosomal protein S5
z: mRNA
x: P-site tRNA fMet
l: 30S ribosomal protein S12
v: Peptide chain release factor 2
w: Alternative ribosome-rescue factor A


Theoretical massNumber of molelcules
Total (without water)1,600,33210
Polyers1,600,33210
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 4 types, 4 molecules aAzx

#1: RNA chain16S rRNA


Mass: 497075.812 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: GenBank: 817573384
#2: RNA chain23S rRNA


Mass: 941790.625 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: GenBank: 42756
#6: RNA chainmRNA


Mass: 5922.644 Da / Num. of mol.: 1 / Source: (synth.) Escherichia coli
#7: RNA chainP-site tRNA fMet


Mass: 24786.785 Da / Num. of mol.: 1 / Source: (synth.) Escherichia coli / References: GenBank: 687670942

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30S ribosomal protein ... , 4 types, 4 molecules cdel

#3: Polypeptide(L)30S ribosomal protein S3


Mass: 26031.316 Da / Num. of mol.: 1 / Details: Gene Name(s): rpsC b3314 JW3276 / Source: (natural) Escherichia coli / References: UniProt: P0A7V3
#4: Polypeptide(L)30S ribosomal protein S4


Mass: 23514.199 Da / Num. of mol.: 1 / Details: Gene Name(s): rpsD ramA b3296 JW3258 / Source: (natural) Escherichia coli / References: UniProt: P0A7V8
#5: Polypeptide(L)30S ribosomal protein S5


Mass: 17629.398 Da / Num. of mol.: 1 / Details: Gene Name(s): rpsE spc b3303 JW3265 / Source: (natural) Escherichia coli / References: UniProt: P0A7W1
#8: Polypeptide(L)30S ribosomal protein S12


Mass: 13768.157 Da / Num. of mol.: 1 / Details: Gene Name(s): rpsL strA b3342 JW3304 / Source: (natural) Escherichia coli / References: UniProt: P0A7S3

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Polypeptide(L) , 2 types, 2 molecules vw

#9: Polypeptide(L)Peptide chain release factor 2 / RF-2


Mass: 43299.844 Da / Num. of mol.: 1 / Details: Gene Name(s): prfB ECK2886 JW5847 supK / Source: (gene. exp.) Escherichia coli / References: UniProt: P07012
#10: Polypeptide(L)Alternative ribosome-rescue factor A


Mass: 6513.396 Da / Num. of mol.: 1 / Details: Gene Name(s): arfA ECK3278 JW3253 yhdL / Source: (gene. exp.) Escherichia coli / References: UniProt: P36675

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE

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Sample preparation

Assembly of specimen
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
Component
IDNameDetailsTypeAssembly id
1Non-stop ribosomal complex with ArfA and RF2RIBOSOME1
230S subunitCOMPLEX2
350S subunitCOMPLEX3
4Alternative ribosome-rescue factor AORGANELLE OR CELLULAR COMPONENT4
5Peptide chain release factor 2ORGANELLE OR CELLULAR COMPONENT5
6P-site tRNA fMetP-site tRNA (fMet) was in vitro transcribed.ORGANELLE OR CELLULAR COMPONENT6
7mRNAORGANELLE OR CELLULAR COMPONENT7
823S rRNAORGANELLE OR CELLULAR COMPONENT8
916S rRNAORGANELLE OR CELLULAR COMPONENT9
1030S ribosomal protein S3ORGANELLE OR CELLULAR COMPONENT10
1130S ribosomal protein S4ORGANELLE OR CELLULAR COMPONENT11
1230S ribosomal protein S5ORGANELLE OR CELLULAR COMPONENT12
1330S ribosomal protein S12ORGANELLE OR CELLULAR COMPONENT13
Specimen supportGrid material: COPPER / Grid mesh size: 400 /inch. / Grid type: C-Flat TM Holey Carbon Grid CF-2/0.5-4C
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 / Details: Grids were blotted for 3.5 s

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Electron microscopy imaging

MicroscopyMicroscope model: JEOL 3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 83822 X / Nominal defocus max: 3000 nm / Nominal defocus min: 700 nm

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Processing

SoftwareName: REFMAC / Version: 5.8.0155 / Classification: refinement
ComputingStructure refinement: REFMAC 5.8.0155
3D reconstructionResolution: 3.7 A / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 155440
Atomic model buildingOverall b value: 108.501 / Ref protocol: FLEXIBLE FIT / Ref space: RECIPROCAL / Target criteria: Average FSC
Refine

B iso mean: 108.51 A2 / Aniso B11: -0.17 A2 / Aniso B12: -0.46 A2 / Aniso B13: -1.7 A2 / Aniso B22: 0.01 A2 / Aniso B23: -0.01 A2 / Aniso B33: 0.16 A2 / Correlation coeff Fo to Fc: 0.596 / R factor R work: 0.43355 / R factor obs: 0.43355 / Highest resolution: 3.7 A / Lowest resolution: 458.11 A / Number reflection obs: 3976064 / Percent reflection obs: 1 / Overall SU B: 6.611 / Overall SU ML: 0.094 / Overall ESU R: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES / Solvent model details: PARAMETERS FOR MASK CACLULATION

Refine id
1
ELECTRON MICROSCOPY
Number of atoms included #1Total: 11360
Refine LS restraints
Refine idTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0050.01412278
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg0.9041.51718210
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg3.8525.000517
ELECTRON MICROSCOPYr_dihedral_angle_2_deg41.52622.139187
ELECTRON MICROSCOPYr_dihedral_angle_3_deg15.79415.000776
ELECTRON MICROSCOPYr_dihedral_angle_4_deg8.72915.00050
ELECTRON MICROSCOPYr_chiral_restr0.0660.2001954
ELECTRON MICROSCOPYr_gen_planes_refined0.0020.0206637
ELECTRON MICROSCOPYr_gen_planes_other
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it2.19514.5572089
ELECTRON MICROSCOPYr_mcbond_other
ELECTRON MICROSCOPYr_mcangle_it4.14921.8152599
ELECTRON MICROSCOPYr_mcangle_other
ELECTRON MICROSCOPYr_scbond_it1.2869.91610189
ELECTRON MICROSCOPYr_scbond_other
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other
ELECTRON MICROSCOPYr_long_range_B_refined9.29320376
ELECTRON MICROSCOPYr_long_range_B_other
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS shellHighest resolution: 3.7 A / R factor R work: 1.519 / Lowest resolution: 3.796 A / Number reflection R free: 0 / Number reflection R work: 295394 / Total number of bins used: 20 / Percent reflection obs: 1

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