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- PDB-4toi: Crystal structure of E.coli ribosomal protein S2 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4toi
TitleCrystal structure of E.coli ribosomal protein S2 in complex with N-terminal domain of S1
Components30S ribosomal protein S2,Ribosomal protein S1
KeywordsRIBOSOMAL PROTEIN / complex / translation
Function / homology
Function and homology information


ribosomal small subunit assembly / cytosolic small ribosomal subunit / cytoplasmic translation / structural constituent of ribosome / translation / zinc ion binding / cytoplasm
Similarity search - Function
Helix hairpin bin / Glucose-6-phosphate isomerase like protein; domain 1 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S2 signature 2. / Ribosomal protein S2 signature 1. / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Helix Hairpins ...Helix hairpin bin / Glucose-6-phosphate isomerase like protein; domain 1 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S2 signature 2. / Ribosomal protein S2 signature 1. / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Helix Hairpins / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Small ribosomal subunit protein uS2 / Ribosomal protein S1 / Small ribosomal subunit protein uS2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli TA206 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsGrishkovskaya, I. / Byrgazov, K. / Moll, I. / Djinovic-Carugo, K.
CitationJournal: Nucleic Acids Res / Year: 2015
Title: Structural basis for the interaction of protein S1 with the Escherichia coli ribosome.
Authors: Konstantin Byrgazov / Irina Grishkovskaya / Stefan Arenz / Nicolas Coudevylle / Hannes Temmel / Daniel N Wilson / Kristina Djinovic-Carugo / Isabella Moll /
Abstract: In Gram-negative bacteria, the multi-domain protein S1 is essential for translation initiation, as it recruits the mRNA and facilitates its localization in the decoding centre. In sharp contrast to ...In Gram-negative bacteria, the multi-domain protein S1 is essential for translation initiation, as it recruits the mRNA and facilitates its localization in the decoding centre. In sharp contrast to its functional importance, S1 is still lacking from the high-resolution structures available for Escherichia coli and Thermus thermophilus ribosomes and thus the molecular mechanism governing the S1-ribosome interaction has still remained elusive. Here, we present the structure of the N-terminal S1 domain D1 when bound to the ribosome at atomic resolution by using a combination of NMR, X-ray crystallography and cryo-electron microscopy. Together with biochemical assays, the structure reveals that S1 is anchored to the ribosome primarily via a stabilizing π-stacking interaction within the short but conserved N-terminal segment that is flexibly connected to domain D1. This interaction is further stabilized by salt bridges involving the zinc binding pocket of protein S2. Overall, this work provides one hitherto enigmatic piece in the 'ribosome puzzle', namely the detailed molecular insight into the topology of the S1-ribosome interface. Moreover, our data suggest novel mechanisms that have the potential to modulate protein synthesis in response to environmental cues by changing the affinity of S1 for the ribosome.
History
DepositionJun 5, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 30S ribosomal protein S2,Ribosomal protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9902
Polymers35,9251
Non-polymers651
Water3,027168
1
A: 30S ribosomal protein S2,Ribosomal protein S1
hetero molecules

A: 30S ribosomal protein S2,Ribosomal protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9804
Polymers71,8502
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area4270 Å2
ΔGint-92 kcal/mol
Surface area32300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.280, 87.280, 94.360
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein 30S ribosomal protein S2,Ribosomal protein S1 / 30S ribosomal protein S2 - Ribosomal protein S1 fusion protein


Mass: 35924.781 Da / Num. of mol.: 1 / Fragment: 1-236,3-84
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Escherichia coli TA206 (bacteria)
Gene: rpsB, BU34_07500, ECs0171, LF82_1969, ECKG_00790 / Production host: Escherichia coli (E. coli)
References: UniProt: C3TPN2, UniProt: F4TQ64, UniProt: P0A7V0*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.46 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1 M HEPES-KOH, pH 7.4, 3 mM MgCl2, 7.5% w/v PEG 6000, 3% w/v 2-methyl-pentanediol-2,4, 100 mM KCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 20, 2012
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→37.79 Å / Num. obs: 18726 / % possible obs: 99 % / Redundancy: 8.1 % / Biso Wilson estimate: 32.2 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.063 / Net I/σ(I): 7.4 / Num. measured all: 151502 / Scaling rejects: 437
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.3-2.384.51.1061.5756016700.5480.54391.3
8.91-37.799.50.07121.734793680.9950.02498.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDS0.1.29data reduction
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.9_1692)refinement
BALBESphasing
Aimlessdata scaling
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2qbf and 2oce

2qbf
PDB Unreleased entry

2oce


Resolution: 2.3→37.79 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2287 949 5.11 %Random selection
Rwork0.1636 17638 --
obs0.1668 18587 98.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.24 Å2 / Biso mean: 42.5864 Å2 / Biso min: 14.98 Å2
Refinement stepCycle: final / Resolution: 2.3→37.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2375 0 1 168 2544
Biso mean--25.18 41.31 -
Num. residues----307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082452
X-RAY DIFFRACTIONf_angle_d1.093313
X-RAY DIFFRACTIONf_chiral_restr0.043374
X-RAY DIFFRACTIONf_plane_restr0.004436
X-RAY DIFFRACTIONf_dihedral_angle_d14.995918
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3003-2.42150.28531290.2292326245592
2.4215-2.57320.27471570.20182468262599
2.5732-2.77180.27851170.18992501261899
2.7718-3.05060.25661470.18712518266599
3.0506-3.49180.22451240.167325672691100
3.4918-4.39830.19351330.133425672700100
4.3983-37.79840.20741420.14726912833100

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