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- PDB-6g63: RNase E in complex with sRNA RrpA -

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Basic information

Entry
Database: PDB / ID: 6g63
TitleRNase E in complex with sRNA RrpA
Components
  • RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
  • Ribonuclease E
KeywordsRNA BINDING PROTEIN / RNase E / small regulatory RNA
Function / homology
Function and homology information


regulation of RNA helicase activity / ribonuclease E / rRNA 5'-end processing / ribonuclease E activity / bacterial degradosome / endoribonuclease complex / DEAD/H-box RNA helicase binding / 7S RNA binding / RNA catabolic process / tRNA processing ...regulation of RNA helicase activity / ribonuclease E / rRNA 5'-end processing / ribonuclease E activity / bacterial degradosome / endoribonuclease complex / DEAD/H-box RNA helicase binding / 7S RNA binding / RNA catabolic process / tRNA processing / mRNA catabolic process / RNA processing / RNA nuclease activity / RNA endonuclease activity / cytoplasmic side of plasma membrane / rRNA processing / protein complex oligomerization / protein homotetramerization / tRNA binding / molecular adaptor activity / rRNA binding / magnesium ion binding / RNA binding / zinc ion binding / membrane / identical protein binding / cytoplasm
Similarity search - Function
Ribonuclease E, catalytic domain / Polyribonucleotide phosphorylase C-terminal / Polyribonucleotide phosphorylase C terminal / Hypothetical Protein Ychn; Chain: A, / : / RNase E/G, Thioredoxin-like domain / Ribonuclease E/G / RNA-binding protein AU-1/Ribonuclease E/G / Ribonuclease E / Ribonuclease E/G family ...Ribonuclease E, catalytic domain / Polyribonucleotide phosphorylase C-terminal / Polyribonucleotide phosphorylase C terminal / Hypothetical Protein Ychn; Chain: A, / : / RNase E/G, Thioredoxin-like domain / Ribonuclease E/G / RNA-binding protein AU-1/Ribonuclease E/G / Ribonuclease E / Ribonuclease E/G family / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Nucleic acid-binding, OB-fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-MONOPHOSPHATE / RNA / RNA (> 10) / Ribonuclease E
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.95 Å
AuthorsBandyra, K.B. / Luisi, B.F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust200873/Z/16/Z United Kingdom
CitationJournal: Mol. Cell / Year: 2018
Title: Substrate Recognition and Autoinhibition in the Central Ribonuclease RNase E.
Authors: Bandyra, K.J. / Wandzik, J.M. / Luisi, B.F.
History
DepositionMar 31, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _entity.formula_weight
Revision 1.2Oct 31, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease E
G: Ribonuclease E
L: Ribonuclease E
N: Ribonuclease E
B: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,4958
Polymers238,0405
Non-polymers4553
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18660 Å2
ΔGint-132 kcal/mol
Surface area102260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.630, 110.630, 466.020
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
Ribonuclease E / / RNase E


Mass: 57495.465 Da / Num. of mol.: 4 / Mutation: D303R,D346R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: rne, ams, hmp1, b1084, JW1071 / Production host: Escherichia coli (E. coli) / References: UniProt: P21513, ribonuclease E
#2: RNA chain RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 8057.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Because of the low resolution, we modelled the RNA structure as two chains in a duplex of polyU:polyA. The sequence of the RNA used in the crystal is ...Details: Because of the low resolution, we modelled the RNA structure as two chains in a duplex of polyU:polyA. The sequence of the RNA used in the crystal is ACGGUUAUAAAUCAACACAUUGAUUUAUAAGCAUGGAAAUCCCCUGAGUGAAACAACGAAUUGCUGUGUGUAGUCUUUGCCCGUCUCCUACGAUGGGCUUUUUUUU
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-U / URIDINE-5'-MONOPHOSPHATE / Uridine monophosphate


Type: RNA linking / Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P

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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: 3.51 Å3/Da / Density % sol: 64.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M KCl, 0.01 M MgCl2, 0.05 M Tris-HCl pH 8.5 and 30% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Oct 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.95→95.8 Å / Num. obs: 28217 / % possible obs: 100 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 8.3
Reflection shellResolution: 3.95→4.19 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 3.95→19.947 Å / SU ML: 0.66 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 32.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2962 1371 4.92 %
Rwork0.2747 --
obs0.2757 27869 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.95→19.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15642 504 2 0 16148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00516451
X-RAY DIFFRACTIONf_angle_d1.01222300
X-RAY DIFFRACTIONf_dihedral_angle_d18.79410141
X-RAY DIFFRACTIONf_chiral_restr0.0542538
X-RAY DIFFRACTIONf_plane_restr0.0082847
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9501-4.09010.36661470.36552647X-RAY DIFFRACTION100
4.0901-4.25230.29981520.30812634X-RAY DIFFRACTION100
4.2523-4.44380.28921350.27162643X-RAY DIFFRACTION100
4.4438-4.67530.30211320.25172629X-RAY DIFFRACTION100
4.6753-4.9640.24531290.27382661X-RAY DIFFRACTION100
4.964-5.34040.38131330.29852672X-RAY DIFFRACTION100
5.3404-5.86540.32171260.2832662X-RAY DIFFRACTION100
5.8654-6.6860.33451540.32542622X-RAY DIFFRACTION100
6.686-8.32070.34311520.30512658X-RAY DIFFRACTION100
8.3207-19.94690.22151110.2272670X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.66340.01580.3904-0.69760.58930.86681.58491.7710.62330.5390.53950.5887-1.2919-1.5827-1.20744.95030.110.3526.09170.72533.7841-42.1366-3.5297-2.2766
21.32271.636-0.93811.53220.0460.4596-0.1533-0.47051.04350.91151.1554-0.6835-2.26180.7148-0.53075.42350.59-0.08823.6951-0.01713.979116.499533.61220.0835
31.63180.4034-1.13640.94050.57382.5754-0.5726-1.8932-1.1136-1.35060.2855-0.7075-0.23682.1654-0.27573.80960.11920.07844.68170.2734.146637.866-47.4112-33.519
41.34511.36081.10021.17350.32465.3279-1.0795-0.21691.0413-1.4572-0.64620.09452.1816-0.05031.26833.9373-0.2239-0.1353.16140.05223.888422.4411-56.876431.4593
52.5248-0.39020.61293.13651.70162.5494-1.2712-0.0816-0.5912-0.32461.0872-0.00820.6999-1.9356-0.62382.53430.8272-0.63891.96530.20662.1197-19.2825-2.1493-22.6854
63.0552-0.99542.49022.63560.0263.84650.3037-0.4402-0.1908-0.75940.26950.7102-0.5869-1.4269-0.36412.00740.875-0.07791.4427-0.05681.3576-7.40933.6202-5.1581
73.127-1.19710.67622.793-1.81194.7764-0.0423-0.3856-0.3588-1.2107-0.278-0.20620.04132.6063-0.81282.55760.8985-0.34651.5959-0.88012.919211.496415.503620.5746
81.8942-0.1427-0.64754.62752.65744.93040.1442-0.04880.2714-0.51570.4897-0.6134-1.195-0.227-0.46662.54610.8306-0.31111.00350.07031.60270.44728.23622.9218
94.23340.1052-0.45668.11081.28684.20970.42770.10120.3942-0.5063-0.07541.13850.81470.4390.17963.2880.897-0.59021.5657-0.33381.514710.0246-47.2181-25.2733
101.26521.52520.56942.44531.27323.193-0.08460.0309-0.1893-0.13310.4678-0.1440.48080.1792-0.40412.00580.7614-0.36321.2532-0.19341.330120.7469-40.0418-6.905
112.0379-0.89291.85492.71291.26365.67490.30740.97540.9280.99770.6178-1.13561.26270.9573-0.71142.78621.1169-0.02062.0039-0.22731.513136.1008-32.233122.9302
123.16840.41061.96741.01611.12293.29750.3765-0.4314-0.4538-0.07880.2805-0.27460.43230.2385-0.54882.11430.6658-0.18941.1246-0.0521.317324.4986-37.88724.6067
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 211 )
2X-RAY DIFFRACTION2chain 'G' and (resid 33 through 211 )
3X-RAY DIFFRACTION3chain 'L' and (resid 33 through 211 )
4X-RAY DIFFRACTION4chain 'N' and (resid 33 through 211 )
5X-RAY DIFFRACTION5chain 'A' and (resid 3 through 32 )
6X-RAY DIFFRACTION6chain 'A' and (resid 212 through 510 )
7X-RAY DIFFRACTION7chain 'G' and (resid 3 through 32 )
8X-RAY DIFFRACTION8chain 'G' and (resid 212 through 510 )
9X-RAY DIFFRACTION9chain 'L' and (resid 3 through 32 )
10X-RAY DIFFRACTION10chain 'L' and (resid 212 through 510 )
11X-RAY DIFFRACTION11chain 'N' and (resid 3 through 32 )
12X-RAY DIFFRACTION12chain 'N' and (resid 212 through 510 )

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