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- PDB-6e4p: Structure of the T. brucei RRM domain in complex with RNA -

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Basic information

Entry
Database: PDB / ID: 6e4p
TitleStructure of the T. brucei RRM domain in complex with RNA
Components
  • RNA (5'-R(P*UP*UP*UP*U)-3')
  • RNA-binding protein, putative
KeywordsRNA BINDING PROTEIN/RNA / RRM / TbRGG2 / kRNA editing / trypanosome / kinetoplastid / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


mitochondrial mRNA processing / mitochondrial mRNA editing complex / cytoplasmic side of mitochondrial outer membrane / kinetoplast / RNA processing / mRNA binding / mitochondrion / nucleus / cytoplasm
Similarity search - Function
RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA-binding protein, putative
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.949 Å
AuthorsSchumacher, M.A.
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: The RRM of the kRNA-editing protein TbRGG2 uses multiple surfaces to bind and remodel RNA.
Authors: Travis, B. / Shaw, P.L.R. / Liu, B. / Ravindra, K. / Iliff, H. / Al-Hashimi, H.M. / Schumacher, M.A.
History
DepositionJul 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 13, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 11, 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

Downloads & links

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Assembly

Deposited unit
J: RNA (5'-R(P*UP*UP*UP*U)-3')
K: RNA (5'-R(P*UP*UP*UP*U)-3')
A: RNA-binding protein, putative
B: RNA-binding protein, putative
C: RNA-binding protein, putative
D: RNA-binding protein, putative
E: RNA-binding protein, putative
F: RNA-binding protein, putative
G: RNA-binding protein, putative
H: RNA-binding protein, putative
I: RNA-binding protein, putative


Theoretical massNumber of molelcules
Total (without water)72,54811
Polymers72,54811
Non-polymers00
Water5,657314
1
J: RNA (5'-R(P*UP*UP*UP*U)-3')
C: RNA-binding protein, putative


Theoretical massNumber of molelcules
Total (without water)8,9782
Polymers8,9782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
K: RNA (5'-R(P*UP*UP*UP*U)-3')
B: RNA-binding protein, putative


Theoretical massNumber of molelcules
Total (without water)8,9782
Polymers8,9782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: RNA-binding protein, putative


Theoretical massNumber of molelcules
Total (without water)7,7991
Polymers7,7991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RNA-binding protein, putative


Theoretical massNumber of molelcules
Total (without water)7,7991
Polymers7,7991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: RNA-binding protein, putative


Theoretical massNumber of molelcules
Total (without water)7,7991
Polymers7,7991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: RNA-binding protein, putative


Theoretical massNumber of molelcules
Total (without water)7,7991
Polymers7,7991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: RNA-binding protein, putative


Theoretical massNumber of molelcules
Total (without water)7,7991
Polymers7,7991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: RNA-binding protein, putative


Theoretical massNumber of molelcules
Total (without water)7,7991
Polymers7,7991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: RNA-binding protein, putative


Theoretical massNumber of molelcules
Total (without water)7,7991
Polymers7,7991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.123, 126.297, 49.203
Angle α, β, γ (deg.)90.000, 118.570, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain RNA (5'-R(P*UP*UP*UP*U)-3')


Mass: 1179.706 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Trypanosoma brucei (eukaryote)
#2: Protein
RNA-binding protein, putative


Mass: 7798.736 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q389P7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 1.85 Å3/Da / Density % sol: 33.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: citrate as precipitant

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.949→35.661 Å / Num. obs: 38345 / % possible obs: 99.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 26.93 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.04 / Rsym value: 0.066 / Net I/σ(I): 17.8
Reflection shellResolution: 1.949→2 Å / Redundancy: 2.5 % / CC1/2: 0.99 / Rpim(I) all: 0.28 / Rsym value: 0.351

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6E4N

6e4n


Resolution: 1.949→35.661 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 23.98
RfactorNum. reflection% reflection
Rfree0.2286 1991 5.2 %
Rwork0.1806 --
obs0.183 38264 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.48 Å2 / Biso mean: 30.01 Å2 / Biso min: 11.43 Å2
Refinement stepCycle: final / Resolution: 1.949→35.661 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4883 122 0 314 5319
Biso mean---34.71 -
Num. residues----637
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055094
X-RAY DIFFRACTIONf_angle_d0.8486912
X-RAY DIFFRACTIONf_chiral_restr0.032810
X-RAY DIFFRACTIONf_plane_restr0.004877
X-RAY DIFFRACTIONf_dihedral_angle_d15.6031833
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9492-1.99790.27861470.21652536268399
1.9979-2.0520.27891390.20626322771100
2.052-2.11230.24571370.194425612698100
2.1123-2.18050.23141300.186826052735100
2.1805-2.25840.24031460.189225932739100
2.2584-2.34880.24511370.188626042741100
2.3488-2.45570.26451410.189725822723100
2.4557-2.58510.23781430.189725902733100
2.5851-2.74710.25361490.196425712720100
2.7471-2.95910.24221500.192925992749100
2.9591-3.25670.23671400.197825982738100
3.2567-3.72750.20191530.168725842737100
3.7275-4.69450.20161510.14825972748100
4.6945-35.66740.21241280.17872621274999
Refinement TLS params.Method: refined / Origin x: 37.5139 Å / Origin y: -26.5283 Å / Origin z: 35.8948 Å
111213212223313233
T0.0806 Å2-0.0049 Å2-0.0036 Å2-0.0858 Å2-0.0004 Å2--0.0732 Å2
L0.1123 °20.0479 °2-0.048 °2-0.1148 °20.122 °2--0.0563 °2
S-0.0034 Å °0.0375 Å °0.0028 Å °-0.0137 Å °0.0158 Å °-0.0292 Å °-0.0229 Å °0.0028 Å °-0.0003 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allJ1 - 3
2X-RAY DIFFRACTION1allK1 - 3
3X-RAY DIFFRACTION1allZ1 - 345
4X-RAY DIFFRACTION1allA200 - 269
5X-RAY DIFFRACTION1allB201 - 269
6X-RAY DIFFRACTION1allC202 - 269
7X-RAY DIFFRACTION1allD199 - 269
8X-RAY DIFFRACTION1allE200 - 269
9X-RAY DIFFRACTION1allF199 - 269
10X-RAY DIFFRACTION1allG200 - 269
11X-RAY DIFFRACTION1allH199 - 269
12X-RAY DIFFRACTION1allI199 - 269

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