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- PDB-6u9x: Structure of T. brucei MERS1-RNA complex -

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Basic information

Entry
Database: PDB / ID: 6u9x
TitleStructure of T. brucei MERS1-RNA complex
Components
  • Mitochondrial edited mRNA stability factor 1
  • RNA (5'-R(*GP*AP*GP*AP*GP*GP*GP*GP*GP*UP*U)-3')
KeywordsRNA BINDING PROTEIN/RNA / MERS1 / mRNA / TmRNA processing / Nudix motif / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homologyNUDIX domain / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / RNA / RNA (> 10) / Mitochondrial edited mRNA stability factor 1
Function and homology information
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsSchumacher, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM130290 United States
CitationJournal: Rna / Year: 2020
Title: Structures of MERS1, the 5' processing enzyme of mitochondrial mRNAs inTrypanosoma brucei.
Authors: Schumacher, M.A. / Henderson, M. / Zeng, W.
History
DepositionSep 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name / _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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
D: Mitochondrial edited mRNA stability factor 1
A: Mitochondrial edited mRNA stability factor 1
H: RNA (5'-R(*GP*AP*GP*AP*GP*GP*GP*GP*GP*UP*U)-3')
K: RNA (5'-R(*GP*AP*GP*AP*GP*GP*GP*GP*GP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)88,9304
Polymers88,9304
Non-polymers00
Water73941
1
D: Mitochondrial edited mRNA stability factor 1
H: RNA (5'-R(*GP*AP*GP*AP*GP*GP*GP*GP*GP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)44,4652
Polymers44,4652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-12 kcal/mol
Surface area15360 Å2
2
A: Mitochondrial edited mRNA stability factor 1
K: RNA (5'-R(*GP*AP*GP*AP*GP*GP*GP*GP*GP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)44,4652
Polymers44,4652
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-10 kcal/mol
Surface area14910 Å2
3
D: Mitochondrial edited mRNA stability factor 1
H: RNA (5'-R(*GP*AP*GP*AP*GP*GP*GP*GP*GP*UP*U)-3')

D: Mitochondrial edited mRNA stability factor 1
H: RNA (5'-R(*GP*AP*GP*AP*GP*GP*GP*GP*GP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)88,9304
Polymers88,9304
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area7880 Å2
ΔGint-40 kcal/mol
Surface area27350 Å2
MethodPISA
4
A: Mitochondrial edited mRNA stability factor 1
K: RNA (5'-R(*GP*AP*GP*AP*GP*GP*GP*GP*GP*UP*U)-3')

A: Mitochondrial edited mRNA stability factor 1
K: RNA (5'-R(*GP*AP*GP*AP*GP*GP*GP*GP*GP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)88,9304
Polymers88,9304
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area7900 Å2
ΔGint-42 kcal/mol
Surface area26360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.445, 89.360, 71.351
Angle α, β, γ (deg.)90.000, 109.510, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Mitochondrial edited mRNA stability factor 1


Mass: 40822.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: MERS1 / Production host: Escherichia coli (E. coli) / References: UniProt: B6SBM0
#2: RNA chain RNA (5'-R(*GP*AP*GP*AP*GP*GP*GP*GP*GP*UP*U)-3')


Mass: 3642.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Trypanosoma brucei (eukaryote)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.4 Å3/Da / Density % sol: 48.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M N-cyclohexyl-3-aminopropanesulfonic acid (CAPS) pH 10.5, 800 mM Potassium phosphate dibasic, 1.2 M sodium phosphate monobasic, 0.2 M lithium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→74.391 Å / Num. obs: 23984 / % possible obs: 92.3 % / Redundancy: 2.5 % / Biso Wilson estimate: 49.94 Å2 / CC1/2: 0.981 / Rpim(I) all: 0.074 / Rsym value: 0.099 / Net I/σ(I): 5.7
Reflection shellResolution: 2.6→2.665 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1259 / CC1/2: 0.839 / Rpim(I) all: 0.389 / Rsym value: 0.486 / % possible all: 72.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.12_2829refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6P5R

6p5r


Resolution: 2.6→74.391 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2499 1997 8.35 %
Rwork0.2179 21911 -
obs0.2207 23908 91.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 173.38 Å2 / Biso mean: 61.3602 Å2 / Biso min: 17.05 Å2
Refinement stepCycle: final / Resolution: 2.6→74.391 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4759 184 0 41 4984
Biso mean---45.39 -
Num. residues----596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035152
X-RAY DIFFRACTIONf_angle_d0.6847061
X-RAY DIFFRACTIONf_chiral_restr0.05757
X-RAY DIFFRACTIONf_plane_restr0.005878
X-RAY DIFFRACTIONf_dihedral_angle_d8.6033061
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6-2.6650.35911140.2922125974
2.665-2.73710.4191260.3043139883
2.7371-2.81760.32331480.2995161295
2.8176-2.90860.34891480.2979162195
2.9086-3.01250.29591450.2848158993
3.0125-3.13320.34151450.2675157794
3.1332-3.27580.33611400.2497154592
3.2758-3.44850.28081480.2394162596
3.4485-3.66450.24471480.2165162595
3.6645-3.94740.23481430.1989156192
3.9474-4.34470.18511480.1776162796
4.3447-4.97320.2231510.1705165495
4.9732-6.26520.2081450.2082159493
6.2652-74.3910.21071480.1991162492
Refinement TLS params.Method: refined / Origin x: 21.6612 Å / Origin y: -44.8791 Å / Origin z: -20.0135 Å
111213212223313233
T0.2174 Å20.0114 Å20.0054 Å2-0.2004 Å2-0.0042 Å2--0.1979 Å2
L0.1986 °20.0605 °20.1132 °2-0.138 °20.0108 °2--0.1371 °2
S-0.0322 Å °-0.0422 Å °-0.0118 Å °-0.0499 Å °0.0548 Å °0.0365 Å °-0.0134 Å °0.0162 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allD59 - 380
2X-RAY DIFFRACTION1allA59 - 380
3X-RAY DIFFRACTION1allH30 - 33
4X-RAY DIFFRACTION1allK30 - 33
5X-RAY DIFFRACTION1allS1 - 41

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