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- PDB-7a9x: Structure of yeast Rmd9p in complex with 16nt target RNA -

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Basic information

Entry
Database: PDB / ID: 7a9x
TitleStructure of yeast Rmd9p in complex with 16nt target RNA
Components
  • Protein RMD9, mitochondrial
  • RNA (5'-R(P*AP*AP*AP*UP*AP*AP*CP*AP*UP*UP*CP*UP*U)-3')
KeywordsRNA BINDING PROTEIN / Mitochondria / Translation / Transcription / Degradation / Ribosome
Function / homology
Function and homology information


3'-UTR-mediated mRNA stabilization / sporulation resulting in formation of a cellular spore / aerobic respiration / translational initiation / regulation of mRNA stability / mRNA 3'-UTR binding / mitochondrial inner membrane / mRNA binding / mitochondrion
Similarity search - Function
Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA-binding protein RMD9, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsHillen, H.S. / Markov, D.A. / Ireneusz, W.D. / Hofmann, K.B. / Cowan, A.T. / Jones, J.L. / Temiakov, D. / Cramer, P. / Anikin, M.
Funding support Germany, 5items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB860 Germany
German Research Foundation (DFG)SPP1935 Germany
European Research Council (ERC)Advanced Grant 693023 Germany
German Research Foundation (DFG)EXC 2067/1- 390729940 Germany
German Research Foundation (DFG)FOR2848 Germany
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: The pentatricopeptide repeat protein Rmd9 recognizes the dodecameric element in the 3'-UTRs of yeast mitochondrial mRNAs.
Authors: Hillen, H.S. / Markov, D.A. / Wojtas, I.D. / Hofmann, K.B. / Lidschreiber, M. / Cowan, A.T. / Jones, J.L. / Temiakov, D. / Cramer, P. / Anikin, M.
History
DepositionSep 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: 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
A: Protein RMD9, mitochondrial
B: RNA (5'-R(P*AP*AP*AP*UP*AP*AP*CP*AP*UP*UP*CP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4633
Polymers75,4272
Non-polymers351
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-38 kcal/mol
Surface area24630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.250, 106.250, 128.520
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Protein RMD9, mitochondrial / Required for meiotic nuclear division protein 9


Mass: 70368.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RMD9, YGL107C, G3075 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: P53140
#2: RNA chain RNA (5'-R(P*AP*AP*AP*UP*AP*AP*CP*AP*UP*UP*CP*UP*U)-3')


Mass: 5059.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.79 Å3/Da / Density % sol: 55.88 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 6.5
Details: Na-Cacodylate, NaCl, LiSO4, CaAcetate, MgCl2, PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→46.02 Å / Num. obs: 59634 / % possible obs: 100 % / Redundancy: 10.7 % / Biso Wilson estimate: 74.15 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.077 / Net I/σ(I): 18.11
Reflection shellResolution: 2.45→2.5 Å / Redundancy: 10.25 % / Rmerge(I) obs: 2.809 / Num. unique obs: 4420 / CC1/2: 0.378 / % possible all: 100

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Processing

Software
NameVersionClassification
Coot0.9model building
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7A9W

7a9w


Resolution: 2.45→46.01 Å / SU ML: 0.3717 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 26.8459 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2327 2986 5.01 %Random selection
Rwork0.1987 56633 --
obs0.2004 59619 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.06 Å2
Refinement stepCycle: LAST / Resolution: 2.45→46.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4198 272 1 79 4550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00194600
X-RAY DIFFRACTIONf_angle_d0.42926283
X-RAY DIFFRACTIONf_chiral_restr0.0345700
X-RAY DIFFRACTIONf_plane_restr0.0033749
X-RAY DIFFRACTIONf_dihedral_angle_d18.16512718
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.490.38021360.35532697X-RAY DIFFRACTION99.79
2.49-2.530.37481440.33752714X-RAY DIFFRACTION99.9
2.53-2.580.341320.3212671X-RAY DIFFRACTION99.86
2.58-2.630.32281460.29662650X-RAY DIFFRACTION99.93
2.63-2.680.32011450.28882744X-RAY DIFFRACTION99.9
2.68-2.740.28371430.26252698X-RAY DIFFRACTION100
2.74-2.80.27431390.26472694X-RAY DIFFRACTION100
2.8-2.870.23821440.26472724X-RAY DIFFRACTION99.97
2.87-2.950.30171490.24142690X-RAY DIFFRACTION100
2.95-3.040.28531400.25482707X-RAY DIFFRACTION100
3.04-3.140.24511440.23362667X-RAY DIFFRACTION99.96
3.14-3.250.29831390.232698X-RAY DIFFRACTION100
3.25-3.380.26451410.22252665X-RAY DIFFRACTION100
3.38-3.530.22911390.20552732X-RAY DIFFRACTION100
3.53-3.720.23291500.20872693X-RAY DIFFRACTION100
3.72-3.950.2441390.18382723X-RAY DIFFRACTION100
3.95-4.260.20661420.17372690X-RAY DIFFRACTION100
4.26-4.690.18411420.16482689X-RAY DIFFRACTION100
4.69-5.360.20961430.16912705X-RAY DIFFRACTION100
5.36-6.750.24331410.20312686X-RAY DIFFRACTION100
6.75-46.010.20651480.16332696X-RAY DIFFRACTION99.65
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.39810319511-1.71889745299-0.9001263533532.767368368710.8957156630433.222703220230.3783411078190.1378540797270.641482635182-0.343887059396-0.142972814467-0.113640646995-0.4311796564490.09687575984480.0003351970194020.766023172902-0.05275254859350.09443133750090.629996178522-0.02919048584930.880864686921-22.36190273783.495032796911.9158621876
22.41886120249-1.798883784260.589223237213.34556693219-0.9730626352491.47376885573-0.152591343686-0.527637888248-0.1719470699120.2961096814570.2708699869320.2977187688610.195846833806-0.3298804995670.0004149408525880.75904412538-0.06387580244570.03969368392520.8259326709830.0124321534380.694133342105-21.134890731662.758875090631.7273955571
34.567538367660.2596024726950.4141949967651.36157395031-1.091771649793.450349300770.003173896075520.733960738984-0.162180816024-0.327499224663-0.306916143289-0.3994769714040.9339082624661.23744437495-0.002250723826370.9274086769610.2963042249520.1066060901031.13082603050.1059546237050.807876279359.2349829059154.544943372817.3173224375
40.447012616674-0.555697119861-0.03525209017860.677312988690.02682296020162.12888351999-0.1717975328320.4077013544480.6232345460640.144170215878-0.115048696512-0.184999218143-0.02401953600030.1543900395588.88491617057E-50.739853654357-0.0698989006773-0.003852881983170.7036131372060.06745708189660.894334361655-14.811498272670.266643960916.9885637351
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 80 through 300 )
2X-RAY DIFFRACTION2chain 'A' and (resid 301 through 439 )
3X-RAY DIFFRACTION3chain 'A' and (resid 440 through 639 )
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 16 )

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