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- PDB-3k4e: Puf3 RNA binding domain bound to Cox17 RNA 3' UTR recognition seq... -

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Basic information

Entry
Database: PDB / ID: 3k4e
TitlePuf3 RNA binding domain bound to Cox17 RNA 3' UTR recognition sequence site A
Components
  • RNA (5'-R(P*CP*UP*UP*GP*UP*AP*UP*AP*UP*A)-3')
  • mRNA-binding protein PUF3
KeywordsRNA Binding protein / RNA / PUF3 / PUMILIO / RNA BINDING / mitochondrial mRNA / Membrane / Mitochondrion / Mitochondrion outer membrane / Phosphoprotein / RNA-binding / RNA Binding protein - RNA COMPLEX
Function / homology
Function and homology information


regulation of ubiquinone biosynthetic process / intracellular mRNA localization / mitochondrion localization / cytoplasmic side of mitochondrial outer membrane / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nuclear-transcribed mRNA catabolic process / aerobic respiration / mitochondrion organization / positive regulation of translation / mRNA 3'-UTR binding ...regulation of ubiquinone biosynthetic process / intracellular mRNA localization / mitochondrion localization / cytoplasmic side of mitochondrial outer membrane / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nuclear-transcribed mRNA catabolic process / aerobic respiration / mitochondrion organization / positive regulation of translation / mRNA 3'-UTR binding / mRNA binding / cytoplasm
Similarity search - Function
Pumilio, RNA binding domain / Pumilio homology domain / Pumilio homology domain (PUM-HD) profile. / Pumilio-family RNA binding repeat / Pumilio RNA-binding repeat profile. / Pumilio RNA-binding repeat / Pumilio-like repeats / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical ...Pumilio, RNA binding domain / Pumilio homology domain / Pumilio homology domain (PUM-HD) profile. / Pumilio-family RNA binding repeat / Pumilio RNA-binding repeat profile. / Pumilio RNA-binding repeat / Pumilio-like repeats / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
RNA / mRNA-binding protein PUF3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsZhu, D. / Stumpf, C.R. / Krahn, J.M. / Wickens, M. / Hall, T.M.T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: A 5' cytosine binding pocket in Puf3p specifies regulation of mitochondrial mRNAs.
Authors: Zhu, D. / Stumpf, C.R. / Krahn, J.M. / Wickens, M. / Hall, T.M.
History
DepositionOct 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 6, 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: mRNA-binding protein PUF3
B: RNA (5'-R(P*CP*UP*UP*GP*UP*AP*UP*AP*UP*A)-3')
C: mRNA-binding protein PUF3
D: RNA (5'-R(P*CP*UP*UP*GP*UP*AP*UP*AP*UP*A)-3')
E: mRNA-binding protein PUF3
F: RNA (5'-R(P*CP*UP*UP*GP*UP*AP*UP*AP*UP*A)-3')


Theoretical massNumber of molelcules
Total (without water)136,3776
Polymers136,3776
Non-polymers00
Water1,67593
1
A: mRNA-binding protein PUF3
B: RNA (5'-R(P*CP*UP*UP*GP*UP*AP*UP*AP*UP*A)-3')


Theoretical massNumber of molelcules
Total (without water)45,4592
Polymers45,4592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-2 kcal/mol
Surface area17540 Å2
MethodPISA
2
C: mRNA-binding protein PUF3
D: RNA (5'-R(P*CP*UP*UP*GP*UP*AP*UP*AP*UP*A)-3')


Theoretical massNumber of molelcules
Total (without water)45,4592
Polymers45,4592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-2 kcal/mol
Surface area17550 Å2
MethodPISA
3
E: mRNA-binding protein PUF3
F: RNA (5'-R(P*CP*UP*UP*GP*UP*AP*UP*AP*UP*A)-3')


Theoretical massNumber of molelcules
Total (without water)45,4592
Polymers45,4592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-2 kcal/mol
Surface area17480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.078, 87.134, 124.910
Angle α, β, γ (deg.)90.00, 116.23, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein mRNA-binding protein PUF3 / Pumilio homology domain family member 3


Mass: 42335.121 Da / Num. of mol.: 3 / Fragment: residues 511-879
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: genomic DNA / Gene: L1325, PUF3, YLL013C / Plasmid: pTYB3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q07807
#2: RNA chain RNA (5'-R(P*CP*UP*UP*GP*UP*AP*UP*AP*UP*A)-3')


Mass: 3123.876 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: RNA oligonucleotides were obtained from Dharmacon, Inc
References: PDB-3K49
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.69 Å3/Da / Density % sol: 54.21 %
Crystal growTemperature: 277 K / pH: 4.8
Details: 20% PEG4000, 0.1 M sodium citrate pH 4.8, 2% dextran sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 12, 2008
RadiationMonochromator: VARIMAX HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 23487 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.153 / Rsym value: 0.153 / Net I/σ(I): 8.6
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.453 / % possible all: 99.9

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Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3K49

3k49


Resolution: 3.2→28.91 Å / Isotropic thermal model: Isotropic / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflection
Rfree0.297 1204 -
Rwork0.247 --
obs0.252 23451 97.8 %
all-23451 -
Displacement parametersBiso mean: 63 Å2
Refinement stepCycle: LAST / Resolution: 3.2→28.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8313 630 0 93 9036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069132
X-RAY DIFFRACTIONf_angle_d0.8412432
X-RAY DIFFRACTIONf_dihedral_angle_d17.0463474
X-RAY DIFFRACTIONf_chiral_restr0.0491449
X-RAY DIFFRACTIONf_plane_restr0.0031488
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2013-3.32930.35831060.29630X-RAY DIFFRACTION82
3.3293-3.48060.32731400.27420X-RAY DIFFRACTION100

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