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- PDB-5l2l: Nab2 Zn fingers 5-7 bound to A11G RNA -

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Basic information

Entry
Database: PDB / ID: 5l2l
TitleNab2 Zn fingers 5-7 bound to A11G RNA
Components
  • Nab2p
  • RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*G)-3')
KeywordsRNA BINDING PROTEIN / Nab2 / Zn finger / RNA
Function / homology
Function and homology information


: / ribonuclease P RNA binding / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 7S RNA binding / poly(A) binding / positive regulation of transcription by RNA polymerase III / poly(A)+ mRNA export from nucleus / regulation of mRNA stability / 5S rRNA binding / tRNA binding ...: / ribonuclease P RNA binding / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 7S RNA binding / poly(A) binding / positive regulation of transcription by RNA polymerase III / poly(A)+ mRNA export from nucleus / regulation of mRNA stability / 5S rRNA binding / tRNA binding / mRNA binding / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
CCCH zinc finger - #40 / CCCH zinc finger / Nuclear abundant poly(A) RNA-binding protein Nab2, N-terminal / Nuclear polyadenylated RNA-binding 2 protein, CCCH zinc finger 1 / Nab2/ZC3H14, N-terminal domain superfamily / : / : / Nuclear abundant poly(A) RNA-bind protein 2 (Nab2) / Nuclear polyadenylated RNA-binding 2 protein CCCH zinc finger 1 / RNA-binding, Nab2-type zinc finger ...CCCH zinc finger - #40 / CCCH zinc finger / Nuclear abundant poly(A) RNA-binding protein Nab2, N-terminal / Nuclear polyadenylated RNA-binding 2 protein, CCCH zinc finger 1 / Nab2/ZC3H14, N-terminal domain superfamily / : / : / Nuclear abundant poly(A) RNA-bind protein 2 (Nab2) / Nuclear polyadenylated RNA-binding 2 protein CCCH zinc finger 1 / RNA-binding, Nab2-type zinc finger / Nab2-type CCCH zinc finger 4 / Nuclear polyadenylated RNA-binding protein Nab2/ZC3H14 / RNA-binding, Nab2-type zinc finger / Few Secondary Structures / Irregular
Similarity search - Domain/homology
RNA / RNA (> 10) / : / Nuclear polyadenylated RNA-binding protein NAB2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae YJM1574 (yeast)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsStewart, M. / Aibara, S.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Structural basis for the dimerization of Nab2 generated by RNA binding provides insight into its contribution to both poly(A) tail length determination and transcript compaction in Saccharomyces cerevisiae.
Authors: Aibara, S. / Gordon, J.M. / Riesterer, A.S. / McLaughlin, S.H. / Stewart, M.
History
DepositionAug 2, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nab2p
B: Nab2p
C: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*G)-3')
D: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*G)-3')
E: Nab2p
F: Nab2p
G: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*G)-3')
H: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,44422
Polymers51,5288
Non-polymers91614
Water12,340685
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14800 Å2
ΔGint-65 kcal/mol
Surface area22830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.669, 85.035, 64.956
Angle α, β, γ (deg.)90.00, 99.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Nab2p


Mass: 8960.466 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae YJM1574 (yeast)
Gene: NAB2, H834_YJM1574G00138 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0C6D5P3, UniProt: P32505*PLUS
#2: RNA chain
RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*G)-3')


Mass: 3921.512 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 685 / 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: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 30% ethanol, PEG6000, ammonium acetate, Tris buffer, pH 7.4. See publication for details.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.55→46.085 Å / Num. obs: 72125 / % possible obs: 99.4 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 20.8
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 1.9 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.55→46.085 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 0.2 / Phase error: 16.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1516 7040 4.95 %
Rwork0.1308 --
obs0.1319 72092 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→46.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2361 908 14 685 3968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083521
X-RAY DIFFRACTIONf_angle_d0.9444958
X-RAY DIFFRACTIONf_dihedral_angle_d14.4962000
X-RAY DIFFRACTIONf_chiral_restr0.049543
X-RAY DIFFRACTIONf_plane_restr0.007474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.56760.28332430.24844437X-RAY DIFFRACTION99
1.5676-1.58610.27942130.23834553X-RAY DIFFRACTION99
1.5861-1.60540.26752570.22174460X-RAY DIFFRACTION99
1.6054-1.62570.2562620.21324514X-RAY DIFFRACTION100
1.6257-1.64710.24892360.19634517X-RAY DIFFRACTION100
1.6471-1.66970.22722330.18394581X-RAY DIFFRACTION99
1.6697-1.69360.21382000.16684443X-RAY DIFFRACTION100
1.6936-1.71880.19312010.16174568X-RAY DIFFRACTION100
1.7188-1.74570.19782170.15064526X-RAY DIFFRACTION99
1.7457-1.77430.17942310.14334485X-RAY DIFFRACTION99
1.7743-1.80490.14282130.12774564X-RAY DIFFRACTION99
1.8049-1.83770.1592760.11584423X-RAY DIFFRACTION100
1.8377-1.87310.13652590.11664533X-RAY DIFFRACTION100
1.8731-1.91130.15652400.1134508X-RAY DIFFRACTION100
1.9113-1.95290.15372150.11974568X-RAY DIFFRACTION100
1.9529-1.99830.16862230.12194479X-RAY DIFFRACTION100
1.9983-2.04830.14952500.12024558X-RAY DIFFRACTION100
2.0483-2.10370.15432600.12034469X-RAY DIFFRACTION99
2.1037-2.16560.15612130.11414491X-RAY DIFFRACTION99
2.1656-2.23550.1492300.11584571X-RAY DIFFRACTION100
2.2355-2.31540.142360.11174495X-RAY DIFFRACTION100
2.3154-2.40810.14742550.10914464X-RAY DIFFRACTION100
2.4081-2.51760.13742110.11444588X-RAY DIFFRACTION100
2.5176-2.65040.17342040.11884496X-RAY DIFFRACTION99
2.6504-2.81640.16612460.13414505X-RAY DIFFRACTION99
2.8164-3.03380.14452200.13724540X-RAY DIFFRACTION100
3.0338-3.3390.14122790.1224482X-RAY DIFFRACTION100
3.339-3.8220.11952690.11474465X-RAY DIFFRACTION99
3.822-4.81450.11812170.11644489X-RAY DIFFRACTION99
4.8145-46.10530.14852310.15674502X-RAY DIFFRACTION99

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