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- PDB-2v75: N-terminal domain of Nab2 -

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Basic information

Entry
Database: PDB / ID: 2v75
TitleN-terminal domain of Nab2
ComponentsNUCLEAR POLYADENYLATED RNA-BINDING PROTEIN NAB2
KeywordsNUCLEAR PROTEIN / METAL-BINDING / NUCLEUS / RNA-BINDING / ZINC-FINGER
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 / mRNA 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
Nuclear abundant poly(A) RNA-bind protein 2, N-terminal domain / 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 abundant poly(A) RNA-bind protein 2, N-terminal domain / 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 / Endonuclease III; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Nuclear polyadenylated RNA-binding protein NAB2
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGrant, R.P. / Marshall, N.J. / Stewart, M.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structure of the N-Terminal Mlp1-Binding Domain of the Saccharomyces Cerevisiae Mrna-Binding Protein, Nab2.
Authors: Grant, R.P. / Marshall, N.J. / Yang, J.-C. / Fasken, M.B. / Kelly, S.M. / Harreman, M.T. / Neuhaus, D. / Corbett, A.H. / Stewart, M.
History
DepositionJul 26, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NUCLEAR POLYADENYLATED RNA-BINDING PROTEIN NAB2


Theoretical massNumber of molelcules
Total (without water)11,3911
Polymers11,3911
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)48.136, 48.136, 81.219
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2023-

HOH

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Components

#1: Protein NUCLEAR POLYADENYLATED RNA-BINDING PROTEIN NAB2


Mass: 11390.797 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-104
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P32505
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.25 Å3/Da / Density % sol: 66 %
Description: NMR STRUCTRE WILL BE PUBLISHED TOGETHER WITH CRYSTAL STRUCTURE
Crystal growDetails: DESCRIBED IN DETAIL IN PUBLICATION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 10, 2006 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 9015 / % possible obs: 96.4 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.1
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.3 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: UNPUBLISHED NMR STRUCTURE

Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.921 / SU B: 6.691 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25 424 4.7 %RANDOM
Rwork0.195 ---
obs0.197 8556 96.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2--0.67 Å20 Å2
3----1.34 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms687 0 0 59 746
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022694
X-RAY DIFFRACTIONr_bond_other_d0.0050.02438
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.972942
X-RAY DIFFRACTIONr_angle_other_deg0.96131085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.696588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.78926.45231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.03515123
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.859152
X-RAY DIFFRACTIONr_chiral_restr0.0910.2117
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02771
X-RAY DIFFRACTIONr_gen_planes_other00.02127
X-RAY DIFFRACTIONr_nbd_refined0.2520.3198
X-RAY DIFFRACTIONr_nbd_other0.2160.3448
X-RAY DIFFRACTIONr_nbtor_refined0.1980.5361
X-RAY DIFFRACTIONr_nbtor_other0.0930.5351
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2670.567
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.310.313
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3020.319
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4590.514
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.2235573
X-RAY DIFFRACTIONr_mcbond_other0.9875180
X-RAY DIFFRACTIONr_mcangle_it4.79410716
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.375284
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.47210226
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 34 -
Rwork0.316 613 -
obs--96.28 %
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)
12.74510.560.01776.0024-0.0124.98330.06530.04610.0987-0.0958-0.01520.2794-0.2125-0.1784-0.0501-0.1565-0.0212-0.0158-0.24460.0301-0.151629.65565.3145-7.176
220.43054.0459-13.339416.07911.162323.89490.4942-1.5147-0.0381.8536-0.0499-0.9140.19731.3243-0.44440.1946-0.1098-0.08-0.125-0.0522-0.140938.644414.4921.2179
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 82
2X-RAY DIFFRACTION2A83 - 94

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