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- PDB-3ktr: Structural basis of ataxin-2 recognition by poly(A)-binding protein -

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Basic information

Entry
Database: PDB / ID: 3ktr
TitleStructural basis of ataxin-2 recognition by poly(A)-binding protein
Components
  • Ataxin-2
  • Polyadenylate-binding protein 1
KeywordsPROTEIN BINDING / protein-protein complex / Acetylation / Alternative splicing / Cytoplasm / Methylation / mRNA processing / mRNA splicing / Nucleus / Phosphoprotein / RNA-binding / Spliceosome / Neurodegeneration / Parkinsonism / Polymorphism / Spinocerebellar ataxia / Triplet repeat expansion
Function / homology
Function and homology information


mCRD-mediated mRNA stability complex / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / RNA metabolic process / translation activator activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA transport / CRD-mediated mRNA stabilization / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Deadenylation of mRNA / negative regulation of receptor internalization ...mCRD-mediated mRNA stability complex / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / RNA metabolic process / translation activator activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA transport / CRD-mediated mRNA stabilization / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Deadenylation of mRNA / negative regulation of receptor internalization / positive regulation of cytoplasmic translation / M-decay: degradation of maternal mRNAs by maternally stored factors / poly(A) binding / P-body assembly / regulatory ncRNA-mediated gene silencing / mRNA stabilization / poly(U) RNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / epidermal growth factor receptor binding / Translation initiation complex formation / cell leading edge / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / positive regulation of viral genome replication / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / stress granule assembly / catalytic step 2 spliceosome / mRNA 3'-UTR binding / AUF1 (hnRNP D0) binds and destabilizes mRNA / trans-Golgi network / mRNA splicing, via spliceosome / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / lamellipodium / regulation of translation / ribonucleoprotein complex / focal adhesion / mRNA binding / perinuclear region of cytoplasm / Golgi apparatus / RNA binding / extracellular exosome / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
LsmAD domain / Ataxin2-like / LsmAD domain / LsmAD / Ataxin 2, SM domain / Ataxin 2 SM domain / Ataxin-2, C-terminal / Ataxin-2 C-terminal region / c-terminal domain of poly(a) binding protein / c-terminal domain of poly(a) binding protein ...LsmAD domain / Ataxin2-like / LsmAD domain / LsmAD / Ataxin 2, SM domain / Ataxin 2 SM domain / Ataxin-2, C-terminal / Ataxin-2 C-terminal region / c-terminal domain of poly(a) binding protein / c-terminal domain of poly(a) binding protein / : / PABP, RNA recognition motif 2 / Polyadenylate binding protein, human types 1, 2, 3, 4 / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / Polyadenylate-binding protein/Hyperplastic disc protein / PABC (PABP) domain / Poly-adenylate binding protein, unique domain / RNA recognition motif domain, eukaryote / RNA recognition motif / : / Sm domain profile. / LSM domain superfamily / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Polyadenylate-binding protein 1 / Ataxin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKozlov, G. / Gehring, K.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural basis of binding of P-body-associated proteins GW182 and ataxin-2 by the Mlle domain of poly(A)-binding protein.
Authors: Kozlov, G. / Safaee, N. / Rosenauer, A. / Gehring, K.
History
DepositionNov 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyadenylate-binding protein 1
B: Ataxin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6665
Polymers11,3612
Non-polymers3053
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-31 kcal/mol
Surface area6270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.093, 60.745, 31.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Polyadenylate-binding protein 1 / Poly(A)-binding protein 1 / PABP 1


Mass: 9421.909 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PABPC1, PAB1, PABP1, PABPC2 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P11940
#2: Protein/peptide Ataxin-2 / Spinocerebellar ataxia type 2 protein / Trinucleotide repeat-containing gene 13 protein


Mass: 1939.090 Da / Num. of mol.: 1 / Fragment: PABPC1-binding fragment / Source method: obtained synthetically / Details: chemically synthesized / Source: (synth.) Homo sapiens (human) / References: UniProt: Q99700
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 1.65 Å3/Da / Density % sol: 25.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 2.2 M ammonium sulfate, 0.2 M CdCl2, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.995 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 30, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.995 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 8296 / Num. obs: 8039 / % possible obs: 96.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 23.1
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 7.4 / Num. unique all: 555 / % possible all: 94

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1I2T

1i2t


Resolution: 1.7→32.88 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.436 / SU ML: 0.076 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24508 393 4.7 %RANDOM
Rwork0.21237 ---
all0.213 8296 --
obs0.213 8039 96.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.196 Å2
Baniso -1Baniso -2Baniso -3
1-2.94 Å20 Å20 Å2
2---1.82 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 1.7→32.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms741 0 11 26 778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022771
X-RAY DIFFRACTIONr_angle_refined_deg1.2772.0161047
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.87599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.72726.12931
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.61215141
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.016153
X-RAY DIFFRACTIONr_chiral_restr0.0820.2121
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02566
X-RAY DIFFRACTIONr_nbd_refined0.210.2376
X-RAY DIFFRACTIONr_nbtor_refined0.3050.2529
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.218
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2690.26
X-RAY DIFFRACTIONr_mcbond_it1.0081.5506
X-RAY DIFFRACTIONr_mcangle_it1.4652797
X-RAY DIFFRACTIONr_scbond_it2.4083279
X-RAY DIFFRACTIONr_scangle_it3.8264.5248
LS refinement shellResolution: 1.7→1.746 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 34 -
Rwork0.237 555 -
obs--93.64 %
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)
115.376913.8241-4.8137.4299-1.871710.3016-1.22170.1369-1.0041-2.46250.7106-0.43890.9550.07720.5111-0.00810.02210.0547-0.0121-0.0054-0.0269-5.5394.3673-18.5746
214.26363.5828-3.33067.1874-5.54459.30850.04170.35310.0280.1081-0.0833-0.1175-0.15680.1460.04150.04660.0236-0.01870.0948-0.00790.0434-9.00149.7884-13.4033
34.92341.53430.62271.97870.53111.26260.0617-0.19420.01250.2071-0.14540.1307-0.0572-0.05420.08370.06550.0055-0.00710.04270.00150.0603-16.4018.1434-1.5191
45.36441.3169-1.550510.71190.83764.3272-0.0895-0.1261-0.12750.1793-0.0159-0.280.02520.21920.10540.0210.0248-0.02280.0928-0.00770.0563-4.06944.4514-5.9208
51.5786-0.5365-0.561117.093113.470610.74050.0935-0.0168-0.09060.22590.0428-0.33730.20070.0402-0.13630.08330.0246-0.02860.04570.01770.0683-10.74093.95264.2273
619.1984-4.3797-3.089437.969517.91520.55890.5321-0.29571.44850.30690.05890.2195-0.5334-0.2075-0.591-0.00830.06330.0493-0.0203-0.0340.1463-14.101619.97714.209
76.0042-4.34896.981629.0083-3.010114.72690.33620.1025-0.1647-0.8678-0.1805-0.48680.46640.768-0.15570.0288-0.01690.00940.047-0.01220.0428-6.068715.20244.0033
819.778812.807626.987810.887317.718147.4686-0.15330.01140.94190.0657-0.22440.32-1.7461-0.5460.37770.16660.06130.01370.00510.0212-0.0003-14.271516.0393-6.5922
933.8176-1.7482-22.369412.4324-11.678545.384-0.44570.8235-1.4504-0.9695-0.00010.61252.01770.46420.44580.04660.0479-0.01240.049-0.04320.059-22.114110.1995-12.1981
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A543 - 555
2X-RAY DIFFRACTION2A556 - 565
3X-RAY DIFFRACTION3A566 - 585
4X-RAY DIFFRACTION4A586 - 597
5X-RAY DIFFRACTION5A598 - 617
6X-RAY DIFFRACTION6A618 - 623
7X-RAY DIFFRACTION7C - A914 - 919
8X-RAY DIFFRACTION8C - A920 - 924
9X-RAY DIFFRACTION9C - A925 - 929

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