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- PDB-3ktp: Structural basis of GW182 recognition by poly(A)-binding protein -

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Basic information

Entry
Database: PDB / ID: 3ktp
TitleStructural basis of GW182 recognition by poly(A)-binding protein
Components
  • Polyadenylate-binding protein 1
  • Trinucleotide repeat-containing gene 6C protein
KeywordsPROTEIN BINDING / protein-protein complex / Methylation / mRNA processing / mRNA splicing / Nucleus / Phosphoprotein / RNA-binding / Spliceosome / RNA-mediated gene silencing / Translation regulation
Function / homology
Function and homology information


negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / mCRD-mediated mRNA stability complex / Regulation of CDH11 mRNA translation by microRNAs / Regulation of NPAS4 mRNA translation / Post-transcriptional silencing by small RNAs / Competing endogenous RNAs (ceRNAs) regulate PTEN translation / Regulation of PTEN mRNA translation / translation activator activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization ...negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / mCRD-mediated mRNA stability complex / Regulation of CDH11 mRNA translation by microRNAs / Regulation of NPAS4 mRNA translation / Post-transcriptional silencing by small RNAs / Competing endogenous RNAs (ceRNAs) regulate PTEN translation / Regulation of PTEN mRNA translation / translation activator activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / Transcriptional Regulation by MECP2 / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / miRNA-mediated post-transcriptional gene silencing / Deadenylation of mRNA / miRNA-mediated gene silencing by inhibition of translation / positive regulation of cytoplasmic translation / mRNA stabilization / poly(A) binding / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / Regulation of RUNX1 Expression and Activity / poly(U) RNA binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Translation initiation complex formation / : / cell leading edge / Regulation of MECP2 expression and activity / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Transcriptional Regulation by VENTX / L13a-mediated translational silencing of Ceruloplasmin expression / positive regulation of viral genome replication / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / catalytic step 2 spliceosome / mRNA 3'-UTR binding / AUF1 (hnRNP D0) binds and destabilizes mRNA / P-body / TP53 Regulates Metabolic Genes / MAPK6/MAPK4 signaling / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Oncogene Induced Senescence / cytoplasmic ribonucleoprotein granule / mRNA splicing, via spliceosome / Pre-NOTCH Transcription and Translation / Regulation of expression of SLITs and ROBOs / cytoplasmic stress granule / lamellipodium / Ca2+ pathway / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / ribonucleoprotein complex / focal adhesion / mRNA binding / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
TNRC6C, RNA recognition motif / Trinucleotide repeat-containing gene 6C protein, UBA domain / GW182, middle domain / M domain of GW182 / TNRC6, PABC binding domain / TNRC6-PABC binding domain / Argonaute hook domain / Argonaute hook / c-terminal domain of poly(a) binding protein / c-terminal domain of poly(a) binding protein ...TNRC6C, RNA recognition motif / Trinucleotide repeat-containing gene 6C protein, UBA domain / GW182, middle domain / M domain of GW182 / TNRC6, PABC binding domain / TNRC6-PABC binding domain / Argonaute hook domain / Argonaute hook / 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 / Polyadenylate-binding protein/Hyperplastic disc protein / Poly-adenylate binding protein, unique domain / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / PABC (PABP) domain / RNA recognition motif domain, eukaryote / RNA recognition motif / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like 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 / Trinucleotide repeat-containing gene 6C protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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: Advisory / Version format compliance
Revision 1.2Sep 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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: Trinucleotide repeat-containing gene 6C protein


Theoretical massNumber of molelcules
Total (without water)11,8852
Polymers11,8852
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-11 kcal/mol
Surface area5730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.461, 38.461, 136.533
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-25-

HOH

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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 Trinucleotide repeat-containing gene 6C protein


Mass: 2462.758 Da / Num. of mol.: 1 / Fragment: PABPC1-binding fragment / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9HCJ0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.12 Å3/Da / Density % sol: 42.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2.0 M ammonium sulfate, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 9, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 16463 / Num. obs: 16216 / % possible obs: 98.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.3 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 34.1
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1041 / % possible all: 82.7

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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: 1.5→37.01 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.832 / SU ML: 0.053 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23067 855 5 %RANDOM
Rwork0.22075 ---
all0.221 16463 --
obs0.221 16216 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.746 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--0.3 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.5→37.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms726 0 0 73 799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022748
X-RAY DIFFRACTIONr_angle_refined_deg1.0051.9891016
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.446594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.58225.86229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.32815132
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.53152
X-RAY DIFFRACTIONr_chiral_restr0.060.2114
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02552
X-RAY DIFFRACTIONr_nbd_refined0.1940.2327
X-RAY DIFFRACTIONr_nbtor_refined0.2930.2505
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0580.250
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.213
X-RAY DIFFRACTIONr_mcbond_it0.5361.5490
X-RAY DIFFRACTIONr_mcangle_it0.752766
X-RAY DIFFRACTIONr_scbond_it1.2553289
X-RAY DIFFRACTIONr_scangle_it1.9984.5249
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 58 -
Rwork0.252 1041 -
obs--86.06 %
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)
130.239614.0274.966713.52852.81345.08681.0222-1.81870.391.4866-0.9958-0.04380.23030.0016-0.02640.2257-0.0817-0.04130.0596-0.0002-0.0877-6.225-25.1755.511
20.36781.01920.36515.69080.1033.49430.04060.0279-0.03530.1963-0.08910.04920.13410.12670.04850.06150.00160.01910.0513-0.00330.0085-10.782-19.386-2.737
30.3035-0.12660.02064.6688-1.24114.73510.01450.088-0.021-0.113-0.0375-0.1423-0.02390.33720.0230.0381-0.00780.0190.08280.00120.0053-6.396-16.138-10.343
43.9644-0.69227.05162.6697-2.673423.71760.1032-0.08290.0324-0.1433-0.1854-0.35760.00361.42950.0821-0.0322-0.04370.01070.18150.0187-0.0291-0.424-14.347-13.515
56.7977-0.8049-6.424631.4749-6.521917.94620.04350.4052-0.2379-1.41420.30941.04481.0778-1.3399-0.35280.144-0.0894-0.09070.05830.0456-0.0388-12.58-14.385-27.996
621.2444-1.8555-22.41974.06812.009849.527-0.1650.7248-0.0497-0.1826-0.09610.1897-0.1833-1.29750.26110.06610.0046-0.00940.0164-0.0119-0.0583-15.406-17.244-17.606
77.51610.5371-3.87913.22273.337612.75540.13330.14860.18-0.0834-0.23440.3153-0.1435-0.40670.10110.01840.0085-0.00810.0722-0.0196-0.0109-18.209-14.921-6.006
812.16396.9969-4.55227.14469.952718.0712-0.15620.2081-0.361-0.2635-0.23770.66020.0527-0.4650.39380.0468-0.021-0.02380.0406-0.0154-0.007-18.175-23.208-10.718
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A541 - 554
2X-RAY DIFFRACTION2A555 - 569
3X-RAY DIFFRACTION3A570 - 595
4X-RAY DIFFRACTION4A596 - 616
5X-RAY DIFFRACTION5A617 - 621
6X-RAY DIFFRACTION6B1384 - 1388
7X-RAY DIFFRACTION7B1389 - 1394
8X-RAY DIFFRACTION8B1395 - 1399

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