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- PDB-2x04: Crystal structure of the PABC-TNRC6C complex -

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Basic information

Entry
Database: PDB / ID: 2x04
TitleCrystal structure of the PABC-TNRC6C complex
Components
  • POLYADENYLATE-BINDING PROTEIN 1
  • TRINUCLEOTIDE REPEAT-CONTAINING GENE 6C PROTEIN
KeywordsPEPTIDE/RNA BINDING PROTEIN / PEPTIDE-RNA BINDING PROTEIN COMPLEX / RNA-MEDIATED GENE SILENCING / NUCLEUS / METHYLATION / SPLICEOSOME / TRANSLATION REGULATION / PROTEIN-PROTEIN COMPLEX / COILED COIL / DEADENYLATION / MRNA SPLICING / PHOSPHOPROTEIN / MRNA PROCESSING / MICRORNA SILENCING
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 / poly(U) RNA binding / Regulation of RUNX1 Expression and Activity / 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 / SAD / Resolution: 1.49 Å
AuthorsJinek, M. / Fabian, M.R. / Coyle, S.M. / Sonenberg, N. / Doudna, J.A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structural Insights Into the Human Gw182-Pabc Interaction in Microrna-Mediated Deadenylation
Authors: Jinek, M. / Fabian, M.R. / Coyle, S.M. / Sonenberg, N. / Doudna, J.A.
History
DepositionDec 4, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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: POLYADENYLATE-BINDING PROTEIN 1
C: TRINUCLEOTIDE REPEAT-CONTAINING GENE 6C PROTEIN
D: TRINUCLEOTIDE REPEAT-CONTAINING GENE 6C PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5676
Polymers21,3754
Non-polymers1922
Water3,909217
1
B: POLYADENYLATE-BINDING PROTEIN 1
D: TRINUCLEOTIDE REPEAT-CONTAINING GENE 6C PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8794
Polymers10,6872
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-22.8 kcal/mol
Surface area5510 Å2
MethodPISA
2
A: POLYADENYLATE-BINDING PROTEIN 1
C: TRINUCLEOTIDE REPEAT-CONTAINING GENE 6C PROTEIN


Theoretical massNumber of molelcules
Total (without water)10,6872
Polymers10,6872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-21.3 kcal/mol
Surface area5440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.110, 72.230, 37.040
Angle α, β, γ (deg.)90.00, 119.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein POLYADENYLATE-BINDING PROTEIN 1 / POLY(A)-BINDING PROTEIN 1 / PABP 1 / POLYA BINDING PROTEIN PABP1


Mass: 8595.959 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN (PABC), RESIDUES 456-530
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11940
#2: Protein/peptide TRINUCLEOTIDE REPEAT-CONTAINING GENE 6C PROTEIN / TNRC6C


Mass: 2091.368 Da / Num. of mol.: 2 / Fragment: DUF DOMAIN, RESIDUES 1382-1399 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q9HCJ0
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE GPLGS AT THE N-TERMINUS IS DERIVED FROM THE EXPRESSION VECTOR

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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: 2.08 Å3/Da / Density % sol: 40.9 % / Description: NONE
Crystal growpH: 4.6
Details: 0.1 M NA-ACETATE PH 4.6, 200 MM AMMONIUM SULFATE, 30% (W/V) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.999954
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999954 Å / Relative weight: 1
Reflection twinOperator: L,-K,H / Fraction: 0.123
ReflectionResolution: 1.5→29.4 Å / Num. obs: 27112 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 3.66 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 3.66 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.87 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.49→29.38 Å / σ(F): 2 / Phase error: 20.91 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.186 1385 5 %
Rwork0.163 --
obs0.164 27601 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.86 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 19.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.7995 Å20 Å20.2947 Å2
2---2.0737 Å20 Å2
3----0.4931 Å2
Refinement stepCycle: LAST / Resolution: 1.49→29.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1414 0 10 217 1641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061493
X-RAY DIFFRACTIONf_angle_d1.0172039
X-RAY DIFFRACTIONf_dihedral_angle_d13.044583
X-RAY DIFFRACTIONf_chiral_restr0.06230
X-RAY DIFFRACTIONf_plane_restr0.005265
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.52730.2534970.22811837X-RAY DIFFRACTION98
1.5273-1.56860.2679980.21411858X-RAY DIFFRACTION98
1.5686-1.61470.21951000.20561899X-RAY DIFFRACTION98
1.6147-1.66680.2398970.19551845X-RAY DIFFRACTION98
1.6668-1.72640.1662980.19221868X-RAY DIFFRACTION98
1.7264-1.79550.2112980.18051858X-RAY DIFFRACTION98
1.7955-1.87720.1682990.1871886X-RAY DIFFRACTION98
1.8772-1.97620.2275990.1781869X-RAY DIFFRACTION98
1.9762-2.10.2258980.17881872X-RAY DIFFRACTION98
2.1-2.2620.1733990.16541866X-RAY DIFFRACTION98
2.262-2.48960.20161000.16371907X-RAY DIFFRACTION98
2.4896-2.84960.1838980.15841860X-RAY DIFFRACTION98
2.8496-3.58910.1788990.13781887X-RAY DIFFRACTION98
3.5891-29.38170.14131010.13281908X-RAY DIFFRACTION98

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