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- PDB-3kuj: Crystal structure of C-terminal domain of PABPC1 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 3kuj
TitleCrystal structure of C-terminal domain of PABPC1 in complex with binding region of eRF3a
Components
  • GSPT1 protein
  • Polyadenylate-binding protein 1
KeywordsPROTEIN BINDING / protein-protein complex / Methylation / mRNA processing / mRNA splicing / Nucleus / Phosphoprotein / RNA-binding / Spliceosome / GTP-binding / Nucleotide-binding
Function / homology
Function and homology information


mCRD-mediated mRNA stability complex / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / translation release factor complex / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / translation activator activity / CRD-mediated mRNA stabilization / translation release factor activity / regulation of translational termination / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Deadenylation of mRNA ...mCRD-mediated mRNA stability complex / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / translation release factor complex / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / translation activator activity / CRD-mediated mRNA stabilization / translation release factor activity / regulation of translational termination / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Deadenylation of mRNA / protein methylation / positive regulation of cytoplasmic translation / poly(A) binding / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / mRNA stabilization / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / poly(U) RNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Translation initiation complex formation / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / cell leading edge / Eukaryotic Translation Termination / 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) / translational termination / cytosolic ribosome / catalytic step 2 spliceosome / mRNA 3'-UTR binding / AUF1 (hnRNP D0) binds and destabilizes mRNA / mRNA splicing, via spliceosome / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / G1/S transition of mitotic cell cycle / cytoplasmic stress granule / lamellipodium / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / translation / ribonucleoprotein complex / focal adhesion / GTPase activity / mRNA binding / GTP binding / RNA binding / extracellular exosome / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
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 ...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 / MLLE domain / : / GTP-eEF1A C-terminal domain-like / : / RNA recognition motif domain, eukaryote / RNA recognition motif / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Translation protein, beta-barrel domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Polyadenylate-binding protein 1 / Eukaryotic peptide chain release factor GTP-binding subunit ERF3B / Eukaryotic peptide chain release factor GTP-binding subunit ERF3A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsKozlov, G. / Gehring, K.
CitationJournal: Plos One / Year: 2010
Title: Molecular basis of eRF3 recognition by the MLLE domain of poly(A)-binding protein.
Authors: Kozlov, G. / Gehring, K.
History
DepositionNov 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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: GSPT1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2894
Polymers11,0972
Non-polymers1922
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-35 kcal/mol
Surface area5690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.217, 50.802, 32.121
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 GSPT1 protein


Mass: 1674.913 Da / Num. of mol.: 1 / Fragment: PABPC1-binding region / Source method: obtained synthetically / Details: chemically synthesized / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96GF2, UniProt: Q8IYD1*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 53 / 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: 1.66 Å3/Da / Density % sol: 26.01 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 1.4M ammonium sulfate, 0.1M citric acid, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 29, 2008 / 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: 1.4→50 Å / Num. all: 14288 / Num. obs: 14231 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.5 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 19.2
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 6.1 / Num. unique all: 997 / % possible all: 99.9

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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: 1.4→33.77 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / SU B: 1.865 / SU ML: 0.039 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.074 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22331 756 5 %RANDOM
Rwork0.19578 ---
obs0.19713 14231 99.36 %-
all-14288 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.223 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.4→33.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms698 0 10 53 761
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022729
X-RAY DIFFRACTIONr_angle_refined_deg1.2492.007992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.037594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.18525.92627
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25115129
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.126152
X-RAY DIFFRACTIONr_chiral_restr0.1060.2118
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02523
X-RAY DIFFRACTIONr_nbd_refined0.2090.2322
X-RAY DIFFRACTIONr_nbtor_refined0.3040.2502
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0730.232
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.212
X-RAY DIFFRACTIONr_mcbond_it0.6621.5477
X-RAY DIFFRACTIONr_mcangle_it1.0132757
X-RAY DIFFRACTIONr_scbond_it1.9453263
X-RAY DIFFRACTIONr_scangle_it2.864.5233
LS refinement shellResolution: 1.4→1.438 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 49 -
Rwork0.218 997 -
obs--96.32 %
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)
121.2737-2.37094.50066.12071.3378.4661-0.28230.2376-0.0071-0.13610.0878-0.0288-0.45860.04840.19460.0766-0.0458-0.0299-0.01540.0081-0.071410.304412.298819.1186
25.69461.66582.26684.5252.36664.09270.0126-0.2426-0.02970.13450.07310.0824-0.09970.2377-0.08570.0629-0.039-0.0210.0610.007-0.012411.41026.265513.6167
30.88150.77460.11472.36910.60110.70730.0158-0.0118-0.06130.0028-0.0356-0.0744-0.00530.00680.01980.0225-0.0058-0.00280.03070.00260.03628.93685.24843.6889
46.0592-1.5579-4.80882.09042.51317.9221-0.05340.0969-0.1638-0.0949-0.00260.0180.1770.04940.0560.0470.0002-0.00140.01830.00930.03377.6936.0921-4.2272
53.8411-3.9714.79411.0162-9.08299.58150.028-0.11-0.2191-0.1350.00980.0020.07680.0515-0.0379-0.00070.00370.01440.03420.0030.057217.3117.7562-1.9525
61.5729-1.912-4.400240.3717-34.722154.512-0.66010.03560.3091.39870.5024-0.24770.5735-0.77520.15770.07520.0061-0.0641-0.0250.0343-0.03713.8192-3.50512.0592
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A544 - 556
2X-RAY DIFFRACTION2A557 - 566
3X-RAY DIFFRACTION3A567 - 596
4X-RAY DIFFRACTION4A597 - 620
5X-RAY DIFFRACTION5B76 - 84
6X-RAY DIFFRACTION6B85 - 90

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