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- PDB-3kus: Crystal structure of the MLLE domain of poly(A)-binding protein i... -

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Basic information

Entry
Database: PDB / ID: 3kus
TitleCrystal structure of the MLLE domain of poly(A)-binding protein in complex with the binding region of Paip2
Components
  • PAIP2 protein
  • Polyadenylate-binding protein 1
KeywordsPROTEIN BINDING / protein-protein complex / Methylation / mRNA processing / mRNA splicing / Nucleus / Phosphoprotein / RNA-binding / Spliceosome
Function / homology
Function and homology information


negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / mCRD-mediated mRNA stability complex / translation activator activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Deadenylation of mRNA / positive regulation of cytoplasmic translation / poly(A) binding / M-decay: degradation of maternal mRNAs by maternally stored factors ...negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / mCRD-mediated mRNA stability complex / translation activator activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Deadenylation of mRNA / 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 / poly(U) RNA binding / regulation of long-term synaptic potentiation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 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) / translation repressor activity / negative regulation of translational initiation / catalytic step 2 spliceosome / mRNA regulatory element binding translation repressor activity / AUF1 (hnRNP D0) binds and destabilizes mRNA / mRNA 3'-UTR binding / memory / Regulation of expression of SLITs and ROBOs / mRNA splicing, via spliceosome / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / lamellipodium / spermatogenesis / negative regulation of translation / ribonucleoprotein complex / translation / focal adhesion / mRNA binding / RNA binding / extracellular exosome / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Polyadenylate-binding protein-interacting protein 2-like / 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 / Polyadenylate-binding protein/Hyperplastic disc protein / Poly-adenylate binding protein, unique domain ...Polyadenylate-binding protein-interacting protein 2-like / 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 / 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 / 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 / Polyadenylate-binding protein-interacting protein 2 / Polyadenylate-binding protein-interacting protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsKozlov, G. / Gehring, K.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Molecular Determinants of PAM2 Recognition by the MLLE Domain of Poly(A)-Binding Protein.
Authors: Kozlov, G. / Menade, M. / Rosenauer, A. / Nguyen, L. / Gehring, K.
History
DepositionNov 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 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: Polyadenylate-binding protein 1
C: PAIP2 protein
D: PAIP2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4066
Polymers22,0754
Non-polymers3302
Water2,306128
1
A: Polyadenylate-binding protein 1
C: PAIP2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1303
Polymers11,0382
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-9 kcal/mol
Surface area5600 Å2
MethodPISA
2
B: Polyadenylate-binding protein 1
D: PAIP2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2763
Polymers11,0382
Non-polymers2381
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-4 kcal/mol
Surface area5610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.396, 31.610, 48.214
Angle α, β, γ (deg.)100.12, 92.26, 98.90
Int Tables number1
Space group name H-MP1

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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.: 2 / 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 PAIP2 protein


Mass: 1615.827 Da / Num. of mol.: 2 / Fragment: PABPC1-binding region / Source method: obtained synthetically / Details: chemically synthesized / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6FID7, UniProt: Q9BPZ3*PLUS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 1.77 Å3/Da / Density % sol: 30.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.3M ammonium sulfate, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.995 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 30, 2009 / 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: 1.4→50 Å / Num. all: 28308 / Num. obs: 27147 / % possible obs: 95.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 33.1
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4 / Num. unique all: 1857 / % possible all: 90.2

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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→47.35 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.765 / SU ML: 0.036 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.069 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20514 1438 5 %RANDOM
Rwork0.17808 ---
obs0.17941 27147 95.73 %-
all-28308 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.843 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.47 Å2-0.1 Å2
2--0.19 Å2-0.15 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.4→47.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1343 0 21 128 1492
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221397
X-RAY DIFFRACTIONr_angle_refined_deg1.0522.0191891
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8645179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.6826.72755
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35715256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.362154
X-RAY DIFFRACTIONr_chiral_restr0.0610.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021016
X-RAY DIFFRACTIONr_nbd_refined0.2090.2695
X-RAY DIFFRACTIONr_nbtor_refined0.30.2974
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0960.270
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.215
X-RAY DIFFRACTIONr_mcbond_it0.771.5925
X-RAY DIFFRACTIONr_mcangle_it1.00521441
X-RAY DIFFRACTIONr_scbond_it1.9973503
X-RAY DIFFRACTIONr_scangle_it3.0854.5447
LS refinement shellResolution: 1.4→1.435 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 97 -
Rwork0.217 1857 -
obs--88.7 %
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)
18.8717-2.36753.45225.555-0.34227.4788-0.08440.1485-0.1403-0.0987-0.0907-0.28970.12520.00140.1751-0.0185-0.01690.0541-0.0489-0.02570.052111.8519-8.1923-19.1301
21.6694-0.6-0.55590.77210.35551.2790.01710.0642-0.0348-0.0141-0.039-0.00770.00950.03270.02180.019-0.00430.00170.026-0.00340.02124.82763.1178-14.4476
34.7283-3.51412.25793.3423-1.69542.01550.00920.08780.0603-0.0469-0.07150.0969-0.03040.01650.06230.0269-0.0094-0.00850.02690.00470.06822.439415.3256-14.7676
40.7434-0.0721-0.43721.9565-0.48213.4662-0.0201-0.0631-0.03470.08990.0461-0.04170.04650.0059-0.0260.01440.0051-0.00410.0532-0.00080.01946.20282.52647.907
54.87611.4273.77971.35921.10014.031-0.0391-0.29210.14830.0906-0.00350.1001-0.1163-0.3710.0427-0.00380.00140.01710.07260.0141-0.0031-3.60461.497310.5462
63.87113.84643.62817.3634.20144.946-0.0683-0.12880.08280.22080.0792-0.1792-0.2573-0.0873-0.01090.05040.0334-0.00250.026-0.01950.0051.11114.1326.9422
73.14533.998-3.096614.8392-5.67855.16610.01550.2145-0.0305-0.2249-0.00070.3785-0.0539-0.2588-0.0148-0.00110.0165-0.03410.0435-0.03180.0255-1.62315.4486-19.8138
814.8829-7.59281.471618.1969-1.73615.56330.1767-0.4033-0.15170.60370.25050.4778-0.4449-0.4923-0.42720.10030.0430.0288-0.004-0.0062-0.06234.376311.300816.742
913.5369-10.9195-5.422421.9669.158911.33740.02050.4111-0.3199-0.62950.0319-0.3126-0.02980.1582-0.0523-0.0029-0.0080.01190.04240.00140.02113.4087-0.75467.6343
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A545 - 556
2X-RAY DIFFRACTION2A557 - 595
3X-RAY DIFFRACTION3A596 - 626
4X-RAY DIFFRACTION4B553 - 585
5X-RAY DIFFRACTION5B586 - 597
6X-RAY DIFFRACTION6B598 - 622
7X-RAY DIFFRACTION7C111 - 121
8X-RAY DIFFRACTION8D110 - 116
9X-RAY DIFFRACTION9D117 - 123

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