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- PDB-3pkn: Crystal structure of MLLE domain of poly(A) binding protein in co... -

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Basic information

Entry
Database: PDB / ID: 3pkn
TitleCrystal structure of MLLE domain of poly(A) binding protein in complex with PAM2 motif of La-related protein 4 (LARP4)
Components
  • La-related protein 4
  • Polyadenylate-binding protein 1
KeywordsPROTEIN BINDING / All helical domain / La-related protein 4
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 / regulation of cell morphogenesis / poly(U) RNA binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Translation initiation complex formation / post-transcriptional regulation of gene expression / : / 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) / cytoskeleton organization / catalytic step 2 spliceosome / AUF1 (hnRNP D0) binds and destabilizes mRNA / mRNA 3'-UTR binding / positive regulation of translation / Regulation of expression of SLITs and ROBOs / mRNA splicing, via spliceosome / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / lamellipodium / ribonucleoprotein complex / translation / focal adhesion / mRNA binding / RNA binding / extracellular exosome / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
LARP4, RNA recognition motif / 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 / La domain containing protein / La domain / Domain in the RNA-binding Lupus La protein; unknown function / La-type HTH domain ...LARP4, RNA recognition motif / 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 / La domain containing protein / La domain / Domain in the RNA-binding Lupus La protein; unknown function / La-type HTH domain / La-type HTH domain profile. / 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 / Winged helix DNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
IODIDE ION / Polyadenylate-binding protein 1 / La-related protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsXie, J. / Kozlov, G. / Gehring, K.
CitationJournal: Mol.Cell.Biol. / Year: 2011
Title: La-Related Protein 4 Binds Poly(A), Interacts with the Poly(A)-Binding Protein MLLE Domain via a Variant PAM2w Motif, and Can Promote mRNA Stability.
Authors: Yang, R. / Gaidamakov, S.A. / Xie, J. / Lee, J. / Martino, L. / Kozlov, G. / Crawford, A.K. / Russo, A.N. / Conte, M.R. / Gehring, K. / Maraia, R.J.
History
DepositionNov 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: 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: La-related protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1874
Polymers10,9642
Non-polymers2232
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-20 kcal/mol
Surface area5510 Å2
MethodPISA
2
A: Polyadenylate-binding protein 1
B: La-related protein 4
hetero molecules

A: Polyadenylate-binding protein 1
B: La-related protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3738
Polymers21,9274
Non-polymers4464
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4340 Å2
ΔGint-54 kcal/mol
Surface area9880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.910, 31.384, 52.647
Angle α, β, γ (deg.)90.00, 104.95, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 9421.909 Da / Num. of mol.: 1 / Fragment: MLLE domain (UNP residues 544-626)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PABPC1, PAB1, PABP1, PABPC2 / Plasmid: pGEX 6p1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P11940
#2: Protein/peptide La-related protein 4 / La ribonucleoprotein domain family member 4


Mass: 1541.725 Da / Num. of mol.: 1 / Fragment: PABP-binding region (UNP residues 13-26) / Source method: obtained synthetically / Details: chemically synthesized peptide / References: UniProt: Q71RC2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 1.78 Å3/Da / Density % sol: 30.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.25 M potassium iodide, 1.9 M ammonium sulfate, 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: A1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 20, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 6954 / Num. obs: 6871 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.8→1.83 Å / % possible all: 89

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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: 3KUS

3kus


Resolution: 1.8→50.83 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.928 / SU B: 7.329 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26933 335 4.6 %RANDOM
Rwork0.22479 ---
all0.227 6954 --
obs0.22683 6871 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.608 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å22.44 Å2
2---1.42 Å20 Å2
3---1.16 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms691 0 6 42 739
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022711
X-RAY DIFFRACTIONr_angle_refined_deg1.1131.999964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.252590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65326.78628
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.70515133
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.305152
X-RAY DIFFRACTIONr_chiral_restr0.0740.2114
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02509
X-RAY DIFFRACTIONr_nbd_refined0.1970.2311
X-RAY DIFFRACTIONr_nbtor_refined0.290.2491
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1020.231
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.26
X-RAY DIFFRACTIONr_mcbond_it0.5861.5461
X-RAY DIFFRACTIONr_mcangle_it0.8892732
X-RAY DIFFRACTIONr_scbond_it1.6773264
X-RAY DIFFRACTIONr_scangle_it2.6414.5231
LS refinement shellResolution: 1.796→1.842 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.491 11 -
Rwork0.251 405 -
obs--80 %
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)
113.25412.1239.54962.65262.347119.6879-0.0725-0.0473-0.2074-0.0210.14610.22380.1886-0.376-0.0737-0.0010.01560.00070.0095-0.01810.04391.6789-9.624710.9066
29.2918-2.0348-5.99095.34226.188723.0041-0.19520.1366-0.3670.04840.07870.11220.61640.02780.11640.0228-0.0078-0.01260.0086-0.00160.0829-4.3795-4.706511.1324
31.79660.3632-2.1051.24380.93485.6609-0.0317-0.1221-0.0738-0.1713-0.02680.0278-0.36750.14220.05850.0427-0.0033-0.0240.05360.00070.0238-9.65767.159317.2392
47.0804-2.1263-0.62345.2398-3.06337.22-0.09080.02090.3735-0.20710.281-0.3357-0.35620.2806-0.19010.0231-0.07740.03830.0356-0.06530.06662.64832.750812.2846
511.4768-10.41818.852613.4215-10.546910.31960.01520.29770.1423-0.2775-0.00410.04590.08490.0246-0.01120.0944-0.07340.01410.0614-0.01130.0328-4.595414.996414.9648
614.40098.9471-6.053623.9897-3.8443.5008-0.30540.3083-0.1686-1.4495-0.033-0.4436-0.3094-0.17640.33830.12130.0316-0.06540.027-0.0372-0.0594-8.740210.61125.8433
77.98414.4543-5.301311.0322-11.009516.5420.2484-0.028-0.2657-0.050.11260.68720.6707-0.8103-0.3610.02-0.0425-0.02990.0409-0.05990.0803-13.331-1.412912.7247
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A544 - 556
2X-RAY DIFFRACTION2A557 - 565
3X-RAY DIFFRACTION3A566 - 585
4X-RAY DIFFRACTION4A586 - 597
5X-RAY DIFFRACTION5A598 - 622
6X-RAY DIFFRACTION6B15 - 21
7X-RAY DIFFRACTION7B22 - 25

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