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

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Basic information

Entry
Database: PDB / ID: 3kut
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


gamma-glutamyltransferase / glutathione gamma-glutamate hydrolase / glutathione hydrolase activity / leukotriene C4 gamma-glutamyl transferase activity / glutathione catabolic process / glutathione biosynthetic process / regulation of long-term synaptic potentiation / translation repressor activity / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity ...gamma-glutamyltransferase / glutathione gamma-glutamate hydrolase / glutathione hydrolase activity / leukotriene C4 gamma-glutamyl transferase activity / glutathione catabolic process / glutathione biosynthetic process / regulation of long-term synaptic potentiation / translation repressor activity / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / memory / spermatogenesis / negative regulation of translation / translation / mRNA binding / metal ion binding / cytoplasm
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 / Poly-adenylate binding protein, unique domain / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase signature. / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase, large subunit, C-terminal 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 / Poly-adenylate binding protein, unique domain / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase signature. / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase, large subunit, C-terminal domain / Gamma-glutamyltranspeptidase, small subunit / Nucleophile aminohydrolases, N-terminal / Prokaryotic membrane lipoprotein lipid attachment site profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Glutathione hydrolase proenzyme / 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: 1.5 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 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)22,4716
Polymers22,4004
Non-polymers712
Water3,171176
1
A: Polyadenylate-binding protein 1
C: PAIP2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2353
Polymers11,2002
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-17 kcal/mol
Surface area6380 Å2
MethodPISA
2
B: Polyadenylate-binding protein 1
D: PAIP2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2353
Polymers11,2002
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-14 kcal/mol
Surface area5820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.309, 31.748, 48.454
Angle α, β, γ (deg.)100.29, 90.37, 99.05
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: 1777.951 Da / Num. of mol.: 2 / Fragment: PABPC1-binding region / Mutation: K116A / Source method: obtained synthetically / Details: chemically synthesized / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6FID7, UniProt: Q9BPZ3*PLUS
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 1.75 Å3/Da / Density % sol: 29.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 2.25M ammonium sulfate, 0.2M KBr, 0.1 M Bis-Tris, pH 6.0, 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: 1.5→50 Å / Num. all: 23114 / Num. obs: 22328 / % possible obs: 96.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.8
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1593 / % possible all: 93.2

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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: 1.5→47.62 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.525 / SU ML: 0.049 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.085 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20065 1188 5.1 %RANDOM
Rwork0.1675 ---
obs0.16917 22328 96.54 %-
all-23114 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.764 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20.38 Å20.22 Å2
2---0.16 Å2-0.18 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.5→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1451 0 2 176 1629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221543
X-RAY DIFFRACTIONr_angle_refined_deg1.1251.9982108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9775212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.53126.92365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73115279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.345154
X-RAY DIFFRACTIONr_chiral_restr0.0630.2247
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021166
X-RAY DIFFRACTIONr_nbd_refined0.2150.2739
X-RAY DIFFRACTIONr_nbtor_refined0.30.21077
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2111
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.298
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.229
X-RAY DIFFRACTIONr_mcbond_it0.811.51037
X-RAY DIFFRACTIONr_mcangle_it0.98521620
X-RAY DIFFRACTIONr_scbond_it2.033545
X-RAY DIFFRACTIONr_scangle_it3.1474.5477
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 96 -
Rwork0.204 1593 -
obs--93.26 %
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)
17.2344-1.05992.5792.911-0.94928.8011-0.0482-0.0784-0.19450.0863-0.081-0.11130.13760.21080.1292-0.02-0.02030.0115-0.06580.00990.039111.9102-8.0093-18.2419
20.9309-0.4597-0.46450.62240.53210.87270.030.01210.0253-0.037-0.0056-0.0507-0.00670.0169-0.02440.0155-0.0020.00440.0046-0.00240.0166.05133.1737-14.083
38.1598-4.91584.43993.8336-3.22034.03970.00810.08210.0654-0.0424-0.01780.0586-0.0514-0.03770.00970.0357-0.01820.00520.0106-0.00390.05522.468516.2654-14.5661
42.3971-1.96661.225110.41353.332912.90490.10650.0382-0.4538-0.29250.0160.33310.0825-0.8276-0.1225-0.0028-0.00250.0031-0.00750.0086-0.04691.6282-1.1252-33.7899
50.4205-0.11760.18911.1141-0.23991.4382-0.0102-0.0857-0.04190.10250.03680.04030.03-0.1216-0.02660.0118-0.00130.01070.0301-0.0012-0.00272.923711.945-40.3278
65.82115.47354.57098.944.87597.1980.0302-0.21440.0840.2472-0.0928-0.1117-0.4072-0.11680.06260.08820.03350.01060.0121-0.01930.00364.733726.9541-37.7708
73.3248-3.1320.885114.2403-0.46738.86420.22720.09060.2992-1.1153-0.0859-0.1633-0.30540.0612-0.14130.10610.02980.0348-0.04810.0021-0.05092.038411.7142-22.5843
85.00734.9713-5.74088.6959-3.39167.9981-0.063-0.1628-0.1880.61450.17120.1211-0.1114-0.4493-0.1081-0.02-0.0017-0.00830.00670.02540.0431-5.5632-2.3906-12.7801
90.9149-2.85380.04611.03113.24795.40320.1004-0.2444-0.03280.31040.00130.028-0.2359-0.0142-0.10160.0715-0.0280.0158-0.0083-0.0176-0.05765.756819.9655-31.9659
1013.4406-4.9918-3.148519.92897.28897.284-0.14090.4415-0.4604-0.5880.2181-0.31960.26620.2179-0.07720.0037-0.01620.010.01260.0159-0.002414.49096.9342-39.9196
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A543 - 556
2X-RAY DIFFRACTION2A557 - 597
3X-RAY DIFFRACTION3A598 - 626
4X-RAY DIFFRACTION4B545 - 556
5X-RAY DIFFRACTION5B557 - 603
6X-RAY DIFFRACTION6B604 - 623
7X-RAY DIFFRACTION7C110 - 116
8X-RAY DIFFRACTION8C117 - 125
9X-RAY DIFFRACTION9D109 - 117
10X-RAY DIFFRACTION10D118 - 123

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