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

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Basic information

Entry
Database: PDB / ID: 3kur
TitleCrystal structure of the MLLE domain of poly(A)-binding protein
ComponentsPolyadenylate-binding protein 1
KeywordsRNA BINDING PROTEIN / all-helical domain / 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 / M-decay: degradation of maternal mRNAs by maternally stored factors / poly(A) binding ...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 / M-decay: degradation of maternal mRNAs by maternally stored factors / poly(A) binding / regulatory ncRNA-mediated gene silencing / mRNA stabilization / poly(U) RNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nuclear-transcribed mRNA catabolic process, nonsense-mediated 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) / catalytic step 2 spliceosome / AUF1 (hnRNP D0) binds and destabilizes mRNA / mRNA 3'-UTR binding / Regulation of expression of SLITs and ROBOs / mRNA splicing, via spliceosome / cytoplasmic stress granule / cytoplasmic ribonucleoprotein granule / lamellipodium / ribonucleoprotein complex / focal adhesion / mRNA binding / RNA binding / extracellular exosome / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
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 ...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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.2Sep 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

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Assembly

Deposited unit
A: Polyadenylate-binding protein 1
B: Polyadenylate-binding protein 1
C: Polyadenylate-binding protein 1
D: Polyadenylate-binding protein 1
E: Polyadenylate-binding protein 1
F: Polyadenylate-binding protein 1
G: Polyadenylate-binding protein 1
H: Polyadenylate-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,12813
Polymers67,9518
Non-polymers1775
Water1,928107
1
A: Polyadenylate-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5292
Polymers8,4941
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polyadenylate-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5292
Polymers8,4941
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Polyadenylate-binding protein 1


Theoretical massNumber of molelcules
Total (without water)8,4941
Polymers8,4941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Polyadenylate-binding protein 1


Theoretical massNumber of molelcules
Total (without water)8,4941
Polymers8,4941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Polyadenylate-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5292
Polymers8,4941
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Polyadenylate-binding protein 1


Theoretical massNumber of molelcules
Total (without water)8,4941
Polymers8,4941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Polyadenylate-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5292
Polymers8,4941
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Polyadenylate-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5292
Polymers8,4941
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.977, 146.977, 83.055
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 8493.868 Da / Num. of mol.: 8 / 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: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 3.3 Å3/Da / Density % sol: 62.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 1.3M ammonium sulfate, 0.5M lithium sulfate, 5% glycerol, pH 6.3, 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: 2.5→103.7 Å / Num. all: 30434 / Num. obs: 29430 / % possible obs: 96.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.3 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 23.1
Reflection shellResolution: 2.5→2.57 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1602 / % possible all: 73.5

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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: 2.5→50 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.91 / SU B: 17.618 / SU ML: 0.191 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.348 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27224 1558 5 %RANDOM
Rwork0.21566 ---
obs0.21841 29430 96.71 %-
all-30434 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.041 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å20 Å20 Å2
2--1.31 Å20 Å2
3----2.61 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 5 107 4496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224453
X-RAY DIFFRACTIONr_angle_refined_deg1.6762.0226020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3855572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.35226.522161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.71915857
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0151516
X-RAY DIFFRACTIONr_chiral_restr0.1170.2731
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023160
X-RAY DIFFRACTIONr_nbd_refined0.2530.22293
X-RAY DIFFRACTIONr_nbtor_refined0.3150.23064
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2168
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.23
X-RAY DIFFRACTIONr_mcbond_it0.771.52991
X-RAY DIFFRACTIONr_mcangle_it1.25124681
X-RAY DIFFRACTIONr_scbond_it2.23931570
X-RAY DIFFRACTIONr_scangle_it3.8044.51338
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.429 105 -
Rwork0.316 1602 -
obs--73.48 %
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)
123.6218-4.2954-11.54775.027-2.981817.96080.6052-0.82020.2188-0.1828-0.2967-0.7002-1.05261.945-0.3085-0.0924-0.2115-0.07310.33870.05190.05019.8881-37.6695-10.8089
27.73490.2059-7.06994.7266-4.287427.10470.6134-0.14890.78090.1253-0.1553-0.1182-1.54330.2708-0.45810.0669-0.09260.02750.119-0.03640.08383.3145-34.6365-15.8636
34.20781.0454-0.43923.97210.33511.99860.07870.56950.0762-0.188-0.1387-0.16340.17820.1750.060.00620.02170.05140.1847-0.00080.05591.8328-41.7545-27.7615
416.24020.296410.936911.11354.481522.9874-0.413-1.4597-0.2632-0.35910.0624-0.0139-2.0164-2.45430.35050.06680.28150.01130.1170.021-0.0014-24.7199-34.7711-25.7421
52.7297-0.10810.11344.4019-1.8856.6941-0.0864-0.0137-0.0122-0.04960.0744-0.1959-0.0214-0.35730.0120.011-0.01370.00320.0995-0.03970.1275-16.1744-44.7043-22.8883
613.86954.40951.59983.32532.26425.74220.47790.3682-0.6667-0.2166-0.0811-0.10070.48550.0803-0.39680.0866-0.00620.00270.0117-0.03840.1763-12.0114-52.0337-28.4567
77.37640.84221.99586.43894.29573.6253-0.286-1.0762-0.83080.22720.4140.02090.73880.0086-0.12790.0487-0.03190.05720.12720.17390.096340.6695-39.06276.3273
836.4236-11.3074-11.53284.31232.35055.5372-0.4269-0.3504-1.4115-0.35770.08380.46490.25930.43870.34310.0842-0.1019-0.03040.12330.05440.059931.5681-35.27099.1105
93.3523-0.8481-1.0585.1051-0.10333.91810.1625-0.46630.19640.10970.07110.1373-0.39510.0289-0.23360.1069-0.11160.02170.13090.02640.010431.138-24.405312.0934
102.7009-1.2127-1.50823.40955.54619.11663.34660.7657-0.19650.1848-2.40570.02661.1281-0.0325-0.94090.3098-0.2722-0.29010.56540.6420.683617.0787-20.5708-12.5273
1140.047516.3568-5.235413.3704-5.750712.54370.31041.7224-0.4007-2.18270.259311.4259-1.0915-0.56970.4051-0.1371-0.37820.00670.1612-0.054925.08-20.3394-10.9802
120.96930.4031-0.29446.2576-2.99576.8130.2585-0.00420.3482-0.02060.09980.2897-0.2191-0.4972-0.35830.1698-0.06410.03840.05450.07930.028730.956-13.8364-1.883
1319.05227.0336-11.79995.3629-3.574713.6130.2840.9220.11980.1526-0.17950.2797-0.6812-1.4389-0.1045-0.01950.1168-0.0950.1713-0.09830.0609-14.3654-39.1258-13.0281
142.4583-0.2793-0.49213.44752.30435.7299-0.0393-0.35830.1869-0.04320.0293-0.0303-0.06830.02980.0099-0.01440.02440.00790.2115-0.03080.0865-6.1276-38.2048-0.9498
159.7392-0.2806-0.29374.35751.41074.24440.3009-0.753-0.52810.5475-0.0160.08310.5983-0.1302-0.28490.10280.04050.07850.1968-0.00450.0321-6.6477-45.31956.2054
163.64285.5676-0.49329.3159-0.56057.5999-0.3091.09690.98890.1498-0.5050.5687-0.6643-0.25070.8140.0266-0.076-0.08210.1459-0.1240.143818.5587-32.50230.4614
176.2684-0.9863-0.35546.4432.56274.2287-0.0917-0.34430.29980.17880.095-0.02610.09910.0201-0.0033-0.03990.0331-0.03620.1327-0.05380.123712.2929-44.6765-1.2409
1828.9929-3.57985.20941.4516-2.51544.40780.2341-1.034-0.42410.2960.2749-0.23830.41510.0836-0.5090.10470.2166-0.05180.1555-0.08530.0339.6888-50.65644.5087
195.4694-1.0725-2.47523.89625.04756.7670.20970.2746-0.1091-1.3752-0.21920.2568-0.6079-0.71280.00950.3126-0.0742-0.11190.00020.0205-0.001833.7307-29.3549-7.7635
201.9476-1.0655-1.56413.67077.51739.60140.17960.5041-0.1202-0.7719-0.12090.4058-0.51340.0521-0.05880.2491-0.1678-0.05050.13190.0656-0.013841.4971-39.1672-14.4025
215.5103-2.70070.14795.41150.28786.17190.12220.08860.1121-0.68930.2261-0.287-0.27460.7085-0.34830.1792-0.22590.03550.1991-0.0527-0.047649.8187-36.6134-10.9651
2229.42811.92831.845813.34033.75193.52460.3804-0.6354-1.34041.0316-0.8533-1.44651.12560.53040.47290.2486-0.03-0.0378-0.06240.22820.017248.4407-55.457711.1267
235.24360.45721.49865.83680.6754.675-0.17160.2807-0.2270.1330.38310.0990.15240.2249-0.21150.0425-0.0511-0.00620.1909-0.0483-0.016252.5198-42.53916.5015
249.8065-4.67175.62963.0522-4.853312.9455-0.41320.70040.2241-0.0570.1947-0.7917-0.2360.93560.21860.0022-0.15040.00750.3545-0.18130.016760.2862-39.47191.3498
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A544 - 555
2X-RAY DIFFRACTION2A556 - 566
3X-RAY DIFFRACTION3A567 - 616
4X-RAY DIFFRACTION4B544 - 556
5X-RAY DIFFRACTION5B557 - 595
6X-RAY DIFFRACTION6B596 - 616
7X-RAY DIFFRACTION7C544 - 559
8X-RAY DIFFRACTION8C560 - 567
9X-RAY DIFFRACTION9C568 - 615
10X-RAY DIFFRACTION10D545 - 556
11X-RAY DIFFRACTION11D557 - 566
12X-RAY DIFFRACTION12D567 - 615
13X-RAY DIFFRACTION13E544 - 555
14X-RAY DIFFRACTION14E556 - 595
15X-RAY DIFFRACTION15E596 - 615
16X-RAY DIFFRACTION16F544 - 560
17X-RAY DIFFRACTION17F561 - 595
18X-RAY DIFFRACTION18F596 - 615
19X-RAY DIFFRACTION19G544 - 560
20X-RAY DIFFRACTION20G561 - 573
21X-RAY DIFFRACTION21G574 - 615
22X-RAY DIFFRACTION22H544 - 556
23X-RAY DIFFRACTION23H557 - 595
24X-RAY DIFFRACTION24H596 - 616

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