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- PDB-3b4d: Crystal Structure of Human PABPN1 RRM -

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Basic information

Entry
Database: PDB / ID: 3b4d
TitleCrystal Structure of Human PABPN1 RRM
ComponentsPolyadenylate-binding protein 2
KeywordsRNA BINDING PROTEIN / RRM fold / ALPHA-BETA Sandwich structure / RNA Binding Domain / RNA Recognition Motif / Acetylation / Alternative splicing / Coiled coil / Cytoplasm / Disease mutation / Methylation / mRNA processing / Nucleus / Polymorphism / RNA-binding / Triplet repeat expansion
Function / homology
Function and homology information


positive regulation of polynucleotide adenylyltransferase activity / Inhibition of Host mRNA Processing and RNA Silencing / Processing of Intronless Pre-mRNAs / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / nuclear inclusion body / poly(A) binding / mRNA 3'-end processing / RNA polymerase binding / RNA Polymerase II Transcription Termination / poly(A)+ mRNA export from nucleus ...positive regulation of polynucleotide adenylyltransferase activity / Inhibition of Host mRNA Processing and RNA Silencing / Processing of Intronless Pre-mRNAs / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / nuclear inclusion body / poly(A) binding / mRNA 3'-end processing / RNA polymerase binding / RNA Polymerase II Transcription Termination / poly(A)+ mRNA export from nucleus / Processing of Capped Intron-Containing Pre-mRNA / RNA processing / muscle contraction / mRNA processing / MAPK cascade / cellular response to lipopolysaccharide / nuclear speck / ribonucleoprotein complex / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
RRM (RNA recognition motif) domain / 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyadenylate-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.001 Å
AuthorsGe, H. / Tong, S. / Teng, M. / Niu, L.
CitationJournal: Proteins / Year: 2008
Title: Crystal structure and possible dimerization of the single RRM of human PABPN1
Authors: Ge, H. / Zhou, D. / Tong, S. / Gao, Y. / Teng, M. / Niu, L.
History
DepositionOct 24, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyadenylate-binding protein 2


Theoretical massNumber of molelcules
Total (without water)10,8611
Polymers10,8611
Non-polymers00
Water1,74797
1
A: Polyadenylate-binding protein 2

A: Polyadenylate-binding protein 2


Theoretical massNumber of molelcules
Total (without water)21,7222
Polymers21,7222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area1540 Å2
ΔGint-7.7 kcal/mol
Surface area8110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.346, 92.346, 92.346
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Polyadenylate-binding protein 2 / Poly(A)-binding protein 2 / Poly(A)-binding protein II / PABII / Polyadenylate-binding nuclear ...Poly(A)-binding protein 2 / Poly(A)-binding protein II / PABII / Polyadenylate-binding nuclear protein 1 / Nuclear poly(A)-binding protein 1


Mass: 10861.189 Da / Num. of mol.: 1 / Fragment: UNP residues 167-254
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PABPN1, PAB2, PABP2 / Plasmid: pET22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q86U42
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 3.02 Å3/Da / Density % sol: 59.29 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 4.2M sodium chloride, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.001→65.233 Å / Num. obs: 9002 / Redundancy: 12.7 % / Rmerge(I) obs: 0.056
Reflection shellResolution: 2.001→2.07 Å / Redundancy: 12.7 %

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
AUTOMARdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.001→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.789 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20732 425 4.7 %RANDOM
Rwork0.17409 ---
obs0.17568 8561 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.155 Å2
Refinement stepCycle: LAST / Resolution: 2.001→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms625 0 0 97 722
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022637
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3121.946856
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.212579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.35622.58131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62315108
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.896156
X-RAY DIFFRACTIONr_chiral_restr0.0950.292
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02487
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1890.2248
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2940.2435
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.262
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.250.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0511.5408
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7162629
X-RAY DIFFRACTIONr_scbond_it2.7753255
X-RAY DIFFRACTIONr_scangle_it4.34.5227
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.002→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 29 -
Rwork0.221 631 -
obs--100 %

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