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- PDB-5im0: Crystal structure of the RNA recognition motif of mRNA decay regu... -

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Basic information

Entry
Database: PDB / ID: 5im0
TitleCrystal structure of the RNA recognition motif of mRNA decay regulator AUF1
Components(Heterogeneous nuclear ribonucleoprotein D0) x 2
KeywordsRNA BINDING PROTEIN / mRNA decay / hnRNP D0 / AUF1 / RNA recognition motif / crystallization
Function / homology
Function and homology information


hepatocyte dedifferentiation / cellular response to putrescine / circadian regulation of translation / response to rapamycin / mCRD-mediated mRNA stability complex / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / response to sodium phosphate / 3'-UTR-mediated mRNA destabilization / positive regulation of telomere capping ...hepatocyte dedifferentiation / cellular response to putrescine / circadian regulation of translation / response to rapamycin / mCRD-mediated mRNA stability complex / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / response to sodium phosphate / 3'-UTR-mediated mRNA destabilization / positive regulation of telomere capping / mRNA 3'-UTR AU-rich region binding / positive regulation of cytoplasmic translation / RNA catabolic process / telomeric DNA binding / minor groove of adenine-thymine-rich DNA binding / Processing of Capped Intron-Containing Pre-mRNA / response to electrical stimulus / RNA processing / positive regulation of telomere maintenance via telomerase / cellular response to nitric oxide / mRNA Splicing - Major Pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / cerebellum development / positive regulation of translation / cellular response to amino acid stimulus / cellular response to estradiol stimulus / liver development / regulation of circadian rhythm / histone deacetylase binding / response to calcium ion / regulation of gene expression / postsynaptic density / ribonucleoprotein complex / chromatin binding / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
CARG-binding factor, N-terminal / CBFNT (NUC161) domain / 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 ...CARG-binding factor, N-terminal / CBFNT (NUC161) domain / 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
Heterogeneous nuclear ribonucleoprotein D0
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsChoi, Y.J. / Chang, J.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation of Korea (NRF)2013R1A1A1061391 Korea, Republic Of
CitationJournal: Biomed Res Int / Year: 2016
Title: Crystal Structure of the N-Terminal RNA Recognition Motif of mRNA Decay Regulator AUF1.
Authors: Choi, Y.J. / Yoon, J.H. / Chang, J.H.
History
DepositionMar 5, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heterogeneous nuclear ribonucleoprotein D0
B: Heterogeneous nuclear ribonucleoprotein D0


Theoretical massNumber of molelcules
Total (without water)19,6562
Polymers19,6562
Non-polymers00
Water4,738263
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint1 kcal/mol
Surface area9970 Å2
Unit cell
Length a, b, c (Å)39.068, 39.411, 93.252
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Heterogeneous nuclear ribonucleoprotein D0 / hnRNP D0 / AU-rich element RNA-binding protein 1


Mass: 10176.004 Da / Num. of mol.: 1 / Fragment: UNP residues 71-156
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNRNPD, AUF1, HNRPD / Production host: Enterobacteria phage L1 (virus) / References: UniProt: Q14103
#2: Protein Heterogeneous nuclear ribonucleoprotein D0 / mRNA decay regulator / hnRNP D0 / AU-rich element RNA-binding protein 1


Mass: 9480.401 Da / Num. of mol.: 1 / Fragment: UNP residues 77-156
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNRNPD, AUF1, HNRPD / Production host: Enterobacteria phage L1 (virus) / References: UniProt: Q14103
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsThe sequence database of chain A and B is Isoform 2 of Q14103.

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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: 1.83 Å3/Da / Density % sol: 32.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 3350, HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 16559 / % possible obs: 99.9 % / Redundancy: 7.1 % / Net I/σ(I): 42.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→26.594 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.04
RfactorNum. reflection% reflection
Rfree0.204 1555 10.11 %
Rwork0.1698 --
obs0.1733 15364 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→26.594 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1280 0 0 263 1543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061302
X-RAY DIFFRACTIONf_angle_d0.9871730
X-RAY DIFFRACTIONf_dihedral_angle_d11.945504
X-RAY DIFFRACTIONf_chiral_restr0.041183
X-RAY DIFFRACTIONf_plane_restr0.005217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6952-1.72170.23391390.20391196X-RAY DIFFRACTION95
1.7217-1.74990.25181410.21361261X-RAY DIFFRACTION100
1.7499-1.78010.27711420.21051269X-RAY DIFFRACTION100
1.7801-1.81250.25511280.19181232X-RAY DIFFRACTION99
1.8125-1.84730.2461430.18841268X-RAY DIFFRACTION100
1.8473-1.8850.21471380.18731248X-RAY DIFFRACTION100
1.885-1.9260.21561370.17551262X-RAY DIFFRACTION100
1.926-1.97080.26871470.17651295X-RAY DIFFRACTION100
1.9708-2.02010.23591400.17241219X-RAY DIFFRACTION100
2.0201-2.07470.21151500.17121285X-RAY DIFFRACTION100
2.0747-2.13570.20271420.17151254X-RAY DIFFRACTION100
2.1357-2.20460.2381400.18321275X-RAY DIFFRACTION100
2.2046-2.28330.23311390.16961242X-RAY DIFFRACTION100
2.2833-2.37470.18841400.16521260X-RAY DIFFRACTION100
2.3747-2.48270.23781470.18151261X-RAY DIFFRACTION100
2.4827-2.61350.21681270.18511277X-RAY DIFFRACTION100
2.6135-2.77710.2161510.17771269X-RAY DIFFRACTION100
2.7771-2.99120.23031440.17491246X-RAY DIFFRACTION100
2.9912-3.29180.1781500.16041272X-RAY DIFFRACTION100
3.2918-3.76690.16441340.14081235X-RAY DIFFRACTION100
3.7669-4.74160.15511480.1361261X-RAY DIFFRACTION100
4.7416-26.59680.17471430.18471251X-RAY DIFFRACTION99

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