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- PDB-6gd3: Structure of HuR RRM3 in complex with RNA (UAUUUA) -

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Basic information

Entry
Database: PDB / ID: 6gd3
TitleStructure of HuR RRM3 in complex with RNA (UAUUUA)
Components
  • ELAV-like protein 1
  • RNA (5'-R(P*UP*AP*UP*UP*UP*A)-3')
KeywordsRNA BINDING PROTEIN
Function / homology
Function and homology information


positive regulation of autophagosome size / lncRNA-mediated post-transcriptional gene silencing / negative regulation of miRNA-mediated gene silencing / HuR (ELAVL1) binds and stabilizes mRNA / regulation of stem cell population maintenance / mRNA 3'-UTR AU-rich region binding / mRNA stabilization / miRNA binding / 3'-UTR-mediated mRNA stabilization / lncRNA binding ...positive regulation of autophagosome size / lncRNA-mediated post-transcriptional gene silencing / negative regulation of miRNA-mediated gene silencing / HuR (ELAVL1) binds and stabilizes mRNA / regulation of stem cell population maintenance / mRNA 3'-UTR AU-rich region binding / mRNA stabilization / miRNA binding / 3'-UTR-mediated mRNA stabilization / lncRNA binding / mRNA destabilization / sarcoplasm / response to glucose / positive regulation of autophagy / positive regulation of superoxide anion generation / positive regulation of translation / mRNA 3'-UTR binding / P-body / protein homooligomerization / protein import into nucleus / cytoplasmic stress granule / double-stranded RNA binding / cytoplasmic vesicle / cell population proliferation / postsynapse / ribonucleoprotein complex / mRNA binding / protein kinase binding / glutamatergic synapse / endoplasmic reticulum / protein homodimerization activity / RNA binding / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
HuR, RNA recognition motif 2 / Splicing factor ELAV/Hu / Paraneoplastic encephalomyelitis antigen / 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
Similarity search - Domain/homology
RNA / ELAV-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsPabis, M. / Sattler, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB1035 Germany
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: HuR biological function involves RRM3-mediated dimerization and RNA binding by all three RRMs.
Authors: Pabis, M. / Popowicz, G.M. / Stehle, R. / Fernandez-Ramos, D. / Asami, S. / Warner, L. / Garcia-Maurino, S.M. / Schlundt, A. / Martinez-Chantar, M.L. / Diaz-Moreno, I. / Sattler, M.
History
DepositionApr 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ELAV-like protein 1
B: ELAV-like protein 1
C: ELAV-like protein 1
P: RNA (5'-R(P*UP*AP*UP*UP*UP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9655
Polymers30,9424
Non-polymers231
Water5,350297
1
A: ELAV-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7242
Polymers9,7011
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ELAV-like protein 1
C: ELAV-like protein 1
P: RNA (5'-R(P*UP*AP*UP*UP*UP*A)-3')


Theoretical massNumber of molelcules
Total (without water)21,2403
Polymers21,2403
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.740, 79.930, 54.870
Angle α, β, γ (deg.)90.00, 90.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ELAV-like protein 1 / Hu-antigen R / HuR


Mass: 9701.152 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELAVL1, HUR / Production host: Escherichia coli (E. coli) / References: UniProt: Q15717
#2: RNA chain RNA (5'-R(P*UP*AP*UP*UP*UP*A)-3')


Mass: 1838.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.39 Å3/Da / Density % sol: 48.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium acetate, 0.01 M calcium chloride, 0.05 M sodium cacodylate pH 6.5 and 10 % (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.007 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007 Å / Relative weight: 1
ReflectionResolution: 1.35→6.04 Å / Num. obs: 62913 / % possible obs: 98.7 % / Redundancy: 3.36 % / Rrim(I) all: 0.072 / Net I/σ(I): 10.84
Reflection shellResolution: 1.35→1.39 Å / Mean I/σ(I) obs: 2.18 / Num. unique obs: 4560 / Rrim(I) all: 0.67 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GD1

6gd1


Resolution: 1.35→6.04 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.932 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.053 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18859 3025 4.9 %RANDOM
Rwork0.16454 ---
obs0.16573 59206 97.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.115 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.35→6.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1946 124 1 297 2368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0192198
X-RAY DIFFRACTIONr_bond_other_d0.0020.021917
X-RAY DIFFRACTIONr_angle_refined_deg2.331.8773008
X-RAY DIFFRACTIONr_angle_other_deg1.1634465
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.255271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.56324.84899
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56515346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.315156
X-RAY DIFFRACTIONr_chiral_restr0.1390.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022424
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02492
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3061.9631021
X-RAY DIFFRACTIONr_mcbond_other2.2961.9611020
X-RAY DIFFRACTIONr_mcangle_it3.2932.9371277
X-RAY DIFFRACTIONr_mcangle_other3.2922.941278
X-RAY DIFFRACTIONr_scbond_it3.62.4971177
X-RAY DIFFRACTIONr_scbond_other3.5992.4981178
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1693.5951719
X-RAY DIFFRACTIONr_long_range_B_refined6.70224.9172555
X-RAY DIFFRACTIONr_long_range_B_other6.57224.2632491
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.383 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 228 -
Rwork0.279 4086 -
obs--97.47 %

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