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- PDB-3hi9: The x-ray crystal structure of the first RNA recognition motif (R... -

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Basic information

Entry
Database: PDB / ID: 3hi9
TitleThe x-ray crystal structure of the first RNA recognition motif (RRM1) of the AU-rich element (ARE) binding protein HuR at 2.0 angstrom resolution
ComponentsELAV-like protein 1
KeywordsTRANSCRIPTION / beta1-alpha1-beta2-beta3-alpha2-beta4 topology / Methylation / Phosphoprotein / RNA-binding
Function / homology
Function and homology information


HuR (ELAVL1) binds and stabilizes mRNA / negative regulation of miRNA-mediated gene silencing / post-transcriptional gene silencing / regulation of stem cell population maintenance / mRNA 3'-UTR AU-rich region binding / mRNA stabilization / lncRNA binding / miRNA binding / 3'-UTR-mediated mRNA stabilization / mRNA destabilization ...HuR (ELAVL1) binds and stabilizes mRNA / negative regulation of miRNA-mediated gene silencing / post-transcriptional gene silencing / regulation of stem cell population maintenance / mRNA 3'-UTR AU-rich region binding / mRNA stabilization / lncRNA binding / miRNA binding / 3'-UTR-mediated mRNA stabilization / mRNA destabilization / sarcoplasm / positive regulation of superoxide anion generation / mRNA 3'-UTR binding / positive regulation of translation / P-body / protein homooligomerization / cytoplasmic stress granule / protein import into nucleus / double-stranded RNA binding / cytoplasmic vesicle / postsynapse / ribonucleoprotein complex / mRNA binding / glutamatergic synapse / protein kinase binding / endoplasmic reticulum / protein homodimerization activity / RNA binding / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
HuR, RNA recognition motif 2 / Splicing factor ELAV/Hu / Paraneoplastic encephalomyelitis antigen / 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 ...HuR, RNA recognition motif 2 / Splicing factor ELAV/Hu / Paraneoplastic encephalomyelitis antigen / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsBenoit, R.M. / Kallen, J.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: The X-ray Crystal Structure of the First RNA Recognition Motif and Site-Directed Mutagenesis Suggest a Possible HuR Redox Sensing Mechanism.
Authors: Benoit, R.M. / Meisner, N.C. / Kallen, J. / Graff, P. / Hemmig, R. / Cebe, R. / Ostermeier, C. / Widmer, H. / Auer, M.
History
DepositionMay 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: 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 / 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: ELAV-like protein 1
B: ELAV-like protein 1
C: ELAV-like protein 1
D: ELAV-like protein 1


Theoretical massNumber of molelcules
Total (without water)37,0104
Polymers37,0104
Non-polymers00
Water3,549197
1
A: ELAV-like protein 1


Theoretical massNumber of molelcules
Total (without water)9,2521
Polymers9,2521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ELAV-like protein 1


Theoretical massNumber of molelcules
Total (without water)9,2521
Polymers9,2521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ELAV-like protein 1


Theoretical massNumber of molelcules
Total (without water)9,2521
Polymers9,2521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ELAV-like protein 1


Theoretical massNumber of molelcules
Total (without water)9,2521
Polymers9,2521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.804, 74.804, 147.361
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 9252.491 Da / Num. of mol.: 4 / Fragment: RRM1 domain: UNP residues 18-99
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELAVL1, HUR / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q15717
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 3.22 Å3/Da / Density % sol: 61.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2 M Di-ammonium citrate, 20% w/v PEG 3350, 5% Glycerol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00778 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 22, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00778 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 32767 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 33.895 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 7.9
Reflection shellResolution: 2→2.08 Å / Redundancy: 3 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 3.2 / Num. measured obs: 11167 / Num. unique all: 3709 / Num. unique obs: 3709 / % possible all: 99.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FXL

1fxl


Resolution: 2→29.76 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.237 / WRfactor Rwork: 0.2 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.847 / SU B: 3.764 / SU ML: 0.104 / SU R Cruickshank DPI: 0.147 / SU Rfree: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1639 5 %RANDOM
Rwork0.197 ---
obs0.199 32762 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 67.53 Å2 / Biso mean: 32.295 Å2 / Biso min: 16.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2→29.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2504 0 0 197 2701
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222539
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.9693430
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2765324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59123.529119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.22515470
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7981525
X-RAY DIFFRACTIONr_chiral_restr0.0950.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021887
X-RAY DIFFRACTIONr_mcbond_it0.9421.51574
X-RAY DIFFRACTIONr_mcangle_it1.81822536
X-RAY DIFFRACTIONr_scbond_it2.7693965
X-RAY DIFFRACTIONr_scangle_it4.8154.5887
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 118 -
Rwork0.291 2239 -
all-2357 -
obs--99.45 %

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