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- PDB-4egl: Crystal structure of two tandem RNA recognition motifs of Human a... -

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Basic information

Entry
Database: PDB / ID: 4egl
TitleCrystal structure of two tandem RNA recognition motifs of Human antigen R
ComponentsELAV-like protein 1
KeywordsRNA BINDING PROTEIN / RRM / RNA Binding / Cytoplasm and Nucleus
Function / homology
Function and homology information


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 / lncRNA binding / 3'-UTR-mediated mRNA stabilization / mRNA destabilization ...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 / lncRNA 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 / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWang, H. / Zeng, F. / Liu, H. / Teng, M. / Li, X.
CitationJournal: To be Published
Title: Crystal structure of two tandem RNA recognition motifs of Human antigen R
Authors: Wang, H. / Zeng, F. / Liu, H. / Teng, M. / Li, X.
History
DepositionMar 31, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_conn / 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_conn.pdbx_leaving_atom_flag / _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: ELAV-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2125
Polymers19,8391
Non-polymers3724
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.181, 132.724, 31.102
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 19839.420 Da / Num. of mol.: 1
Fragment: N-terminal RRM1 and RRM2 domain, UNP residues 18-186
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3

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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: 2.14 Å3/Da / Density % sol: 42.58 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.5M Lithium sulfate monohydrate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 0.99985 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 21, 2010
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99985 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 4179 / Num. obs: 4062 / % possible obs: 97.3 %
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 2.26 / Rsym value: 0.366 / % possible all: 92.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FXL

1fxl


Resolution: 2.9→39.33 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.854 / Occupancy max: 1 / Occupancy min: 0.22 / SU B: 52.296 / SU ML: 0.448 / Cross valid method: THROUGHOUT / ESU R Free: 0.486 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2944 186 4.6 %RANDOM
Rwork0.26315 ---
obs0.26458 3862 97.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.645 Å2
Baniso -1Baniso -2Baniso -3
1--6.55 Å20 Å20 Å2
2---4.55 Å20 Å2
3---11.1 Å2
Refinement stepCycle: LAST / Resolution: 2.9→39.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1176 0 20 0 1196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211209
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.251.9691635
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0765163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.82123.69646
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.9715165
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.828157
X-RAY DIFFRACTIONr_chiral_restr0.0780.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021911
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.3511.5814
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.65321275
X-RAY DIFFRACTIONr_scbond_it0.7743395
X-RAY DIFFRACTIONr_scangle_it1.3874.5360
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.896→2.971 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 12 -
Rwork0.322 247 -
obs--88.7 %
Refinement TLS params.Method: refined / Origin x: -4.8111 Å / Origin y: 15.3323 Å / Origin z: -2.3802 Å
111213212223313233
T0.2474 Å2-0.0424 Å20.0143 Å2-0.2886 Å20.0385 Å2--0.1296 Å2
L2.1312 °20.4044 °20.3163 °2-9.2277 °2-1.4865 °2--0.7021 °2
S-0.0893 Å °0.2178 Å °0.113 Å °-0.4114 Å °0.2808 Å °-0.1234 Å °0.0336 Å °-0.0856 Å °-0.1915 Å °

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