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- PDB-6gd2: Structure of HuR RRM3 in complex with RNA -

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Basic information

Entry
Database: PDB / ID: 6gd2
TitleStructure of HuR RRM3 in complex with RNA
Components
  • ELAV-like protein 1
  • RNA (5'-R(P*UP*UP*UP*AP*UP*UP*U)-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 / RNA (> 10) / ELAV-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
D: RNA (5'-R(P*UP*UP*UP*AP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)33,7204
Polymers33,7204
Non-polymers00
Water4,143230
1
A: ELAV-like protein 1
B: ELAV-like protein 1
D: RNA (5'-R(P*UP*UP*UP*AP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)24,0193
Polymers24,0193
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-18 kcal/mol
Surface area10260 Å2
MethodPISA
2
C: ELAV-like protein 1


Theoretical massNumber of molelcules
Total (without water)9,7011
Polymers9,7011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.120, 80.480, 54.440
Angle α, β, γ (deg.)90.00, 90.69, 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*UP*UP*AP*UP*UP*U)-3')


Mass: 4616.649 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.22 Å3/Da / Density % sol: 44.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.5, 10% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Aug 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.9→8.5 Å / Num. obs: 23114 / % possible obs: 99.6 % / Redundancy: 4.06 % / Rrim(I) all: 0.116 / Net I/σ(I): 9.09
Reflection shellResolution: 1.9→1.95 Å / Mean I/σ(I) obs: 2.38 / Rrim(I) all: 0.6 / % possible all: 100

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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: 1.9→8.5 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.52 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24513 1159 5.1 %RANDOM
Rwork0.1916 ---
obs0.19428 21702 98.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.636 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0.01 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.9→8.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1900 142 0 230 2272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192167
X-RAY DIFFRACTIONr_bond_other_d0.0020.021878
X-RAY DIFFRACTIONr_angle_refined_deg1.8231.8742965
X-RAY DIFFRACTIONr_angle_other_deg1.14534369
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1285261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.4962598
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.33915335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.887156
X-RAY DIFFRACTIONr_chiral_restr0.1390.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022370
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02479
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_it2.312.467996
X-RAY DIFFRACTIONr_mcbond_other2.3032.465995
X-RAY DIFFRACTIONr_mcangle_it3.4333.6741246
X-RAY DIFFRACTIONr_mcangle_other3.4333.6761247
X-RAY DIFFRACTIONr_scbond_it3.1643.0311171
X-RAY DIFFRACTIONr_scbond_other3.153.0281170
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8524.4081710
X-RAY DIFFRACTIONr_long_range_B_refined6.92730.2932455
X-RAY DIFFRACTIONr_long_range_B_other6.92130.2892454
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.947 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 87 -
Rwork0.276 1528 -
obs--99.81 %

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