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- PDB-4ed5: Crystal structure of the two N-terminal RRM domains of HuR comple... -

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Basic information

Entry
Database: PDB / ID: 4ed5
TitleCrystal structure of the two N-terminal RRM domains of HuR complexed with RNA
Components
  • 5'-R(*A*UP*UP*UP*UP*UP*AP*UP*UP*UP*U)-3'
  • ELAV-like protein 1
KeywordsRNA BINDING PROTEIN/RNA / RRM / RNA binding / Nucleus / RNA BINDING PROTEIN-RNA complex
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
1-METHOXY-2-(2-METHOXYETHOXY)ETHANE / RNA / RNA (> 10) / ELAV-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, H. / Zeng, F. / Liu, Q. / Niu, L. / Teng, M. / Li, X.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: The structure of the ARE-binding domains of Hu antigen R (HuR) undergoes conformational changes during RNA binding.
Authors: Wang, H. / Zeng, F. / Liu, Q. / Liu, H. / Liu, Z. / Niu, L. / Teng, M. / Li, X.
History
DepositionMar 27, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)47,26614
Polymers46,3634
Non-polymers90310
Water4,540252
1
A: ELAV-like protein 1
D: 5'-R(*A*UP*UP*UP*UP*UP*AP*UP*UP*UP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,08412
Polymers23,1812
Non-polymers90310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-12 kcal/mol
Surface area9670 Å2
MethodPISA
2
B: ELAV-like protein 1
C: 5'-R(*A*UP*UP*UP*UP*UP*AP*UP*UP*UP*U)-3'


Theoretical massNumber of molelcules
Total (without water)23,1812
Polymers23,1812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-25 kcal/mol
Surface area9400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.770, 62.750, 53.290
Angle α, β, γ (deg.)90.00, 111.89, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / RNA chain , 2 types, 4 molecules ABCD

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


Mass: 19812.375 Da / Num. of mol.: 2 / Fragment: RRM1/RRM2 domains, 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: RNA chain 5'-R(*A*UP*UP*UP*UP*UP*AP*UP*UP*UP*U)-3'


Mass: 3368.946 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Non-polymers , 4 types, 262 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-M2M / 1-METHOXY-2-(2-METHOXYETHOXY)ETHANE / Diglyme


Mass: 134.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.29 Å3/Da / Density % sol: 46.25 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18% PEG 5000, 0.1M HEPES, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 0.9793 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 19, 2012
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→35.08 Å / Num. all: 28267 / Num. obs: 27777 / % possible obs: 98.3 %
Reflection shellResolution: 2→2.11 Å / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 4.8 / Rsym value: 0.226 / % possible all: 98.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→35.08 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.884 / SU B: 10.318 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25651 1393 5 %RANDOM
Rwork0.20873 ---
obs0.21115 26384 98.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.901 Å2
Baniso -1Baniso -2Baniso -3
1--1.15 Å20 Å2-0.52 Å2
2--2.11 Å20 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 2→35.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2526 349 59 252 3186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223035
X-RAY DIFFRACTIONr_angle_refined_deg1.2172.1214151
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3855343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.96822.762105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.10915435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6751524
X-RAY DIFFRACTIONr_chiral_restr0.0740.2486
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212106
X-RAY DIFFRACTIONr_mcbond_it0.4161.51689
X-RAY DIFFRACTIONr_mcangle_it0.822705
X-RAY DIFFRACTIONr_scbond_it1.50731346
X-RAY DIFFRACTIONr_scangle_it2.5174.51446
LS refinement shellResolution: 2.004→2.056 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 89 -
Rwork0.231 1942 -
obs--97.74 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5405-0.1034-0.3070.1219-0.0271.55110.01420.0176-0.00370.03120.0128-0.00140.01030.0527-0.0270.1441-0.0011-0.01290.0994-0.00140.1499-14.8556-1.1936-4.5015
22.0883-0.02830.32440.17430.09544.27090.03580.28690.03890.0214-0.0231-0.0103-0.0301-0.3691-0.01270.10630.03560.01250.16950.03580.1495-44.45420.4721-20.9817
314.6682-1.9251-1.46531.94393.75147.6362-0.17410.379-0.5320.6175-0.28680.25361.2644-0.58080.46080.2357-0.06250.05880.0902-0.05760.0454-42.8444-6.3734-21.9508
412.8439-0.1202-9.15441.3730.9667.0924-0.6021-0.2398-0.8435-0.16070.092-0.18480.34880.1920.510.15920.01450.02890.06430.03050.1059-16.3048-8.0399-4.4849
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 185
2X-RAY DIFFRACTION2B18 - 186
3X-RAY DIFFRACTION3C2 - 11
4X-RAY DIFFRACTION4D2 - 11

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