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- PDB-6gc5: Molecular basis for AU-rich element recognition and dimerization ... -

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Basic information

Entry
Database: PDB / ID: 6gc5
TitleMolecular basis for AU-rich element recognition and dimerization by the HuR C-terminal RRM
Components
  • AU-rich RNA
  • ELAV-like protein 1
KeywordsRNA BINDING PROTEIN / Elav / HuR / RRM3 / dimer / RRM
Function / homology
Function and homology information


positive regulation of autophagosome size / lncRNA-mediated post-transcriptional gene silencing / negative regulation of miRNA-mediated gene silencing / regulation of stem cell population maintenance / HuR (ELAVL1) binds and stabilizes mRNA / 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 / regulation of stem cell population maintenance / HuR (ELAVL1) binds and stabilizes mRNA / 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 superoxide anion generation / positive regulation of autophagy / positive regulation of translation / mRNA 3'-UTR binding / P-body / protein homooligomerization / cytoplasmic stress granule / protein import into nucleus / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRipin, N. / Allain, F.H.
Funding support Switzerland, Czech Republic, 2items
OrganizationGrant numberCountry
European Union289007 Switzerland
Czech Science FoundationP305/12/G034 Czech Republic
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Molecular basis for AU-rich element recognition and dimerization by the HuR C-terminal RRM.
Authors: Ripin, N. / Boudet, J. / Duszczyk, M.M. / Hinniger, A. / Faller, M. / Krepl, M. / Gadi, A. / Schneider, R.J. / Sponer, J. / Meisner-Kober, N.C. / Allain, F.H.
History
DepositionApr 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 27, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: ELAV-like protein 1
E: AU-rich RNA
F: AU-rich RNA
G: AU-rich RNA
H: AU-rich RNA


Theoretical massNumber of molelcules
Total (without water)53,2058
Polymers53,2058
Non-polymers00
Water3,441191
1
A: ELAV-like protein 1
B: ELAV-like protein 1
E: AU-rich RNA
F: AU-rich RNA


Theoretical massNumber of molelcules
Total (without water)26,6034
Polymers26,6034
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: ELAV-like protein 1
D: ELAV-like protein 1
G: AU-rich RNA
H: AU-rich RNA


Theoretical massNumber of molelcules
Total (without water)26,6034
Polymers26,6034
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: ELAV-like protein 1
E: AU-rich RNA


Theoretical massNumber of molelcules
Total (without water)13,3012
Polymers13,3012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-6 kcal/mol
Surface area4970 Å2
MethodPISA
4
B: ELAV-like protein 1
F: AU-rich RNA


Theoretical massNumber of molelcules
Total (without water)13,3012
Polymers13,3012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-7 kcal/mol
Surface area4490 Å2
MethodPISA
5
C: ELAV-like protein 1
G: AU-rich RNA


Theoretical massNumber of molelcules
Total (without water)13,3012
Polymers13,3012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-5 kcal/mol
Surface area4920 Å2
MethodPISA
6
D: ELAV-like protein 1
H: AU-rich RNA


Theoretical massNumber of molelcules
Total (without water)13,3012
Polymers13,3012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-7 kcal/mol
Surface area4660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.287, 40.258, 106.496
Angle α, β, γ (deg.)90.00, 132.95, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 9932.361 Da / Num. of mol.: 4
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
AU-rich RNA


Mass: 3368.946 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.23 Å3/Da / Density % sol: 44.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20 mM Tris (pH8), 100 mM NaCl, 10% (w/v) Glycerol, 1mM TCEP precipitant: 2 M Ammonium sulfate, 0.1 M Bis-Tris well

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→77.95 Å / Num. obs: 35681 / % possible obs: 95.1 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04556 / Rrim(I) all: 0.05447 / Net I/σ(I): 15.23
Reflection shellResolution: 1.9→1.968 Å / Rmerge(I) obs: 0.6683 / Num. unique obs: 3148 / CC1/2: 0.854 / % possible all: 81.19

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Processing

Software
NameClassification
XDSdata scaling
XDSdata reduction
PHASERphasing
PHENIXrefinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HI9

3hi9


Resolution: 1.9→77.946 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.99
RfactorNum. reflection% reflection
Rfree0.2312 1784 5.01 %
Rwork0.2007 --
obs0.2023 35638 94.99 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Bsol: 53.915 Å2 / ksol: 0.344 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.7789 Å20 Å22.0232 Å2
2--17.0258 Å2-0 Å2
3----7.2469 Å2
Refinement stepCycle: LAST / Resolution: 1.9→77.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2320 304 0 191 2815
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152831
X-RAY DIFFRACTIONf_angle_d1.2163753
X-RAY DIFFRACTIONf_dihedral_angle_d12.004959
X-RAY DIFFRACTIONf_chiral_restr0.09434
X-RAY DIFFRACTIONf_plane_restr0.006423
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.95140.46981090.4235207177
1.9514-2.00880.3141390.264262595
2.0088-2.07370.25061350.2256256496
2.0737-2.14780.26341390.201265197
2.1478-2.23380.27231380.2044262096
2.2338-2.33550.25441300.2022244991
2.3355-2.45860.23151400.1928266697
2.4586-2.61270.25151420.1897268398
2.6127-2.81440.26151400.1976267698
2.8144-3.09760.21721430.2032270698
3.0976-3.54590.19891410.1953269198
3.5459-4.46740.2071410.1685266196
4.46740.2241470.2089279197
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)
10.75530.55760.07190.4478-0.07610.4110.15060.059-0.0754-0.0071-0.0281-0.07750.00260.0581-0.12460.2854-0.0352-0.01420.2378-0.01540.3103219.91936.259939.8626
20.21470.3112-0.46082.2483-1.13041.21330.1439-0.03520.1544-0.0653-0.288-0.6403-0.1570.26580.13390.2963-0.08020.02760.32710.02420.4255235.01640.437541.0334
30.8014-0.47680.17880.61330.12911.64470.0779-0.00680.3359-0.11880.0250.2838-0.3029-0.4949-0.07240.30630.00560.03180.25430.01040.3392211.604637.838443.031
41.40780.289-0.04620.1393-0.42112.04550.1634-0.2891-0.66880.2089-0.222-0.20350.51950.38370.06440.2703-0.00060.01720.1793-0.010.3139219.510833.391949.0948
51.04190.2842-0.88880.5656-0.37350.90270.17790.72780.0272-0.1162-0.2281-0.12850.25790.4917-0.03270.26020.024-0.03680.59910.03720.2311216.21130.761218.4162
68.3479-0.4347-0.84011.4658-0.66961.78320.28750.95320.885-0.3980.0486-0.2285-0.71790.5364-0.21880.3736-0.0521-0.01630.4408-0.0190.2898215.77236.425726.3701
71.17490.5953-0.72230.4178-0.35390.44260.1790.42190.0439-0.1298-0.0133-0.18440.43161.05740.10570.3180.1668-0.00680.8623-0.05350.2287220.959728.22922.1981
80.48810.33390.25730.2537-0.02271.69410.12220.102-0.0875-0.0950.17880.06360.27940.2825-0.3760.32730.0212-0.01530.42470.05850.2978212.127828.285824.1994
92.47211.1489-1.4274.64540.90621.4334-0.0124-0.2249-0.26280.6014-0.22080.24840.1034-0.73970.10760.2887-0.0241-0.07530.38570.00150.269204.052435.228523.0813
102.30290.1906-0.3540.1830.02471.33620.1960.77390.3591-0.09650.10070.22020.33350.365-0.1810.3384-0.0334-0.08010.56930.06950.2767212.602334.406714.8296
111.1854-0.3766-0.14731.2829-0.43650.21410.36270.31260.0056-0.324-0.1986-0.1102-0.2376-0.2966-0.23030.3183-0.0184-00.43130.03070.2985195.209538.11265.2872
122.15541.0436-0.86181.5770.81071.8845-0.13970.3405-0.2924-0.2203-0.0552-0.17840.397-0.1340.12170.3466-0.04930.01430.3543-0.02730.3365188.795433.432210.6968
131.82520.53260.65314.3359-2.50281.96730.15430.29260.39210.3759-0.15780.2402-0.6578-0.22290.01720.30510.0608-0.00650.35560.04320.328187.672140.946211.0902
141.1133-0.3799-0.60651.03330.57010.477-0.08220.0743-0.1423-0.52150.23250.40870.50250.1792-0.01380.4630.042-0.0620.48590.10.3137190.705241.7153-6.2492
150.9937-0.0584-0.66780.31360.62171.66170.2597-0.21570.40160.1705-0.20910.0566-0.821-0.1988-0.1010.3340.01940.00050.23910.010.344192.713441.638812.4605
162.3282-0.486-0.81650.6805-0.10440.4744-0.0358-0.68970.04310.1824-0.01920.2167-0.27960.401-0.04940.3439-0.0164-0.01410.36090.02470.2791197.576435.464919.0596
171.9069-0.27220.06980.1579-0.57333.65290.1430.1719-0.361-0.1124-0.0169-0.15860.68730.1054-0.08580.2908-0.0144-0.02610.27930.02380.2553200.64833.71517.6652
184.424-2.21590.4363.0559-0.38570.75240.22061.1102-0.225-0.0703-0.25550.3869-0.3057-0.0729-0.00030.3654-0.02530.00260.4878-0.0480.3304171.056531.988914.4437
191.12050.9318-0.18321.29391.05554.33740.04730.25730.53430.1244-0.1120.0715-0.3468-0.42540.07160.30050.03320.00120.35680.05660.3402178.949337.443114.5761
202.43550.2576-2.40262.89150.48782.72990.09060.5876-0.5151-0.1179-0.0846-0.20180.3513-0.30280.14190.28090.01240.05050.431-0.05040.3121179.949430.259113.9065
210.135-0.19860.34820.3013-0.49050.9680.05580.1388-0.0497-0.13360.10540.0005-0.01170.06750.45730.32190.0113-0.04961.1302-0.35440.2091166.951629.42064.6724
220.47490.0358-0.34110.5608-0.52251.08680.02650.0222-0.17230.066-0.1734-0.00010.0432-0.08030.11370.2927-0.01070.04180.3887-0.00790.2973176.389832.861622.5373
231.1624-1.60530.69265.5189-1.40770.9797-0.03350.38520.3530.2213-0.2968-0.4219-0.2159-0.35210.27180.25410.03670.06370.3469-0.00780.2851167.18636.220418.5975
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 243:275)
2X-RAY DIFFRACTION2chain 'A' and (resseq 276:286)
3X-RAY DIFFRACTION3chain 'A' and (resseq 287:305)
4X-RAY DIFFRACTION4chain 'A' and (resseq 306:321)
5X-RAY DIFFRACTION5chain 'B' and (resseq 243:256)
6X-RAY DIFFRACTION6chain 'B' and (resseq 257:267)
7X-RAY DIFFRACTION7chain 'B' and (resseq 268:286)
8X-RAY DIFFRACTION8chain 'B' and (resseq 287:294)
9X-RAY DIFFRACTION9chain 'B' and (resseq 295:305)
10X-RAY DIFFRACTION10chain 'B' and (resseq 306:322)
11X-RAY DIFFRACTION11chain 'C' and (resseq 243:256)
12X-RAY DIFFRACTION12chain 'C' and (resseq 257:267)
13X-RAY DIFFRACTION13chain 'C' and (resseq 268:275)
14X-RAY DIFFRACTION14chain 'C' and (resseq 276:286)
15X-RAY DIFFRACTION15chain 'C' and (resseq 287:294)
16X-RAY DIFFRACTION16chain 'C' and (resseq 295:305)
17X-RAY DIFFRACTION17chain 'C' and (resseq 306:321)
18X-RAY DIFFRACTION18chain 'D' and (resseq 242:256)
19X-RAY DIFFRACTION19chain 'D' and (resseq 257:267)
20X-RAY DIFFRACTION20chain 'D' and (resseq 268:275)
21X-RAY DIFFRACTION21chain 'D' and (resseq 276:286)
22X-RAY DIFFRACTION22chain 'D' and (resseq 287:305)
23X-RAY DIFFRACTION23chain 'D' and (resseq 306:322)

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