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- PDB-1fxl: CRYSTAL STRUCTURE OF HUD AND AU-RICH ELEMENT OF THE C-FOS RNA -

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Basic information

Entry
Database: PDB / ID: 1fxl
TitleCRYSTAL STRUCTURE OF HUD AND AU-RICH ELEMENT OF THE C-FOS RNA
Components
  • 5'-R(P*UP*UP*UP*UP*AP*UP*UP*UP*U)-3'
  • PARANEOPLASTIC ENCEPHALOMYELITIS ANTIGEN HUD
KeywordsTRANSCRIPTION/RNA / PROTEIN-RNA COMPLEX / HuD / AU-Rich Element / TRANSCRIPTION-RNA COMPLEX
Function / homology
Function and homology information


positive regulation of 3'-UTR-mediated mRNA stabilization / regeneration / pre-mRNA intronic pyrimidine-rich binding / regulation of translation at postsynapse / cerebral cortex neuron differentiation / mRNA 3'-UTR AU-rich region binding / apical dendrite / poly(A) binding / positive regulation of dendrite development / dendrite morphogenesis ...positive regulation of 3'-UTR-mediated mRNA stabilization / regeneration / pre-mRNA intronic pyrimidine-rich binding / regulation of translation at postsynapse / cerebral cortex neuron differentiation / mRNA 3'-UTR AU-rich region binding / apical dendrite / poly(A) binding / positive regulation of dendrite development / dendrite morphogenesis / 3'-UTR-mediated mRNA stabilization / associative learning / RNA processing / response to endoplasmic reticulum stress / RNA splicing / cellular response to nerve growth factor stimulus / locomotory behavior / response to cocaine / mRNA 3'-UTR binding / mRNA processing / nuclear envelope / growth cone / postsynapse / perikaryon / ribosome / ribonucleoprotein complex / axon / glutamatergic synapse / dendrite / cytoplasm
Similarity search - Function
HuD, RNA recognition motif 3 / 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 ...HuD, RNA recognition motif 3 / 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
RNA / ELAV-like protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsWang, X. / Hall, T.M.T.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Structural basis for recognition of AU-rich element RNA by the HuD protein.
Authors: Wang, X. / Tanaka Hall, T.M.
History
DepositionSep 26, 2000Deposition site: NDB / Processing site: NDB
Revision 1.0Feb 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: 5'-R(P*UP*UP*UP*UP*AP*UP*UP*UP*U)-3'
A: PARANEOPLASTIC ENCEPHALOMYELITIS ANTIGEN HUD


Theoretical massNumber of molelcules
Total (without water)21,2812
Polymers21,2812
Non-polymers00
Water3,945219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.310, 99.380, 33.340
Angle α, β, γ (deg.)90.00, 106.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain 5'-R(P*UP*UP*UP*UP*AP*UP*UP*UP*U)-3'


Mass: 2733.574 Da / Num. of mol.: 1 / Fragment: FRAGMENT OF THE C-FOS AU-RICH ELEMENT / Source method: obtained synthetically
#2: Protein PARANEOPLASTIC ENCEPHALOMYELITIS ANTIGEN HUD / HUD / HU-ANTIGEN D


Mass: 18547.186 Da / Num. of mol.: 1 / Fragment: N-TERMINAL TWO RRM-DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: BRAIN / Plasmid: PPROEXHTC / Production host: Escherichia coli (E. coli) / References: UniProt: P26378
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.26 Å3/Da / Density % sol: 45.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 3350, Ammonium sulfate, Calcium chloride, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2(NH4)2SO411
3CaCl211
4Tris11
Crystal
*PLUS
Density % sol: 43 %
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 %(w/v)PEG33501reservoir
250 mMTris1reservoir
3200 mM1reservoirNH4Cl
410 mM1reservoirCaCl2

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1931
2931
Diffraction source
SourceSiteBeamlineTypeIDWavelength
ROTATING ANODERIGAKU RUH3R11.5418
SYNCHROTRONNSLS X9B21.072
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV1IMAGE PLATEMar 6, 2000
ADSC QUANTUM2CCDMar 23, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.0721
ReflectionResolution: 1.8→30.45 Å / Num. all: 16220 / Num. obs: 16220 / % possible obs: 92.3 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 12.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.329 / Num. unique all: 1485 / % possible all: 85.1
Reflection
*PLUS
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.8→30.45 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: A final round of refinement was performed by using all data including reflections set aside for cross-validation in a "free" R-factor set. For last nucleotide U11, only the 5' phosphate group was observed.
RfactorNum. reflection% reflectionSelection details
Rfree0.239 931 -RANDOM
Rwork0.192 ---
obs0.193 15853 90.3 %-
all-16220 --
Refinement stepCycle: LAST / Resolution: 1.8→30.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1304 167 0 219 1690
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.21
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / σ(F): 0 / % reflection Rfree: 6 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.1 Å2
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.19

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