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- PDB-1g2e: CRYSTAL STRUCTURE OF HUD AND AU-RICH ELEMENT OF THE TUMOR NECROSI... -

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Basic information

Entry
Database: PDB / ID: 1g2e
TitleCRYSTAL STRUCTURE OF HUD AND AU-RICH ELEMENT OF THE TUMOR NECROSIS FACTOR ALPHA RNA
Components
  • 5'-R(P*UP*AP*UP*UP*UP*AP*UP*UP*UP*A)-3'
  • PARANEOPLASTIC ENCEPHALOMYELITIS ANTIGEN HUD
KeywordsTRANSCRIPTION/RNA / PROTEIN-RNA COMPLEX / HuD / AU-Rich Element / TUMOR NECROSIS FACTOR / 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 / cellular response to nerve growth factor stimulus / RNA splicing / locomotory behavior / response to cocaine / mRNA 3'-UTR binding / mRNA processing / nuclear envelope / growth cone / perikaryon / postsynapse / 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 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
DepositionOct 18, 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 1.3Aug 2, 2023Group: Database references / Refinement description / Category: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)21,6332
Polymers21,6332
Non-polymers00
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.37, 100.15, 33.27
Angle α, β, γ (deg.)90.0, 106.59, 90.0
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 3085.820 Da / Num. of mol.: 1
Fragment: FRAGMENT OF AU-RICH ELEMENT OF THE TUMOR NECROSIS FACTOR ALPHA RNA
Source method: obtained synthetically
#2: Protein PARANEOPLASTIC ENCEPHALOMYELITIS ANTIGEN HUD


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 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P26378
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.24 Å3/Da / Density % sol: 45.11 %
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

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 5, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→30.38 Å / Num. all: 8327 / Num. obs: 8327 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 31.4 Å2 / Rsym value: 0.106 / Net I/σ(I): 8.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 725 / Rsym value: 0.299 / % possible all: 83.8
Reflection
*PLUS
Rmerge(I) obs: 0.106
Reflection shell
*PLUS
Highest resolution: 2.3 Å

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FXL

1fxl


Resolution: 2.3→30.38 Å / Isotropic thermal model: Isotropic RESTRAINED / Cross valid method: THROUGHOUT / 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 A11, only the 5' phosphate ...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 A11, only the 5' phosphate group and ribose group are observed.
RfactorNum. reflection% reflectionSelection details
Rfree0.238 516 -RANDOM
Rwork0.174 ---
obs0.174 8121 95.5 %-
all-8327 --
Displacement parametersBiso mean: 25.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.3→30.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1304 197 0 154 1655
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.28
X-RAY DIFFRACTIONc_dihedral_angle_d
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / σ(F): 0 / % reflection Rfree: 6 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.7 Å2

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