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- PDB-1ec6: CRYSTAL STRUCTURE OF NOVA-2 KH3 K-HOMOLOGY RNA-BINDING DOMAIN BOU... -

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Basic information

Entry
Database: PDB / ID: 1ec6
TitleCRYSTAL STRUCTURE OF NOVA-2 KH3 K-HOMOLOGY RNA-BINDING DOMAIN BOUND TO 20-MER RNA HAIRPIN
Components
  • 20-MER RNA HAIRPIN
  • RNA-BINDING PROTEIN NOVA-2
KeywordsRNA BINDING PROTEIN/RNA / KH domain / alpha-beta fold / RNA-binding motif / protein/RNA structure / RNA BINDING PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


regulation of axon guidance / regulation of RNA metabolic process / sequence-specific mRNA binding / negative regulation of cold-induced thermogenesis / regulation of alternative mRNA splicing, via spliceosome / central nervous system neuron development / mRNA splicing, via spliceosome / neuron differentiation / mRNA binding / RNA binding ...regulation of axon guidance / regulation of RNA metabolic process / sequence-specific mRNA binding / negative regulation of cold-induced thermogenesis / regulation of alternative mRNA splicing, via spliceosome / central nervous system neuron development / mRNA splicing, via spliceosome / neuron differentiation / mRNA binding / RNA binding / nucleus / cytoplasm
Similarity search - Function
: / : / : / K Homology domain, type 1 / KH domain / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / K Homology domain ...: / : / : / K Homology domain, type 1 / KH domain / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA-binding protein Nova-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsLewis, H.A. / Musunuru, K. / Jensen, K.B. / Edo, C. / Chen, H.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2000
Title: Sequence-specific RNA binding by a Nova KH domain: implications for paraneoplastic disease and the fragile X syndrome.
Authors: Lewis, H.A. / Musunuru, K. / Jensen, K.B. / Edo, C. / Chen, H. / Darnell, R.B. / Burley, S.K.
History
DepositionJan 25, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.4Feb 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

Downloads & links

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Assembly

Deposited unit
C: 20-MER RNA HAIRPIN
D: 20-MER RNA HAIRPIN
A: RNA-BINDING PROTEIN NOVA-2
B: RNA-BINDING PROTEIN NOVA-2


Theoretical massNumber of molelcules
Total (without water)31,5594
Polymers31,5594
Non-polymers00
Water3,063170
1
D: 20-MER RNA HAIRPIN
A: RNA-BINDING PROTEIN NOVA-2


Theoretical massNumber of molelcules
Total (without water)15,7802
Polymers15,7802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 20-MER RNA HAIRPIN
B: RNA-BINDING PROTEIN NOVA-2


Theoretical massNumber of molelcules
Total (without water)15,7802
Polymers15,7802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.850, 51.210, 128.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: RNA chain 20-MER RNA HAIRPIN


Mass: 6341.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Product of SELEX protein binding study
#2: Protein RNA-BINDING PROTEIN NOVA-2 / ASTROCYTIC NOVA-LIKE RNA-BINDING PROTEIN


Mass: 9437.835 Da / Num. of mol.: 2 / Fragment: KH3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UNW9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.5 Å3/Da / Density % sol: 50.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 25% PEG 5000, 150 mM ammonium sulfate, 100 mM MES, pH 6.5, VAPOR DIFFUSION, temperature 293.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1MES11
2(NH4)2SO411
3PEG 500011
4(NH4)2SO412
5PEG 500012
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop / Details: protein:RNA 1:1.25 ratio
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 %PEG5000 MME1reservoir
2150 mMammonium sulfate1reservoir
3100 mMMES1reservoirpH6.5
40.155 mMprotein1drop
51

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.935
DetectorType: OTHER / Detector: CCD / Date: Sep 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.935 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 12459 / Num. obs: 12004 / % possible obs: 96.5 % / Observed criterion σ(I): 3 / Redundancy: 5.3 % / Biso Wilson estimate: 46.4 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 16.9
Reflection shellHighest resolution: 2.4 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.215 / % possible all: 93.7
Reflection
*PLUS
Num. obs: 67678 / % possible obs: 98 % / Num. measured all: 143241
Reflection shell
*PLUS
% possible obs: 93.7 % / Rmerge(I) obs: 0.211

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Processing

Software
NameVersionClassification
CNSrefinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
CNSphasing
RefinementResolution: 2.4→20 Å / Cross valid method: THROUGHOUT / σ(I): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.291 1245 10 %random
Rwork0.208 ---
all0.224 ---
obs0.215 12459 --
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1286 838 0 170 2294
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.48
X-RAY DIFFRACTIONc_bond_d0.0091
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor obs: 0.208 / Num. reflection obs: 67678
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4

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