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- PDB-1dt4: CRYSTAL STRUCTURE OF NOVA-1 KH3 K-HOMOLOGY RNA-BINDING DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1dt4
TitleCRYSTAL STRUCTURE OF NOVA-1 KH3 K-HOMOLOGY RNA-BINDING DOMAIN
ComponentsNEURO-ONCOLOGICAL VENTRAL ANTIGEN 1
KeywordsIMMUNE SYSTEM / KH DOMAIN / ALPHA-BETA FOLD / RNA-BINDING MOTIF
Function / homology
Function and homology information


sequence-specific mRNA binding / negative regulation of cold-induced thermogenesis / regulation of alternative mRNA splicing, via spliceosome / RNA processing / RNA splicing / mRNA 3'-UTR binding / mRNA splicing, via spliceosome / nervous system development / intracellular membrane-bounded organelle / mRNA binding ...sequence-specific mRNA binding / negative regulation of cold-induced thermogenesis / regulation of alternative mRNA splicing, via spliceosome / RNA processing / RNA splicing / mRNA 3'-UTR binding / mRNA splicing, via spliceosome / nervous system development / intracellular membrane-bounded organelle / mRNA binding / nucleolus / RNA binding / nucleoplasm / 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-binding protein Nova-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsLewis, H.A. / Chen, H. / Edo, C. / Buckanovich, R.J. / Yang, Y.Y.L.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Crystal structures of Nova-1 and Nova-2 K-homology RNA-binding domains.
Authors: Lewis, H.A. / Chen, H. / Edo, C. / Buckanovich, R.J. / Yang, Y.Y. / Musunuru, K. / Zhong, R. / Darnell, R.B. / Burley, S.K.
History
DepositionJan 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 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 / struct_ref_seq_dif
Item: _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NEURO-ONCOLOGICAL VENTRAL ANTIGEN 1


Theoretical massNumber of molelcules
Total (without water)7,8951
Polymers7,8951
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.670, 44.670, 84.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein NEURO-ONCOLOGICAL VENTRAL ANTIGEN 1


Mass: 7895.203 Da / Num. of mol.: 1 / Fragment: THIRD K-HOMOLOGY DOMAIN / Mutation: A37C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: NEURON / Organ: BRAIN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P51513

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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: 2.65 Å3/Da / Density % sol: 53.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4
Details: Li2SO4, sodium acetate, sodium cloride, pH 4.0, VAPOR DIFFUSION, temperature 293.0K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.8 M1reservoirLi2SO4
2100 mM1reservoirNaAc
310 mg/mlprotein1drop
4300 mM1dropNaCl
520 mMHEPES1drop

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 2659 / Num. obs: 2473 / % possible obs: 91.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4.3 % / Biso Wilson estimate: 56.6 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 24.3
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.19 / Num. unique all: 250 / % possible all: 90.3

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Processing

Software
NameVersionClassification
CNSrefinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
CNSphasing
RefinementResolution: 2.6→20 Å / σ(F): 3 / σ(I): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.282 228 random
Rwork0.222 --
all0.242 2916 -
obs0.228 2660 -
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms514 0 0 0 514
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.0077
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / σ(F): 3 / Rfactor obs: 0.245 / Rfactor Rfree: 0.31
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.8
LS refinement shell
*PLUS
Rfactor Rfree: 0.316 / Rfactor obs: 0.313

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