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- PDB-1dtj: CRYSTAL STRUCTURE OF NOVA-2 KH3 K-HOMOLOGY RNA-BINDING DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1dtj
TitleCRYSTAL STRUCTURE OF NOVA-2 KH3 K-HOMOLOGY RNA-BINDING DOMAIN
ComponentsRNA-BINDING NEUROONCOLOGICAL VENTRAL ANTIGEN 2
KeywordsIMMUNE SYSTEM / KH domain / alpha-beta fold RNA-binding motif
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 / neuron differentiation / mRNA splicing, via spliceosome / 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 / neuron differentiation / mRNA splicing, via spliceosome / mRNA binding / RNA binding / nucleus / cytoplasm
Similarity search - Function
: / : / : / K Homology domain, type 1 / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / Ribosomal Protein S8; Chain: A, domain 1 / K Homology domain, type 1 superfamily / K Homology domain ...: / : / : / K Homology domain, type 1 / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / Ribosomal Protein S8; Chain: A, domain 1 / 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-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsLewis, H.A. / Chen, H. / Edo, C. / Buckanovich, R.J. / Yang, Y.Y.L. / Musunuru, K. / Zhong, R. / Darnell, R.B. / Burley, S.K.
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 12, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 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 / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_sheet.number_strands
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: RNA-BINDING NEUROONCOLOGICAL VENTRAL ANTIGEN 2
B: RNA-BINDING NEUROONCOLOGICAL VENTRAL ANTIGEN 2
C: RNA-BINDING NEUROONCOLOGICAL VENTRAL ANTIGEN 2
D: RNA-BINDING NEUROONCOLOGICAL VENTRAL ANTIGEN 2


Theoretical massNumber of molelcules
Total (without water)33,1544
Polymers33,1544
Non-polymers00
Water3,801211
1
A: RNA-BINDING NEUROONCOLOGICAL VENTRAL ANTIGEN 2


Theoretical massNumber of molelcules
Total (without water)8,2891
Polymers8,2891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA-BINDING NEUROONCOLOGICAL VENTRAL ANTIGEN 2


Theoretical massNumber of molelcules
Total (without water)8,2891
Polymers8,2891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA-BINDING NEUROONCOLOGICAL VENTRAL ANTIGEN 2


Theoretical massNumber of molelcules
Total (without water)8,2891
Polymers8,2891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RNA-BINDING NEUROONCOLOGICAL VENTRAL ANTIGEN 2


Theoretical massNumber of molelcules
Total (without water)8,2891
Polymers8,2891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.500, 61.100, 97.300
Angle α, β, γ (deg.)90.00, 98.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
RNA-BINDING NEUROONCOLOGICAL VENTRAL ANTIGEN 2


Mass: 8288.556 Da / Num. of mol.: 4 / Fragment: THIRD KH DOMAIN OF NOVA-2 / Mutation: I10M
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: Q9UNW9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.95 Å3/Da / Density % sol: 58.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 3
Details: (NH4)2SO4, MPD, sodium chloride, pH 3.0, VAPOR DIFFUSION, temperature 277.0K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.4 Mammonium sulfate1reservoir
22 %MPD1reservoir
350 mMFormic acid1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.981
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Apr 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.981 Å / Relative weight: 1
ReflectionResolution: 2→15 Å / Num. all: 26192 / Num. obs: 25590 / % possible obs: 99 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4.1 % / Biso Wilson estimate: 32.9 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 15.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.197 / % possible all: 99.2
Reflection shell
*PLUS
% possible obs: 99.2 %

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Processing

Software
NameVersionClassification
CNSrefinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
CNSphasing
RefinementResolution: 2→15 Å / σ(F): 3 / σ(I): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.279 2465 random
Rwork0.225 --
all0.236 26192 -
obs0.229 25590 -
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1917 0 0 211 2128
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_bond_d0.017

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