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- PDB-2anr: Crystal structure (II) of Nova-1 KH1/KH2 domain tandem with 25nt ... -

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Basic information

Entry
Database: PDB / ID: 2anr
TitleCrystal structure (II) of Nova-1 KH1/KH2 domain tandem with 25nt RNA hairpin
Components
  • 5'-R(*CP*(5BU)P*CP*GP*CP*GP*GP*AP*UP*CP*AP*GP*UP*CP*AP*CP*CP*CP*AP*AP*GP*CP*GP*AP*G)-3'
  • RNA-binding protein Nova-1
KeywordsRNA-BINDING PROTEIN/RNA / Protein-RNA complex / KH domain / Hairpin / RNA-BINDING PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


regulation of RNA metabolic process / regulation of mRNA processing / 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 ...regulation of RNA metabolic process / regulation of mRNA processing / 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 / RNA (> 10) / RNA-binding protein Nova-1 / RNA-binding protein Nova-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsMalinina, L. / Teplova, M. / Musunuru, K. / Teplov, A. / Darnell, J.C. / Burley, S.K. / Darnell, R.B. / Patel, D.J.
CitationJournal: Structure / Year: 2011
Title: Protein-RNA and protein-protein recognition by dual KH1/2 domains of the neuronal splicing factor Nova-1.
Authors: Teplova, M. / Malinina, L. / Darnell, J.C. / Song, J. / Lu, M. / Abagyan, R. / Musunuru, K. / Teplov, A. / Burley, S.K. / Darnell, R.B. / Patel, D.J.
History
DepositionAug 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 2, 2011Group: Database references
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 20, 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 1.7Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.8Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.9Dec 20, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / pdbx_struct_mod_residue / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_mutation ..._entity.pdbx_description / _entity.pdbx_mutation / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.entity_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5'-R(*CP*(5BU)P*CP*GP*CP*GP*GP*AP*UP*CP*AP*GP*UP*CP*AP*CP*CP*CP*AP*AP*GP*CP*GP*AP*G)-3'
A: RNA-binding protein Nova-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4615
Polymers27,3742
Non-polymers883
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)159.453, 37.885, 38.523
Angle α, β, γ (deg.)90.00, 96.64, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain 5'-R(*CP*(5BU)P*CP*GP*CP*GP*GP*AP*UP*CP*AP*GP*UP*CP*AP*CP*CP*CP*AP*AP*GP*CP*GP*AP*G)-3'


Mass: 8090.747 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein RNA-binding protein Nova-1 / Neuro-oncological ventral antigen 1 / Ventral neuron-specific protein 1


Mass: 19282.838 Da / Num. of mol.: 1 / Fragment: KH1/KH2 domains / Mutation: E218N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Genus: Homo / Gene: Nova1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9JKN6, UniProt: P51513*PLUS
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.4 Å3/Da / Density % sol: 48.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.6
Details: PEG 4000, isopropanol, potassium cloride, magnesium cloride, pH 5.6, VAPOR DIFFUSION, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2isopropanol11
3potassium chloride11
4magnesium chloride11
5H2O11
6PEG 400012
7potassium chloride12
8magnesium chloride12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.919826 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 7, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919826 Å / Relative weight: 1
ReflectionResolution: 1.94→39.6 Å / Num. obs: 16720 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.55 % / Rmerge(I) obs: 0.114 / Χ2: 0.988
Reflection shellResolution: 1.94→2.01 Å / % possible obs: 72.4 % / Rmerge(I) obs: 0.464 / Num. measured obs: 1303 / Χ2: 0.728 / % possible all: 89.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ANN

2ann


Resolution: 1.94→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / SU B: 6.103 / SU ML: 0.169 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.218 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.268 830 5.1 %RANDOM
Rwork0.227 ---
all0.23 16805 --
obs0.23 16202 94.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.996 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å20 Å2-1.85 Å2
2---0.38 Å20 Å2
3----1.76 Å2
Refinement stepCycle: LAST / Resolution: 1.94→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1177 531 3 106 1817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211796
X-RAY DIFFRACTIONr_angle_refined_deg1.6822.032535
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.175152
X-RAY DIFFRACTIONr_chiral_restr0.110.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021121
X-RAY DIFFRACTIONr_nbd_refined0.2110.2806
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.286
X-RAY DIFFRACTIONr_metal_ion_refined0.2620.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.25
X-RAY DIFFRACTIONr_mcbond_it0.6361.5765
X-RAY DIFFRACTIONr_mcangle_it1.08421238
X-RAY DIFFRACTIONr_scbond_it1.69931029
X-RAY DIFFRACTIONr_scangle_it2.2334.51297
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.409 61
Rwork0.344 1045
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.77871.05711.33322.73560.19232.3635-0.02630.0314-0.13310.6712-0.0459-0.47160.01070.00390.07220.19490.0523-0.07890.0778-0.01040.236863.58144.874810.8711
21.21810.37491.22972.72820.68842.14220.13390.24520.0350.0746-0.0422-0.1659-0.0263-0.4289-0.09170.09280.05760.10820.30520.00560.140448.8347-16.8254-1.6941
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AB3 - 1783 - 178
22BA201 - 2251 - 25

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