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- PDB-3iwn: Co-crystal structure of a bacterial c-di-GMP riboswitch -

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Basic information

Entry
Database: PDB / ID: 3iwn
TitleCo-crystal structure of a bacterial c-di-GMP riboswitch
Components
  • C-di-GMP riboswitch
  • U1 small nuclear ribonucleoprotein A
KeywordsRNA/RNA BINDING PROTEIN / riboswitch / RNA / U1A / RNA-RNA BINDING PROTEIN COMPLEX / Acetylation / mRNA processing / mRNA splicing / Nucleus / Phosphoprotein / Ribonucleoprotein / RNA-binding / Spliceosome
Function / homology
Function and homology information


U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm ...U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
U1 small nuclear ribonucleoprotein A, RNA recognition motif 2 / U1 small nuclear ribonucleoprotein A, RNA recognition motif 1 / 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 ...U1 small nuclear ribonucleoprotein A, RNA recognition motif 2 / U1 small nuclear ribonucleoprotein A, RNA recognition motif 1 / 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
Chem-C2E / RNA / RNA (> 10) / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsKulshina, N. / Baird, N.J. / Ferre-D'Amare, A.R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch.
Authors: Kulshina, N. / Baird, N.J. / Ferre-D'Amare, A.R.
History
DepositionSep 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / struct_ref_seq / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 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: C-di-GMP riboswitch
B: C-di-GMP riboswitch
C: U1 small nuclear ribonucleoprotein A
D: U1 small nuclear ribonucleoprotein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6596
Polymers81,2794
Non-polymers1,3812
Water00
1
A: C-di-GMP riboswitch
C: U1 small nuclear ribonucleoprotein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3303
Polymers40,6392
Non-polymers6901
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint3 kcal/mol
Surface area18770 Å2
MethodPISA
2
B: C-di-GMP riboswitch
D: U1 small nuclear ribonucleoprotein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3303
Polymers40,6392
Non-polymers6901
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint0 kcal/mol
Surface area19010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.800, 91.000, 280.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: RNA chain C-di-GMP riboswitch


Mass: 30087.014 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: in vitro transcription
#2: Protein U1 small nuclear ribonucleoprotein A / U1 snRNP protein A / U1A protein / U1-A


Mass: 10552.307 Da / Num. of mol.: 2 / Fragment: UNP residues 6-96, RRM 1 domain / Mutation: Y31H, Q36R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPA, U1A / Plasmid: pT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P09012
#3: Chemical ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate


Mass: 690.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O14P2

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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: 2.49 Å3/Da / Density % sol: 50.68 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG3350 0.1M Tris pH8.5 0.3M ammonium acetate pH7.0 3mM MgCl2 1 mM spermine , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 11, 2009 / Details: Double crystal, Si(111)
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 11257 / % possible obs: 84 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.179 / Net I/σ(I): 7.9
Reflection shellResolution: 3.2→3.25 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 2.2 / % possible all: 75.4

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→29.85 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 35958.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.292 1155 10.3 %RANDOM
Rwork0.222 ---
obs0.222 11257 79.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 0.152628 Å2 / ksol: 0.2 e/Å3
Displacement parametersBiso mean: 49.5 Å2
Baniso -1Baniso -2Baniso -3
1--8.95 Å2-0 Å2-0 Å2
2--3.43 Å2-0 Å2
3---5.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 3.2→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1429 3984 92 0 5505
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.99
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.481.5
X-RAY DIFFRACTIONc_mcangle_it0.872
X-RAY DIFFRACTIONc_scbond_it0.492
X-RAY DIFFRACTIONc_scangle_it0.842.5
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.356 139 9.7 %
Rwork0.299 1287 -
obs--62.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramCNS_TOPAR:dna-rna.top
X-RAY DIFFRACTION3c2e.parc2e.top

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