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- PDB-4w92: Crystal structure of Bacillus subtilis cyclic-di-AMP riboswitch ydaO -

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Basic information

Entry
Database: PDB / ID: 4w92
TitleCrystal structure of Bacillus subtilis cyclic-di-AMP riboswitch ydaO
Components
  • C-di-AMP ribsoswitch
  • U1 small nuclear ribonucleoprotein A
Keywordsrna binding protein/rna / riboswitch / cyclic-di-AMP / protein-RNA complex / rna binding protein-rna complex
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-2BA / : / RNA / RNA (> 10) / RNA (> 100) / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesHomo sapiens (human)
Bacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.209 Å
AuthorsJones, C.P. / Ferre-D'Amare, A.R.
CitationJournal: Embo J. / Year: 2014
Title: Crystal structure of a c-di-AMP riboswitch reveals an internally pseudo-dimeric RNA.
Authors: Jones, C.P. / Ferre-D'Amare, A.R.
History
DepositionAug 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2Dec 3, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / refine_hist
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: U1 small nuclear ribonucleoprotein A
C: C-di-AMP ribsoswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,53211
Polymers48,9932
Non-polymers1,5409
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-58 kcal/mol
Surface area21730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.281, 83.062, 233.573
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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Protein / RNA chain , 2 types, 2 molecules BC

#1: Protein U1 small nuclear ribonucleoprotein A / U1A


Mass: 10692.992 Da / Num. of mol.: 1 / Fragment: unp residues 6-96 / Mutation: Y31H, Q36R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPA / Plasmid: pIDTBlue / Production host: Escherichia coli (E. coli) / References: UniProt: P09012
#2: RNA chain C-di-AMP ribsoswitch


Mass: 38299.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)

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Non-polymers , 4 types, 9 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-2BA / (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide / bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate


Mass: 658.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O12P2

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Details

Has protein modificationY

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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: 2.98 Å3/Da / Density % sol: 58.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 / Details: PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 7, 2014
RadiationMonochromator: Double crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 9964 / % possible obs: 99.2 % / Redundancy: 12.2 % / Biso Wilson estimate: 86.47 Å2 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.056 / Rrim(I) all: 0.165 / Χ2: 1.611 / Net I/av σ(I): 18.267 / Net I/σ(I): 5.1 / Num. measured all: 122045
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
3.2-3.266.84380.5130.4911.08891.1
3.26-3.318.94770.5850.4261.10695.2
3.31-3.389.64690.5690.4431.13598.9
3.38-3.4510.15060.590.411.21199.8
3.45-3.5211.64820.8520.2911.27999.80.962
3.52-3.611.84990.840.281.2021000.9310.973
3.6-3.6912.34810.8780.251.3221000.8450.882
3.69-3.7912.85050.9270.2111.2551000.7290.76
3.79-3.91134820.950.181.2331000.6280.653
3.91-4.0313.45110.9590.1561.2991000.5520.574
4.03-4.1813.54880.9710.1321.2331000.4690.488
4.18-4.3413.75010.9860.1051.3631000.3730.388
4.34-4.5413.95060.9840.0921.3991000.330.343
4.54-4.7813.64930.9870.0671.5381000.2390.248
4.78-5.0813.85080.9990.0611.5381000.2130.222
5.08-5.4713.55040.9940.0461.6981000.1630.17
5.47-6.0213.15180.9970.041.7661000.1390.145
6.02-6.8912.75110.9960.0352.05899.40.120.125
6.89-8.6713.65240.9950.0272.5561000.0950.099
8.67-5012.256110.0183.91599.30.0590.062

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
RefinementResolution: 3.209→48.787 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.01 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2892 1807 9.93 %Random selection
Rwork0.2517 16383 --
obs0.2553 8069 98.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 211.66 Å2 / Biso mean: 100.4238 Å2 / Biso min: 31.58 Å2
Refinement stepCycle: final / Resolution: 3.209→48.787 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms658 2033 98 0 2789
Biso mean--54.75 --
Num. residues----186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033044
X-RAY DIFFRACTIONf_angle_d0.7284599
X-RAY DIFFRACTIONf_chiral_restr0.027596
X-RAY DIFFRACTIONf_plane_restr0.002215
X-RAY DIFFRACTIONf_dihedral_angle_d14.7531399
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2094-3.29620.42041100.36841008111881
3.2962-3.39310.3711430.33571278142197
3.3931-3.50260.36811440.31491269141399
3.5026-3.62780.33051390.298212531392100
3.6278-3.7730.30611450.282413211466100
3.773-3.94460.33281400.252512821422100
3.9446-4.15250.25241390.236812791418100
4.1525-4.41250.27271420.235912741416100
4.4125-4.75290.2481390.222912751414100
4.7529-5.23070.27561390.208912961435100
5.2307-5.98650.24211490.214612881437100
5.9865-7.53780.25791460.24512791425100
7.5378-48.79270.29551320.24941281141399
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)
10.35240.06150.10970.0350.00640.03880.29280.0493-0.0660.21930.03710.02290.0478-0.09530.15581.6375-0.0885-0.11461.01330.19890.320940.6191-153.6712761.2609
20.11960.148-0.02370.21140.05250.28610.11310.1188-0.17720.2978-0.0073-0.1534-0.1006-0.064-0.00180.9646-0.2246-0.23491.1274-0.20020.391842.0671-156.7037751.529
30.09390.02550.19990.06160.10150.4392-0.5817-0.4298-0.8025-0.2099-0.1138-0.0995-0.22260.2676-0.03280.56630.06360.03711.28020.11941.478742.3941-160.2353738.1968
40.101-0.10730.02330.1083-0.02840.0574-0.30510.120.5288-0.0649-0.3469-0.41030.5209-0.2137-0.00080.5328-0.005-0.07540.5896-0.15970.900331.7124-156.4511744.7798
50.01160.0112-0.00490.0045-0.01170.0283-0.3122-0.02620.4368-0.03820.43370.2939-0.2574-0.135600.8237-0.16360.12910.7703-0.17990.858834.212-149.7389748.5748
6-0.00070.0020.0028-0.0031-0.00350.01990.1436-0.4390.20580.1575-0.1514-0.2241-0.08650.20780.14670.2376-0.1356-0.57290.709-0.13812.199347.735-153.6299741.488
70.0007-0.0232-0.01620.76410.50860.33720.0080.1327-0.0862-0.3612-0.0129-0.1121-0.04230.0789-0.4890.769-0.1652-0.05290.4765-0.41830.271436.1333-151.64752.7831
80.1593-0.14830.15150.4666-0.04350.18010.17490.0652-0.1714-0.0874-0.01780.0276-0.0721-0.04680.62080.8561-0.063-0.04460.9745-0.00430.139432.9802-159.9406757.4525
90.1718-0.52920.1682.0975-1.08770.8872-1.11930.4721-0.0511.02430.1184-0.7037-0.24380.2474-0.01950.6225-0.0682-0.13051.1105-0.01841.520637.6691-166.1625745.1451
100.16610.38530.10951.54320.4670.13360.2075-0.55650.07630.5088-0.09690.0076-0.20340.47750.06980.9658-0.0982-0.24251.1078-0.04070.548842.5954-155.232755.972
110.0422-0.01940.11880.18650.03830.378-0.0115-0.07750.00390.01760.00290.0247-0.0162-0.07340.00911.1457-0.1441-0.60771.36970.45160.642939.6864-141.0731756.5213
122.82151.1766-0.92731.83230.66280.9908-0.25370.35410.3026-0.46860.15940.4643-0.1921-0.5839-0.00560.8264-0.0866-0.37981.01940.17341.459765.6915-146.0327723.8217
130.2013-0.14490.23470.246-0.07170.2679-0.5088-0.97721.33380.58780.08120.9739-0.1022-0.05950.00010.9320.03810.18161.2013-0.14861.548783.7583-146.7647738.8935
140.1148-0.3513-0.15581.8913-0.41071.4443-0.21580.0550.577-0.24910.18850.7734-0.099-0.4259-0.00010.7796-0.1147-0.10790.9828-0.09021.329574.2971-142.9455724.4702
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 6 through 10 )B0
2X-RAY DIFFRACTION2chain 'B' and (resid 11 through 15 )B0
3X-RAY DIFFRACTION3chain 'B' and (resid 16 through 22 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 23 through 37 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 38 through 45 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 46 through 54 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 55 through 61 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 62 through 72 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 73 through 82 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 83 through 91 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 92 through 96 )B0
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 65 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 66 through 82 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 83 through 119 )C0

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