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- PDB-4w90: Crystal structure of Bacillus subtilis cyclic-di-AMP riboswitch ydaO -

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Basic information

Entry
Database: PDB / ID: 4w90
TitleCrystal structure of Bacillus subtilis cyclic-di-AMP riboswitch ydaO
Components
  • U1 small nuclear ribonucleoprotein A
  • riboswitch a pseudo-dimeric RNA
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: 3.118 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 15, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Nov 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_assembly / pdbx_struct_assembly_prop / 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_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 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 / struct_conn
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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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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: riboswitch a pseudo-dimeric RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4319
Polymers48,9932
Non-polymers1,4387
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-35 kcal/mol
Surface area20120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.280, 84.850, 230.536
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein U1 small nuclear ribonucleoprotein A / U1A


Mass: 10692.992 Da / Num. of mol.: 1 / Mutation: Y31H, Q36R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo Sapiens (human) / Gene: U1A protein / Plasmid: pIDTBlue / Production host: Escherichia coli (E. coli) / References: UniProt: P09012
#2: RNA chain riboswitch a pseudo-dimeric RNA


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)
#3: 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
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg

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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: 2.96 Å3/Da / Density % sol: 58.43 %
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: May 2, 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: 3.118→50 Å / Num. obs: 9322 / % possible obs: 87 % / Redundancy: 10.4 % / Biso Wilson estimate: 91.66 Å2 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.055 / Rrim(I) all: 0.14 / Χ2: 2.407 / Net I/av σ(I): 23.61 / Net I/σ(I): 7.4 / Num. measured all: 96691
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
3.16-3.2110.34770.4590.7031.55991.9
3.21-3.2710.34710.6050.5571.71387.4
3.27-3.3410.44680.6250.4881.77290.2
3.34-3.410.74540.7050.4431.85288.3
3.4-3.4810.44810.8250.3461.95788.6
3.48-3.5610.44650.8610.2922.08989.30.9440.992
3.56-3.6510.74550.8640.2631.98489.60.8570.899
3.65-3.7510.64780.9210.2042.11886.60.6580.692
3.75-3.8610.54490.9270.172.14788.90.550.578
3.86-3.9810.44810.9560.1412.11388.70.4480.472
3.98-4.1210.94570.9670.1052.19286.40.3410.358
4.12-4.2910.54610.9830.092.37686.70.2860.301
4.29-4.4810.64530.9830.072.39986.90.2240.235
4.48-4.7210.44650.990.0512.43686.40.1620.17
4.72-5.0110.54690.9960.0492.5886.40.1510.16
5.01-5.410.44640.9940.0392.75485.90.1220.128
5.4-5.9410.44570.9950.0332.96985.30.1020.108
5.94-6.810.24630.9960.033.08184.50.0910.096
6.8-8.569.74760.9960.0253.51183.80.0780.082
8.56-509.54780.9980.0194.85679.80.0550.058

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Processing

Software
NameVersionClassificationNB
PHENIX(phenix.refine: 1.9_1692)refinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
RefinementResolution: 3.118→46.937 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2883 1713 9.9 %Random selection
Rwork0.23 15586 --
obs0.2357 9322 86.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 247.32 Å2 / Biso mean: 109.537 Å2 / Biso min: 40.14 Å2
Refinement stepCycle: final / Resolution: 3.118→46.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms639 2146 93 0 2878
Biso mean--79.73 --
Num. residues----191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033150
X-RAY DIFFRACTIONf_angle_d0.7914779
X-RAY DIFFRACTIONf_chiral_restr0.034624
X-RAY DIFFRACTIONf_plane_restr0.004219
X-RAY DIFFRACTIONf_dihedral_angle_d15.9061457
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1185-3.21020.37121410.35051228136983
3.2102-3.31380.3861470.3311347149489
3.3138-3.43220.34561410.33051331147289
3.4322-3.56960.33931460.27981319146588
3.5696-3.7320.3321490.25811338148789
3.732-3.92860.31251420.24951332147488
3.9286-4.17460.26241480.21741296144486
4.1746-4.49670.2931470.20471308145586
4.4967-4.94880.25371290.18421307143687
4.9488-5.66380.22431500.18161260141085
5.6638-7.13180.26461400.21851269140984
7.1318-46.94230.2921330.22091251138482
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)
10.08870.09870.16750.04470.12010.33080.13310.7023-0.0550.6887-0.21230.53720.0262-0.5108-0.08881.002-0.2460.2831.4926-0.08620.5581-11.286203.3053277.21
21.193-0.6108-0.11620.31240.05840.02020.24740.3026-0.64230.1759-0.0680.4855-0.2220.1431-0.01220.6472-0.032-0.03620.66850.14550.4251-1.6366200.6172275.5787
30.2534-0.330.22590.4409-0.29920.2020.1182-0.0984-0.08690.12130.1410.30270.0699-0.33010.64160.8224-0.21730.81450.96880.52551.2526-17.0836199.2448270.9587
40.0537-0.0060.02380.01-0.02420.03420.1013-0.192-0.08050.9235-0.2074-0.10720.3468-0.18710.00051.2313-0.015-0.19570.98290.24640.7153-5.5391197.4798282.1994
50.1034-0.15840.06850.2594-0.20830.32240.1493-0.28510.01550.08290.002-0.05640.1633-0.08590.93311.23210.15320.08930.92010.3128-0.839-2.6716205.9133286.7375
60.0387-0.03840.01990.0351-0.01090.04-0.2754-0.1321-0.2762-0.3448-0.08770.56120.44010.1529-0.00090.6255-0.0960.05851.14690.02020.7551-7.4196212.0699274.5345
71.55110.23951.45440.90820.02491.387-0.6104-0.4039-0.90840.3623-0.7577-0.06830.22690.4126-1.42511.7617-0.42970.84851.06990.0130.911-10.6767195.5901285.9792
80.50980.7061.08580.34270.19760.7493-0.19740.8675-0.0593-0.45080.5682-0.57740.15020.3540.00051.0366-0.10710.28370.8284-0.23311.0749-38.4847187.9554242.5155
90.69240.00140.19070.09730.12270.19010.1836-0.7880.73830.0993-1.04410.79770.3073-0.2211-0.04450.9511-0.0720.25651.0371-0.04231.1208-29.2905194.7221269.457
100.44050.51960.42462.33861.37922.42950.4179-0.076-2.3082-0.32510.5573-0.29320.2233-0.31330.7710.48780.0566-0.10641.06440.37161.0236-52.7722190.4686270.7883
110.6199-0.44360.89831.50510.00651.4634-0.22860.0513-0.8227-0.32020.2436-0.5560.21290.129500.8332-0.06690.16870.7361-0.04111.1404-43.233188.31254.2268
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 7 through 22 )B0
2X-RAY DIFFRACTION2chain 'B' and (resid 23 through 45 )B0
3X-RAY DIFFRACTION3chain 'B' and (resid 46 through 54 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 55 through 61 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 62 through 72 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 73 through 82 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 83 through 96 )B0
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 33 )C0
9X-RAY DIFFRACTION9chain 'C' and (resid 34 through 65 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 66 through 82 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 83 through 119 )C0

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