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- PDB-3irw: Structure of a c-di-GMP riboswitch from V. cholerae -

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Basic information

Entry
Database: PDB / ID: 3irw
TitleStructure of a c-di-GMP riboswitch from V. cholerae
Components
  • U1 small nuclear ribonucleoprotein A
  • c-di-GMP Riboswitch
KeywordsRNA binding protein/RNA / riboswitch / c-di-GMP / RNA / 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-C2E / IRIDIUM HEXAMMINE ION / RNA / RNA (> 10) / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesHomo sapiens (human)
Vibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsSmith, K.D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Structural basis of ligand binding by a c-di-GMP riboswitch.
Authors: Smith, K.D. / Lipchock, S.V. / Ames, T.D. / Wang, J. / Breaker, R.R. / Strobel, S.A.
History
DepositionAug 24, 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_conn / 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_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
P: U1 small nuclear ribonucleoprotein A
R: c-di-GMP Riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,67214
Polymers41,2832
Non-polymers3,38912
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-34 kcal/mol
Surface area18100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.461, 45.123, 76.573
Angle α, β, γ (deg.)90.00, 96.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / RNA chain , 2 types, 2 molecules PR

#1: Protein U1 small nuclear ribonucleoprotein A / U1 snRNP protein A / U1A protein / U1-A


Mass: 11340.315 Da / Num. of mol.: 1 / Fragment: RNA Binding Domain / Mutation: Y31H, Q36R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPA / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: P09012
#2: RNA chain c-di-GMP Riboswitch


Mass: 29942.773 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: In vitro synthesis from a plasmid dna template of natural sequence from vibrio cholerae
Source: (synth.) Vibrio cholerae (bacteria)

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Non-polymers , 4 types, 104 molecules

#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 / Cyclic di-GMP


Mass: 690.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#4: Chemical
ChemComp-IRI / IRIDIUM HEXAMMINE ION


Mass: 294.400 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: H18IrN6
#5: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.06 Å3/Da / Density % sol: 40.15 %
Crystal growTemperature: 298 K / pH: 6
Details: 22% PEG550mme, 50 mM MES, pH 6.0, 5 mM MgSO4, 300 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1050, 1.1054, 1.0762
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 26, 2009
Details: CRYOGENICALLY COOLED DOUBLE CRYSTAL MONOCHROMETER WITH HORIZONTAL FOCUSING SAGITTAL BEND SECOND MONO CRYSTAL WITH 4:1 MAGNIFICATION RATIO AND VERTICALLY FOCUSING MIRROR.
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMETER WITH HORIZONTAL FOCUSING SAGITTAL BEND SECOND MONO CRYSTAL WITH 4:1 MAGNIFICATION RATIO AND VERTICALLY FOCUSING MIRROR.
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.1051
21.10541
31.07621
ReflectionResolution: 2.7→50 Å / Num. obs: 8935 / % possible obs: 94.8 % / Observed criterion σ(I): 1.9 / Redundancy: 2.7 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 12.5
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 1.9 / % possible all: 82.4

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Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEphasing
REFMAC5.4.0077refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.7→43.69 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / SU ML: 0.32 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R Free: 0.411
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 439 4.9 %RANDOM
Rwork0.196 ---
obs0.199 8497 94.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.651 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20 Å21.44 Å2
2---4.89 Å20 Å2
3---4.4 Å2
Refinement stepCycle: LAST / Resolution: 2.7→43.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms734 1961 111 92 2898
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0213045
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9532.7764631
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.686589
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.39223.23534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.32715150
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.926156
X-RAY DIFFRACTIONr_chiral_restr
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021519
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.125449
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.84810727
X-RAY DIFFRACTIONr_scbond_it1.90152596
X-RAY DIFFRACTIONr_scangle_it3.102103904
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 19 -
Rwork0.311 477 -
obs--72.51 %
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)
19.2098-0.4908-0.80683.56361.64020.79180.0919-0.7027-0.1654-0.01150.0286-0.11360.3680.297-0.12050.25630.14550.11240.35140.03790.053218.422-30.654-11.934
21.1305-0.9168-0.94292.05940.02341.98430.28260.02110.0458-0.2669-0.2328-0.09990.06560.152-0.04980.20470.0236-0.01940.1259-0.00470.07094.529-25.86-6.55
30.183-0.3101-0.2750.69660.8511.27970.0584-0.01680.1455-0.0360.0024-0.10030.00430.0515-0.06070.2272-0.07770.01680.2474-0.00870.188210.587-22.0712.318
40000000000000000.1906000.190600.19065.204-4.45937.533
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1R8 - 14
2X-RAY DIFFRACTION1R92 - 97
3X-RAY DIFFRACTION2R15 - 47
4X-RAY DIFFRACTION3R48 - 91
5X-RAY DIFFRACTION3R660 - 669
6X-RAY DIFFRACTION4P7 - 96

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