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- PDB-3mut: Crystal Structure of the G20A/C92U mutant c-di-GMP riboswith boun... -

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Basic information

Entry
Database: PDB / ID: 3mut
TitleCrystal Structure of the G20A/C92U mutant c-di-GMP riboswith bound to c-di-GMP
Components
  • G20A/C92U mutant c-di-GMP riboswitch
  • U1 small nuclear ribonucleoprotein A
KeywordsRNA BINDING PROTEIN/RNA / RNA / riboswitch / c-di-GMP / 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 / RNA / RNA (> 10) / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsStrobel, S.A. / Smith, K.D.
CitationJournal: Biochemistry / Year: 2010
Title: Structural and biochemical determinants of ligand binding by the c-di-GMP riboswitch .
Authors: Smith, K.D. / Lipchock, S.V. / Livingston, A.L. / Shanahan, C.A. / Strobel, S.A.
History
DepositionMay 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 6, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_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 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: G20A/C92U mutant c-di-GMP riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0075
Polymers41,2682
Non-polymers7393
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-15 kcal/mol
Surface area19140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.690, 45.430, 78.930
Angle α, β, γ (deg.)90.00, 95.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 11340.315 Da / Num. of mol.: 1 / Fragment: UNP residues 1-98 / 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 G20A/C92U mutant c-di-GMP riboswitch


Mass: 29927.758 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: in vitro transcribed from linear DNA
#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.: 1 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#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.: 21 / 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: 2.15 Å3/Da / Density % sol: 42.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 25% PEG 550 MME, 5 mM MgSO4, 50 mM MES, pH 6.0, 300 mM NaCl. Streak seeding after 3-6 hours, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 19, 2009 / Details: Pt-coated mirror
RadiationMonochromator: Si-111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3→80 Å / Num. all: 6668 / Num. obs: 6354 / % possible obs: 98 % / Redundancy: 6.5 % / Biso Wilson estimate: 101.7 Å2 / Rmerge(I) obs: 0.177 / Net I/σ(I): 8.8
Reflection shellResolution: 3→3.1 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 1.9 / Num. unique all: 216 / % possible all: 84.7

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3IRW

3irw


Resolution: 3→49.49 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.884 / SU B: 77.811 / SU ML: 0.673 / Cross valid method: THROUGHOUT / ESU R Free: 0.547 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2679 322 4.8 %RANDOM
Rwork0.23259 ---
obs0.23435 6354 96.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 85.96 Å2
Baniso -1Baniso -2Baniso -3
1-3.51 Å20 Å26.43 Å2
2---6.38 Å20 Å2
3---4.02 Å2
Refinement stepCycle: LAST / Resolution: 3→49.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms734 1983 48 21 2786
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0213030
X-RAY DIFFRACTIONr_angle_refined_deg1.1712.7714574
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.404589
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.43723.23534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.7715150
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.213156
X-RAY DIFFRACTIONr_chiral_restr0.0530.2577
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021530
X-RAY DIFFRACTIONr_mcbond_it1.3145449
X-RAY DIFFRACTIONr_mcangle_it2.29910727
X-RAY DIFFRACTIONr_scbond_it1.29852581
X-RAY DIFFRACTIONr_scangle_it2.218103846
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 15 -
Rwork0.303 216 -
obs-216 93.15 %
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)
110.2785-1.1689-2.261930.5923-4.707410.48241.12910.66261.1342-0.4782-0.04410.5001-0.45341.2048-1.0850.23820.0653-0.00171.13570.09870.4215-5.969618.0518-38.6103
22.6350.557-0.81362.4247-0.55362.48190.22710.0505-0.16880.0755-0.04690.2369-0.1328-0.5152-0.18020.40170.05150.08050.25060.00950.3755-8.0154-2.74030.7024
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1P7 - 93
2X-RAY DIFFRACTION2R8 - 98

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