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

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Basic information

Entry
Database: PDB / ID: 3muv
TitleCrystal Structure of the G20A/C92U mutant c-di-GMP riboswith bound to c-di-AMP
Components
  • G20A/C92U mutant c-di-GMP riboswitch
  • U1 small nuclear ribonucleoprotein A
KeywordsRNA binding PROTEIN/rna / RNA / riboswitch / c-di-AMP / 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-2BA / 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
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 1.2Sep 6, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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 / _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.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

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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)41,9514
Polymers41,2682
Non-polymers6832
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-15 kcal/mol
Surface area18690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.870, 45.898, 75.696
Angle α, β, γ (deg.)90.00, 95.48, 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-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.: 1 / Source method: obtained synthetically / Formula: C20H24N10O12P2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.05 Å3/Da / Density % sol: 39.93 %
Crystal growTemperature: 298 K / pH: 6
Details: 25% PEG 550 MME, 5 mM MgSO4, 50 mM MES, pH 6.0, 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: X25 / Wavelength: 1.1
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: 3.2→80 Å / Num. obs: 4829 / % possible obs: 90 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.197 / Net I/σ(I): 5.6
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 2.2 / % possible all: 63.6

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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: 3.2→48.65 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26 244 -RANDOM
Rwork0.187 ---
obs0.19 4829 90.3 %-
Displacement parametersBiso mean: 41.09 Å2
Baniso -1Baniso -2Baniso -3
1-2.4 Å20 Å23.54 Å2
2---4.9 Å20 Å2
3---3.17 Å2
Refinement stepCycle: LAST / Resolution: 3.2→48.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms734 1960 45 16 2755
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.005
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.112
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.054
X-RAY DIFFRACTIONr_gen_planes_refined0.002
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.28 Å
RfactorNum. reflection% reflection
Rfree0.292 13 -
Rwork0.268 --
obs--65.45 %
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)
14.0414-0.9426-1.82018.34731.50895.96360.16270.03040.1401-0.2249-0.17410.5480.1029-0.08670.01130.0147-0.0044-0.00970.0757-0.00220.0445.5613-5.384437.4749
21.7297-0.6927-0.56211.45760.45061.8520.120.14460.1799-0.03430.0062-0.3486-0.16270.259-0.12620.1123-0.06160.04780.0898-0.01650.08378.2087-26.03410.2245
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1P7 - 93
2X-RAY DIFFRACTION2R8 - 98

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