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- PDB-3mxh: Native structure of a c-di-GMP riboswitch from V. cholerae -

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Basic information

Entry
Database: PDB / ID: 3mxh
TitleNative structure of a c-di-GMP riboswitch from V. cholerae
Components
  • U1 small nuclear ribonucleoprotein A
  • c-di-GMP riboswitch
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: 2.3 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 7, 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 / pdbx_initial_refinement_model / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_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: c-di-GMP riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0958
Polymers41,2832
Non-polymers8126
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-40 kcal/mol
Surface area19250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.243, 45.652, 80.248
Angle α, β, γ (deg.)90.00, 93.74, 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 c-di-GMP riboswitch


Mass: 29942.773 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: in vitro transcribed from linear DNA
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.22 Å3/Da / Density % sol: 44.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / 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: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 26, 2009 / Details: VERTICALLY FOCUSING MIRROR
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→80 Å / Num. all: 15607 / Num. obs: 15201 / % possible obs: 97.4 % / Redundancy: 5.3 % / Biso Wilson estimate: 62.4 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 14.6
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1019 / % possible all: 89.9

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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: 2.3→30.34 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 17.433 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23913 816 5.1 %RANDOM
Rwork0.20157 ---
obs0.20342 15201 97.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.319 Å2
Baniso -1Baniso -2Baniso -3
1-2.92 Å20 Å23.33 Å2
2---0.5 Å20 Å2
3----1.98 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms712 1984 51 169 2916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0213020
X-RAY DIFFRACTIONr_angle_refined_deg0.9362.7774567
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.313586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97223.23534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.2715144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.356156
X-RAY DIFFRACTIONr_chiral_restr0.0460.2573
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021519
X-RAY DIFFRACTIONr_mcbond_it0.9185434
X-RAY DIFFRACTIONr_mcangle_it1.57610703
X-RAY DIFFRACTIONr_scbond_it1.38252586
X-RAY DIFFRACTIONr_scangle_it2.122103863
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 49 -
Rwork0.465 1019 -
obs-1019 90.66 %
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)
117.12762.51071.18957.0041-1.96067.0560.1639-0.8546-0.53770.849-0.17760.41280.091-0.38560.01370.46320.01990.16010.29310.01950.1569-14.2399-4.380322.302
22.22310.7402-1.47792.5465-0.03422.2971-0.04680.4048-0.0374-0.41740.06280.1106-0.0508-0.2331-0.0160.28170.0457-0.0720.10410.02790.1784-2.2192-1.7566-6.0709
32.08780.70140.63732.3987-0.4765.0541-0.01470.29560.0208-0.16950.01960.3893-0.3833-0.625-0.00490.25490.08140.01890.24560.02220.319-15.0206-4.0062.999
49.28112.4823-3.61523.3611-4.25775.42480.9414-0.05541.76230.29470.40191.1096-0.4251-0.3753-1.34320.34270.0481-0.08760.5249-0.07481.1319-17.716810.0842-32.7336
58.55981.6941-1.420126.6322-7.78610.88290.56420.51061.8324-0.9445-0.06860.4835-0.61970.2963-0.49560.24820.052-0.00080.35780.02150.796-7.016816.3283-40.3012
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1R8 - 20
2X-RAY DIFFRACTION2R21 - 65
3X-RAY DIFFRACTION3R75 - 98
4X-RAY DIFFRACTION4R660 - 669
5X-RAY DIFFRACTION5P7 - 93

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