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- PDB-8gxb: Crystal structure of NAD+ -II riboswitch in complex with NAD+ -

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Basic information

Entry
Database: PDB / ID: 8gxb
TitleCrystal structure of NAD+ -II riboswitch in complex with NAD+
Components
  • NAD+ II riboswitch
  • U1 small nuclear ribonucleoprotein A
KeywordsPROTEIN/RNA / riboswitch / NAD+ / noncoding RNA / RNA / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / RNA / RNA (> 10) / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesStreptococcus sp. (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsXu, X.C. / Ren, A.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Structure-based investigations of the NAD+-II riboswitch.
Authors: Xu, X. / Egger, M. / Li, C. / Chen, H. / Micura, R. / Ren, A.
History
DepositionSep 19, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 29, 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
A: NAD+ II riboswitch
B: NAD+ II riboswitch
C: U1 small nuclear ribonucleoprotein A
D: U1 small nuclear ribonucleoprotein A
E: U1 small nuclear ribonucleoprotein A
F: U1 small nuclear ribonucleoprotein A
G: U1 small nuclear ribonucleoprotein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,43228
Polymers95,6437
Non-polymers1,78921
Water5,314295
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.460, 122.611, 154.649
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: RNA chain NAD+ II riboswitch


Mass: 19798.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. (bacteria)
Production host: in vitro transcription vector pT7-TP(deltai) (others)
#2: Protein
U1 small nuclear ribonucleoprotein A / U1 snRNP A / U1-A / U1A


Mass: 11209.120 Da / Num. of mol.: 5 / Mutation: Y31H, Q36R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPA / Production host: Escherichia coli (E. coli) / References: UniProt: P09012
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.85 Å3/Da / Density % sol: 51.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2M KCl, 0.01M MgCl2, 0.05M MES pH 5.6, 5% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 57920 / % possible obs: 95 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.989 / Χ2: 0.056 / Net I/σ(I): 2.9 / Num. measured all: 734175
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.15-2.235.31.07683460.475172.9
2.23-2.325.70.94395460.489182.5
2.32-2.426.30.84108630.494194.4
2.42-2.556.90.701115140.499199.9
2.55-2.7170.488115270.5431100
2.71-2.926.80.313114790.6021100
2.92-3.217.30.187115330.7081100
3.21-3.6770.127115190.8971100
3.67-4.637.30.101114980.9671100
4.63-3070.079115580.8561100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LAS

6las


Resolution: 2.15→28.73 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2685 2910 5.04 %
Rwork0.2191 --
obs0.2215 57691 95.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→28.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3791 2624 107 295 6817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086886
X-RAY DIFFRACTIONf_angle_d1.2429874
X-RAY DIFFRACTIONf_dihedral_angle_d21.6932011
X-RAY DIFFRACTIONf_chiral_restr0.0661195
X-RAY DIFFRACTIONf_plane_restr0.008779
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.180.40981140.34721907X-RAY DIFFRACTION72
2.18-2.220.41831010.34182091X-RAY DIFFRACTION77
2.22-2.260.42031280.32392166X-RAY DIFFRACTION82
2.26-2.30.39811360.3242293X-RAY DIFFRACTION85
2.3-2.350.37541350.31962488X-RAY DIFFRACTION93
2.35-2.40.32441570.31742614X-RAY DIFFRACTION96
2.4-2.460.37261480.30532665X-RAY DIFFRACTION100
2.46-2.520.32791440.30372711X-RAY DIFFRACTION100
2.52-2.590.34951410.28672706X-RAY DIFFRACTION100
2.59-2.660.37261330.2852730X-RAY DIFFRACTION100
2.66-2.750.34321200.28022739X-RAY DIFFRACTION100
2.75-2.850.28841430.26312700X-RAY DIFFRACTION100
2.85-2.960.32191390.28432712X-RAY DIFFRACTION100
2.96-3.10.32381550.24872712X-RAY DIFFRACTION100
3.1-3.260.25531230.2222764X-RAY DIFFRACTION100
3.26-3.460.25431610.20422708X-RAY DIFFRACTION100
3.46-3.730.2251480.21012749X-RAY DIFFRACTION100
3.73-4.10.2451450.18252796X-RAY DIFFRACTION100
4.1-4.70.23031400.17332774X-RAY DIFFRACTION100
4.7-5.910.22281410.16712818X-RAY DIFFRACTION100
5.91-28.730.21841580.18182938X-RAY DIFFRACTION100

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