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

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Basic information

Entry
Database: PDB / ID: 8gxc
TitleCrystal structure of NAD+ -II riboswitch in complex with NMN
Components
  • 61-mer RNA
  • U1 small nuclear ribonucleoprotein A
KeywordsPROTEIN/RNA / riboswitch / coenzyme / 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
BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / 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: 2.5 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 1.2Nov 8, 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
A: 61-mer RNA
B: 61-mer RNA
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)96,70225
Polymers95,6437
Non-polymers1,05918
Water2,918162
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.588, 122.677, 154.378
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: RNA chain 61-mer RNA


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-NMN / BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / NICOTINAMIDE MONONUCLEOTIDE


Mass: 335.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H16N2O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.9 Å3/Da / Density % sol: 57.59 %
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: 1.102 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.102 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 38926 / % possible obs: 100 % / Redundancy: 13 % / Rmerge(I) obs: 0.242 / Rpim(I) all: 0.071 / Rrim(I) all: 0.253 / Χ2: 1.12 / Net I/σ(I): 2.5 / Num. measured all: 505554
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.5912.21.06937800.8390.3131.1160.49399.9
2.59-2.6913.10.87138300.9240.2480.9060.525100
2.69-2.8213.50.70938490.9350.2010.7380.572100
2.82-2.9613.40.53738320.9660.1520.5580.633100
2.96-3.1512.70.35438620.9690.1040.3690.857100
3.15-3.3913.30.2838770.9840.0810.2921.121100
3.39-3.7313.70.2538730.9890.0720.261.331100
3.73-4.2713.10.2239050.9740.0640.231.594100
4.27-5.3812.50.20639620.9830.0610.2151.918100
5.38-5012.30.17741560.9810.0540.1852.106100

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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: 8GXB

8gxb


Resolution: 2.5→39.53 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 33.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2689 1888 4.9 %
Rwork0.2242 36669 -
obs0.2264 38557 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.32 Å2 / Biso mean: 59.3569 Å2 / Biso min: 33.47 Å2
Refinement stepCycle: final / Resolution: 2.5→39.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3809 2624 60 162 6655
Biso mean--57.35 58.19 -
Num. residues----591
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.570.37081520.34127352887100
2.57-2.640.41651520.331227622914100
2.64-2.730.38241540.326627802934100
2.73-2.830.43361280.317127992927100
2.83-2.940.35361450.310527892934100
2.94-3.070.34591350.2752791292699
3.07-3.230.31041650.255727892954100
3.23-3.440.27381420.218527992941100
3.44-3.70.32371310.221628122943100
3.7-4.070.24781380.207428582996100
4.07-4.660.24571440.188128512995100
4.66-5.870.20041400.189728953035100
5.87-39.530.20291620.186430093171100

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