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- PDB-7d7v: Crystal Structure of the Domain1 of NAD+ Riboswitch with nicotina... -

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Basic information

Entry
Database: PDB / ID: 7d7v
TitleCrystal Structure of the Domain1 of NAD+ Riboswitch with nicotinamide adenine dinucleotide (NAD+) and U1A protein
Components
  • 17delU1A (58-MER)
  • U1 small nuclear ribonucleoprotein A
KeywordsRNA / riboswitch / RNA structure / RNA folding / RNA-ligand interactions / RNA crystallography
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 / 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
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / RNA / RNA (> 10) / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesAcidobacterium capsulatum ATCC 51196 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsChen, H. / Ren, A.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Structural distinctions between NAD+ riboswitch domains 1 and 2 determine differential folding and ligand binding.
Authors: Chen, H. / Egger, M. / Xu, X. / Flemmich, L. / Krasheninina, O. / Sun, A. / Micura, R. / Ren, A.
History
DepositionOct 6, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed
Revision 1.2Dec 23, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 17delU1A (58-MER)
C: U1 small nuclear ribonucleoprotein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,33312
Polymers28,9522
Non-polymers1,38110
Water73941
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.593, 68.593, 333.848
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

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RNA chain / Protein , 2 types, 2 molecules AC

#1: RNA chain 17delU1A (58-MER)


Mass: 18270.900 Da / Num. of mol.: 1 / Mutation: G4del A51del G29C30G31A32 TO AUUGCACUCC
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidobacterium capsulatum ATCC 51196 (bacteria)
Production host: in vitro transcription vector pT7-TP(deltai) (others)
#2: Protein U1 small nuclear ribonucleoprotein A / U1A


Mass: 10681.421 Da / Num. of mol.: 1 / Mutation: Y27H, Q32R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPA / Production host: bacterium (bacteria) / References: UniProt: P09012

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Non-polymers , 4 types, 51 molecules

#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.92 Å3/Da / Density % sol: 68.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Mg(OAc)2, 0.1 M C2H6AsNaO2, pH 6.5, 30% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 12481 / % possible obs: 99.6 % / Redundancy: 21.4 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.016 / Rrim(I) all: 0.084 / Χ2: 0.842 / Net I/σ(I): 5.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.919.80.76111910.9570.1540.7790.42599.2
2.9-3.0221.90.39711950.9780.0760.4060.43999.1
3.02-3.1521.30.22511940.9930.0430.2290.46899.2
3.15-3.3221.10.15512050.9960.030.1580.4999.7
3.32-3.5320.50.12612130.9980.0250.1290.51599.6
3.53-3.819.80.09812440.9980.020.10.54599.6
3.8-4.1818.10.08112150.9990.0170.0830.57899.8
4.18-4.7921.10.06412670.9990.0130.0660.64799.9
4.79-6.0323.50.05613050.9990.0110.0570.621100
6.03-5025.60.06114520.9990.0120.0622.763100

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Processing

Software
NameVersionClassification
PHENIXv1.14refinement
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→50 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.308 602 -
Rwork0.25 --
obs-12306 99.11 %
Displacement parametersBiso max: 139.72 Å2 / Biso mean: 76.524 Å2 / Biso min: 31.73 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms746 1242 52 41 2081
LS refinement shellResolution: 2.8→3.0795 Å
RfactorNum. reflection
Rfree0.3619 153
Rwork0.3608 -
obs-2810

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