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- PDB-6sqn: Structure of the U1A variant A1-98 Y31H/Q36R/F56W triple mutant c... -

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Basic information

Entry
Database: PDB / ID: 6sqn
TitleStructure of the U1A variant A1-98 Y31H/Q36R/F56W triple mutant co-crystallized with RNA
Components
  • RNA hairpin
  • U1 small nuclear ribonucleoprotein A
KeywordsRNA BINDING PROTEIN / U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A / U1A / RNA hairpin / co-crystallization
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
RNA / RNA (> 10) / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsRosenbach, H. / Span, I.
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Expanding crystallization tools for nucleic acid complexes using U1A protein variants.
Authors: Rosenbach, H. / Victor, J. / Borggrafe, J. / Biehl, R. / Steger, G. / Etzkorn, M. / Span, I.
History
DepositionSep 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: U1 small nuclear ribonucleoprotein A
B: U1 small nuclear ribonucleoprotein A
C: U1 small nuclear ribonucleoprotein A
X: RNA hairpin
Y: RNA hairpin
Z: RNA hairpin


Theoretical massNumber of molelcules
Total (without water)53,5776
Polymers53,5776
Non-polymers00
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8190 Å2
ΔGint-26 kcal/mol
Surface area20640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.938, 96.938, 258.730
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein U1 small nuclear ribonucleoprotein A / U1A


Mass: 11248.156 Da / Num. of mol.: 3
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
#2: RNA chain RNA hairpin


Mass: 6610.940 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 3.36 Å3/Da / Density % sol: 63.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.2 M ammonium sulfate, 0.1 M tri-potassium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.05→51.74 Å / Num. obs: 49417 / % possible obs: 100 % / Redundancy: 38 % / CC1/2: 0.999 / Rmerge(I) obs: 0.199 / Rrim(I) all: 0.201 / Net I/σ(I): 18.2
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 39.6 % / Rmerge(I) obs: 2.383 / Num. unique obs: 2231 / CC1/2: 0.683 / Rrim(I) all: 2.414 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1URN

1urn


Resolution: 2.05→48.52 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.229 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.137
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2488 2509 5.1 %RANDOM
Rwork0.2297 ---
obs0.2306 46908 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 107.5 Å2 / Biso mean: 36.892 Å2 / Biso min: 14.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å2-0 Å2
3---0.14 Å2
Refinement stepCycle: final / Resolution: 2.05→48.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2335 993 0 95 3423
Biso mean---33.89 -
Num. residues----336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0123484
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182784
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.5214901
X-RAY DIFFRACTIONr_angle_other_deg1.4231.8286511
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9595284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.00221.463123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.86715471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8521518
X-RAY DIFFRACTIONr_chiral_restr0.0910.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023114
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02749
LS refinement shellResolution: 2.05→2.053 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 171 -
Rwork0.301 3372 -
all-3543 -
obs--99.33 %

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