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

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Basic information

Entry
Database: PDB / ID: 6sqq
TitleStructure of the U1A variant A1-98 Y31H/Q36R/F56W triple mutant in complex with RNA obtained by soaking
Components
  • RNA hairpin
  • U1 small nuclear ribonucleoprotein A
KeywordsRNA BINDING PROTEIN / U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A / U1A / RNA hairpin / soaking
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
RNA / RNA (> 10) / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: U1 small nuclear ribonucleoprotein A
BBB: U1 small nuclear ribonucleoprotein A
CCC: U1 small nuclear ribonucleoprotein A
XXX: RNA hairpin
YYY: RNA hairpin
ZZZ: RNA hairpin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9957
Polymers53,9716
Non-polymers241
Water46826
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8250 Å2
ΔGint-25 kcal/mol
Surface area20200 Å2
Unit cell
Length a, b, c (Å)96.080, 96.080, 258.010
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: 11379.352 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: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.62 Å3/Da / Density % sol: 65.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.2 M ammonium sulfate, 0.2 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: 2.37→51.6 Å / Num. obs: 29657 / % possible obs: 100 % / Redundancy: 38.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.29 / Rrim(I) all: 0.293 / Net I/σ(I): 12.4
Reflection shellResolution: 2.37→2.41 Å / Redundancy: 40.2 % / Rmerge(I) obs: 2.601 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1460 / CC1/2: 0.753 / Rrim(I) all: 2.633 / % possible all: 99.9

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Processing

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

1urn


Resolution: 2.37→51.031 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.894 / SU B: 8.263 / SU ML: 0.188 / Cross valid method: FREE R-VALUE / ESU R: 0.28 / ESU R Free: 0.244
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2941 1498 5.066 %
Rwork0.2452 --
all0.248 --
obs-29570 99.939 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.941 Å2
Baniso -1Baniso -2Baniso -3
1-0.775 Å20.387 Å20 Å2
2--0.775 Å20 Å2
3----2.513 Å2
Refinement stepCycle: LAST / Resolution: 2.37→51.031 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2269 1008 1 26 3304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123443
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182729
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.5164849
X-RAY DIFFRACTIONr_angle_other_deg1.3231.8396381
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0595277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59121.28125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.20115459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.341519
X-RAY DIFFRACTIONr_chiral_restr0.0870.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023076
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02754
X-RAY DIFFRACTIONr_nbd_refined0.1990.2504
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.22570
X-RAY DIFFRACTIONr_nbtor_refined0.1910.21470
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21321
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.274
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1150.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0830.213
X-RAY DIFFRACTIONr_nbd_other0.2310.227
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0480.23
X-RAY DIFFRACTIONr_mcbond_it2.9734.1091111
X-RAY DIFFRACTIONr_mcbond_other2.9724.1071110
X-RAY DIFFRACTIONr_mcangle_it4.1356.1421384
X-RAY DIFFRACTIONr_mcangle_other4.1346.1441385
X-RAY DIFFRACTIONr_scbond_it4.2594.9872332
X-RAY DIFFRACTIONr_scbond_other4.2514.9852331
X-RAY DIFFRACTIONr_scangle_it6.0297.3723464
X-RAY DIFFRACTIONr_scangle_other6.0297.3743465
X-RAY DIFFRACTIONr_lrange_it7.47247.0473865
X-RAY DIFFRACTIONr_lrange_other7.47447.0443864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.4310.3851100.3282015X-RAY DIFFRACTION99.7184
2.431-2.4980.373960.3151986X-RAY DIFFRACTION100
2.498-2.5710.3061020.2761933X-RAY DIFFRACTION100
2.571-2.650.3271050.2831871X-RAY DIFFRACTION100
2.65-2.7360.361040.2641802X-RAY DIFFRACTION99.9476
2.736-2.8330.333910.31755X-RAY DIFFRACTION99.9459
2.833-2.9390.389940.291691X-RAY DIFFRACTION100
2.939-3.0590.345810.2751651X-RAY DIFFRACTION100
3.059-3.1950.347730.2731611X-RAY DIFFRACTION99.9407
3.195-3.3510.254680.2571518X-RAY DIFFRACTION100
3.351-3.5330.267680.2291460X-RAY DIFFRACTION100
3.533-3.7470.233690.21372X-RAY DIFFRACTION100
3.747-4.0060.259840.1911289X-RAY DIFFRACTION100
4.006-4.3260.247830.1911196X-RAY DIFFRACTION100
4.326-4.7390.24660.1811123X-RAY DIFFRACTION100
4.739-5.2980.265630.2161032X-RAY DIFFRACTION100
5.298-6.1180.335480.261917X-RAY DIFFRACTION100
6.118-7.4910.267430.26806X-RAY DIFFRACTION100
7.491-10.590.286310.244646X-RAY DIFFRACTION100
10.59-51.0310.45190.369398X-RAY DIFFRACTION99.0499

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