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- PDB-6sr7: Structure of the U1A variant A1-98 Y31H/Q36R/K98W -

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Basic information

Entry
Database: PDB / ID: 6sr7
TitleStructure of the U1A variant A1-98 Y31H/Q36R/K98W
ComponentsU1 small nuclear ribonucleoprotein A
KeywordsRNA BINDING PROTEIN / U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A / U1A
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
U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 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 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Derived calculations
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
DDD: U1 small nuclear ribonucleoprotein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6855
Polymers45,5894
Non-polymers961
Water1,45981
1
AAA: U1 small nuclear ribonucleoprotein A


Theoretical massNumber of molelcules
Total (without water)11,3971
Polymers11,3971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: U1 small nuclear ribonucleoprotein A


Theoretical massNumber of molelcules
Total (without water)11,3971
Polymers11,3971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: U1 small nuclear ribonucleoprotein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4932
Polymers11,3971
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
DDD: U1 small nuclear ribonucleoprotein A


Theoretical massNumber of molelcules
Total (without water)11,3971
Polymers11,3971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.258, 76.258, 151.481
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
U1 small nuclear ribonucleoprotein A / U1A


Mass: 11397.345 Da / Num. of mol.: 4
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.42 Å3/Da / Density % sol: 49.08 %
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: Dec 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.86→68.11 Å / Num. obs: 38415 / % possible obs: 100 % / Redundancy: 24.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.142 / Rrim(I) all: 0.145 / Net I/σ(I): 14.8
Reflection shellResolution: 1.86→1.89 Å / Rmerge(I) obs: 0.923 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1842 / CC1/2: 0.54 / Rrim(I) all: 0.956 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→68.11 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.563 / SU ML: 0.106 / Cross valid method: FREE R-VALUE / ESU R: 0.147 / ESU R Free: 0.139
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.256 1920 5.008 %
Rwork0.2214 --
all0.223 --
obs-38337 99.945 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.351 Å2
Baniso -1Baniso -2Baniso -3
1--0.551 Å20 Å20 Å2
2---0.551 Å20 Å2
3---1.103 Å2
Refinement stepCycle: LAST / Resolution: 1.86→68.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2902 0 5 81 2988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132973
X-RAY DIFFRACTIONr_bond_other_d0.0030.0172888
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.6433981
X-RAY DIFFRACTIONr_angle_other_deg1.3651.5846698
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5085352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.83121.688154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53515589
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0751520
X-RAY DIFFRACTIONr_chiral_restr0.0810.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023221
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02647
X-RAY DIFFRACTIONr_nbd_refined0.2010.2467
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.22372
X-RAY DIFFRACTIONr_nbtor_refined0.1650.21390
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1260.21251
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.10.275
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1550.215
X-RAY DIFFRACTIONr_nbd_other0.2340.299
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.160.217
X-RAY DIFFRACTIONr_mcbond_it2.4082.7071414
X-RAY DIFFRACTIONr_mcbond_other2.4052.7051413
X-RAY DIFFRACTIONr_mcangle_it3.5134.0411761
X-RAY DIFFRACTIONr_mcangle_other3.5134.0431762
X-RAY DIFFRACTIONr_scbond_it3.1833.1791559
X-RAY DIFFRACTIONr_scbond_other3.1813.1791556
X-RAY DIFFRACTIONr_scangle_it5.0344.572219
X-RAY DIFFRACTIONr_scangle_other5.0384.5682214
X-RAY DIFFRACTIONr_lrange_it6.47830.6473136
X-RAY DIFFRACTIONr_lrange_other6.4830.6343132
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.9080.3271140.312625X-RAY DIFFRACTION99.4915
1.908-1.9610.3331340.2722589X-RAY DIFFRACTION100
1.961-2.0170.2641500.2422490X-RAY DIFFRACTION100
2.017-2.0790.2911310.2332433X-RAY DIFFRACTION100
2.079-2.1480.2571380.2182354X-RAY DIFFRACTION100
2.148-2.2230.2371200.2062283X-RAY DIFFRACTION100
2.223-2.3070.2541150.2022241X-RAY DIFFRACTION100
2.307-2.4010.2791140.2162134X-RAY DIFFRACTION100
2.401-2.5080.231080.2112052X-RAY DIFFRACTION100
2.508-2.630.2431140.2111972X-RAY DIFFRACTION100
2.63-2.7720.2651150.2231856X-RAY DIFFRACTION100
2.772-2.9410.278930.2451790X-RAY DIFFRACTION100
2.941-3.1430.293750.2381686X-RAY DIFFRACTION100
3.143-3.3950.25630.2151606X-RAY DIFFRACTION100
3.395-3.7190.248700.2161462X-RAY DIFFRACTION100
3.719-4.1580.169750.1771333X-RAY DIFFRACTION100
4.158-4.80.221620.1821180X-RAY DIFFRACTION100
4.8-5.8780.32560.2361027X-RAY DIFFRACTION100
5.878-8.3060.252430.264810X-RAY DIFFRACTION100
8.306-68.110.319300.246494X-RAY DIFFRACTION100

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