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- PDB-1urn: U1A MUTANT/RNA COMPLEX + GLYCEROL -

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Basic information

Entry
Database: PDB / ID: 1urn
TitleU1A MUTANT/RNA COMPLEX + GLYCEROL
Components
  • PROTEIN (U1A)
  • RNA (5'-R(*AP*AP*UP*CP*CP*AP*UP*UP*GP*CP*AP*CP*UP*CP*CP*GP*G P*AP*UP*UP*U)-3')
KeywordsTRANSCRIPTION/RNA / PROTEIN-RNA COMPLEX / SINGLE STRAND / OVERHANGING BASE / HAIRPIN LOOP / TRANSCRIPTION-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
RNA / RNA (> 10) / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.92 Å
AuthorsOubridge, C. / Ito, N. / Evans, P.R. / Teo, C.-H. / Nagai, K.
CitationJournal: Nature / Year: 1994
Title: Crystal structure at 1.92 A resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin.
Authors: Oubridge, C. / Ito, N. / Evans, P.R. / Teo, C.H. / Nagai, K.
History
DepositionJan 4, 1995Processing site: NDB
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: RNA (5'-R(*AP*AP*UP*CP*CP*AP*UP*UP*GP*CP*AP*CP*UP*CP*CP*GP*G P*AP*UP*UP*U)-3')
Q: RNA (5'-R(*AP*AP*UP*CP*CP*AP*UP*UP*GP*CP*AP*CP*UP*CP*CP*GP*G P*AP*UP*UP*U)-3')
R: RNA (5'-R(*AP*AP*UP*CP*CP*AP*UP*UP*GP*CP*AP*CP*UP*CP*CP*GP*G P*AP*UP*UP*U)-3')
A: PROTEIN (U1A)
B: PROTEIN (U1A)
C: PROTEIN (U1A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,86411
Polymers53,4606
Non-polymers4045
Water7,548419
1
P: RNA (5'-R(*AP*AP*UP*CP*CP*AP*UP*UP*GP*CP*AP*CP*UP*CP*CP*GP*G P*AP*UP*UP*U)-3')
A: PROTEIN (U1A)


Theoretical massNumber of molelcules
Total (without water)17,8202
Polymers17,8202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
Q: RNA (5'-R(*AP*AP*UP*CP*CP*AP*UP*UP*GP*CP*AP*CP*UP*CP*CP*GP*G P*AP*UP*UP*U)-3')
B: PROTEIN (U1A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0405
Polymers17,8202
Non-polymers2203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
R: RNA (5'-R(*AP*AP*UP*CP*CP*AP*UP*UP*GP*CP*AP*CP*UP*CP*CP*GP*G P*AP*UP*UP*U)-3')
C: PROTEIN (U1A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0044
Polymers17,8202
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.000, 97.000, 255.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.49289, 0.86995, -0.01564), (-0.86755, -0.49274, -0.06753), (-0.06646, -0.01971, 0.99759)
Vector: 45.23, 88.184, 4.302)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 6 .. A 96 B 6 .. B 96 0.273 M2 A 6 .. A 96 C 6 .. C 96 0.341 M3 C 3 .. C 96 B 3 .. B 96 0.296 M4 P 1 .. P 12 Q 1 .. Q 12 0.429 M4 P 16 .. P 19 Q 16 .. Q 19 0.633 M5 P 1 .. P 12 R 1 .. R 12 0.597 M5 P 16 .. P 19 R 16 .. R 19 0.697 M6 R 3 .. R 12 Q 3 .. Q 12 0.347 M6 R 16 .. R 19 Q 16 .. Q 19 0.896

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Components

#1: RNA chain RNA (5'-R(*AP*AP*UP*CP*CP*AP*UP*UP*GP*CP*AP*CP*UP*CP*CP*GP*G P*AP*UP*UP*U)-3')


Mass: 6610.940 Da / Num. of mol.: 3 / Source method: obtained synthetically
#2: Protein PROTEIN (U1A)


Mass: 11209.120 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: FETAL BRAIN CDNA LIBRARY / Plasmid: PKN172 / Species (production host): Escherichia coli / Gene (production host): U1A (2-98, Y31H, Q36R) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / Keywords: MUTANT Y31H, Q36R / References: UniProt: P09012
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCOMPND MOLECULE_NAME: U1A. A PROTEIN FROM U1 SMALL RIBONUCLEOPROTEIN (U1SNRNP) THE PROTEIN IS IN ...COMPND MOLECULE_NAME: U1A. A PROTEIN FROM U1 SMALL RIBONUCLEOPROTEIN (U1SNRNP) THE PROTEIN IS IN THE PDB AS 1NRC (CURRENTLY CA ONLY). MOLECULE_NAME: RNA 21MER. SEQUENCE BASED ON HAIRPIN II OF U1 RNA.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 62.06 %
Crystal growMethod: vapor diffusion, hanging drop
Details: VAPOR DIFFUSION, HANGING DROP CRYSTALLIZATION CONDITIONS: 1.8M (NH4)2 SO4, 40MM TRIS-HCL PH 7.0, 5MM SPERMINE TRANSFERRED TO 1.9M (NH4)2 SO4, 40MM TRIS-HCL PH 7.0, 5MM SPERMINE, 25% GLYCEROL ...Details: VAPOR DIFFUSION, HANGING DROP CRYSTALLIZATION CONDITIONS: 1.8M (NH4)2 SO4, 40MM TRIS-HCL PH 7.0, 5MM SPERMINE TRANSFERRED TO 1.9M (NH4)2 SO4, 40MM TRIS-HCL PH 7.0, 5MM SPERMINE, 25% GLYCEROL FOR 15 MINUTES BEFORE FREEZING.
Crystal
*PLUS
Density % sol: 61 %
Crystal grow
*PLUS
Temperature: 20-25 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.8 Mammonium sulfate1reservoir
240 mMTris-HCl1reservoir
35 mMspermine1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.882 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.882 Å / Relative weight: 1
ReflectionRedundancy: 7.7 % / Rmerge(I) obs: 0.038
Reflection shellRedundancy: 7.7 % / Rmerge(I) obs: 0.038
Reflection
*PLUS
Highest resolution: 1.92 Å / Lowest resolution: 33.5 Å / Num. obs: 54400 / % possible obs: 99.7 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.038

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.92→10 Å / σ(F): 0
Details: THE B/Q COMPLEX HAS THE BEST-ORDERED RNA CHAIN, SO IS PROBABLY THE MOST USEFUL TO LOOK AT. THE 3' END OF ALL THREE RNA CHAINS IS POORLY ORDERED. MOST OF U 21 IS OMITTED, BUT RESIDUE U 21 IS ...Details: THE B/Q COMPLEX HAS THE BEST-ORDERED RNA CHAIN, SO IS PROBABLY THE MOST USEFUL TO LOOK AT. THE 3' END OF ALL THREE RNA CHAINS IS POORLY ORDERED. MOST OF U 21 IS OMITTED, BUT RESIDUE U 21 IS ALSO UNCERTAIN IN CHAINS P AND Q.
RfactorNum. reflection
Rwork0.207 -
obs-54007
Refinement stepCycle: LAST / Resolution: 1.92→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2308 1177 25 419 3929
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0350.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0330.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.63
X-RAY DIFFRACTIONp_mcangle_it2.95
X-RAY DIFFRACTIONp_scbond_it3.35
X-RAY DIFFRACTIONp_scangle_it5.27
X-RAY DIFFRACTIONp_plane_restr0.0090.02
X-RAY DIFFRACTIONp_chiral_restr0.1190.15
X-RAY DIFFRACTIONp_singtor_nbd0.1850.3
X-RAY DIFFRACTIONp_multtor_nbd0.2330.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROTIN/PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.92 Å / Lowest resolution: 10 Å / σ(F): 0 / Rfactor obs: 0.207 / Rfactor Rfree: 0.242
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19.3 Å2

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