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- PDB-1a9n: CRYSTAL STRUCTURE OF THE SPLICEOSOMAL U2B''-U2A' PROTEIN COMPLEX ... -

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Basic information

Entry
Database: PDB / ID: 1a9n
TitleCRYSTAL STRUCTURE OF THE SPLICEOSOMAL U2B''-U2A' PROTEIN COMPLEX BOUND TO A FRAGMENT OF U2 SMALL NUCLEAR RNA
Components
  • RNA (5'-R(*CP*CP*UP*GP*GP*UP*AP*UP*UP*GP*CP*AP*GP*UP*AP*CP*CP*UP*CP*CP*AP*GP* GP*U)-3')
  • SPLICEOSOMAL U2B''
  • U2A'
KeywordsRNA BINDING PROTEIN/RNA / COMPLEX (NUCLEAR PROTEIN-RNA) / RNA / SNRNP / RIBONUCLEOPROTEIN / RNA BINDING PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


small nuclear ribonucleoprotein complex / U2-type precatalytic spliceosome / U2-type spliceosomal complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U2 snRNP / U1 snRNP / U2 snRNA binding / U1 snRNA binding / catalytic step 2 spliceosome ...small nuclear ribonucleoprotein complex / U2-type precatalytic spliceosome / U2-type spliceosomal complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U2 snRNP / U1 snRNP / U2 snRNA binding / U1 snRNA binding / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / fibrillar center / cytoplasmic ribonucleoprotein granule / spermatogenesis / nuclear speck / nuclear body / RNA binding / nucleoplasm / nucleus
Similarity search - Function
U2 small nuclear ribonucleoprotein B'', RNA recognition motif 2 / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 1 / U2 small nuclear ribonucleoprotein A' / U2A'/phosphoprotein 32 family A, C-terminal / occurring C-terminal to leucine-rich repeats / Leucine-rich repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / RRM (RNA recognition motif) domain ...U2 small nuclear ribonucleoprotein B'', RNA recognition motif 2 / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 1 / U2 small nuclear ribonucleoprotein A' / U2A'/phosphoprotein 32 family A, C-terminal / occurring C-terminal to leucine-rich repeats / Leucine-rich repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / RRM (RNA recognition motif) domain / Leucine-rich repeat profile. / Leucine-rich repeat / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Leucine-rich repeat domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / U2 small nuclear ribonucleoprotein B'' / U2 small nuclear ribonucleoprotein A'
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2.38 Å
AuthorsPrice, S.R. / Evans, P.R. / Nagai, K.
CitationJournal: Nature / Year: 1998
Title: Crystal structure of the spliceosomal U2B"-U2A' protein complex bound to a fragment of U2 small nuclear RNA.
Authors: Price, S.R. / Evans, P.R. / Nagai, K.
History
DepositionApr 8, 1998Deposition site: BNL / Processing site: NDB
Revision 1.0Sep 23, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Q: RNA (5'-R(*CP*CP*UP*GP*GP*UP*AP*UP*UP*GP*CP*AP*GP*UP*AP*CP*CP*UP*CP*CP*AP*GP* GP*U)-3')
R: RNA (5'-R(*CP*CP*UP*GP*GP*UP*AP*UP*UP*GP*CP*AP*GP*UP*AP*CP*CP*UP*CP*CP*AP*GP* GP*U)-3')
A: U2A'
C: U2A'
B: SPLICEOSOMAL U2B''
D: SPLICEOSOMAL U2B''


Theoretical massNumber of molelcules
Total (without water)77,9966
Polymers77,9966
Non-polymers00
Water00
1
Q: RNA (5'-R(*CP*CP*UP*GP*GP*UP*AP*UP*UP*GP*CP*AP*GP*UP*AP*CP*CP*UP*CP*CP*AP*GP* GP*U)-3')
A: U2A'
B: SPLICEOSOMAL U2B''


Theoretical massNumber of molelcules
Total (without water)38,9983
Polymers38,9983
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
R: RNA (5'-R(*CP*CP*UP*GP*GP*UP*AP*UP*UP*GP*CP*AP*GP*UP*AP*CP*CP*UP*CP*CP*AP*GP* GP*U)-3')
C: U2A'
D: SPLICEOSOMAL U2B''


Theoretical massNumber of molelcules
Total (without water)38,9983
Polymers38,9983
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.370, 128.240, 66.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.902213, -0.022157, -0.430722), (0.083146, -0.97101, 0.224112), (-0.423201, -0.23801, -0.874215)17.155, -23.71, 69.781
2given(0.876212, 0.1497, -0.458085), (0.035702, -0.968083, -0.248076), (-0.480601, 0.201013, -0.85359)18.27396, -24.52502, 70.57467
3given(0.905594, 0.085398, -0.41546), (-0.01754, -0.971143, -0.237851), (-0.423783, 0.222683, -0.877963)17.08585, -23.77819, 69.50339

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Components

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


Mass: 7622.534 Da / Num. of mol.: 2 / Fragment: U2 HAIRPIN IV
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
#2: Protein U2A' / U2A'


Mass: 20226.555 Da / Num. of mol.: 2
Fragment: N-TERMINAL DOMAIN, RESIDUES 1 - 176 OF U2 A', A COMPONENT OF U2 SNRNP
Mutation: C89D, S119C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: CDNA CLONE; / Plasmid: PET3 / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
Keywords: RESIDUES 1 - 176 OF U2 A', WHICH IS A COMPONENT OF U2 SNRNP
References: UniProt: P09661
#3: Protein SPLICEOSOMAL U2B'' / SPLICEOSOMAL U2B''


Mass: 11149.093 Da / Num. of mol.: 2
Fragment: RESIDUES 4 - 99 OF U2 B'', A COMPONENT OF U2 SNRNP
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: CDNA CLONE / Plasmid: PET3 / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
Keywords: RESIDUES 4 - 99 OF U2 B'', WHICH IS A COMPONENT OF U2 SNRNP
References: UniProt: P08579
Has protein modificationY
Sequence detailsTHE NUMBERING USED IN CHAINS B, D, Q, AND R IS CHOSEN TO CORRESPOND TO THE HOMOLOGOUS U1A FOUND IN ...THE NUMBERING USED IN CHAINS B, D, Q, AND R IS CHOSEN TO CORRESPOND TO THE HOMOLOGOUS U1A FOUND IN PDB ENTRY 1URN.

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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: 2.69 Å3/Da / Density % sol: 42 %
Crystal growpH: 7.3
Details: 50MM NACL, 9MM MGCL2, 0.25 MM SPERMINE, 0.25% N-OCTYL-BETA-D-GLUCOPYRANOSIDE, 50MM TRIS-CL PH 7.3, 1% PEG600
Components of the solutions
IDNameCrystal-IDSol-ID
1NACL11
2MGCL211
3SPERMINE11
4N-OCTYL-BETA-D-GLUCOPYRANOSIDE11
5TRIS11
6PEG 60011
7TRIS12
8PEG 60012
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mM1reservoirNaCl
29 mg/ml1reservoirMgCl2
30.25 mMspermine1reservoir
40.25 %n-octyl-beta-D-glucopyranoside1reservoir
550 mMTris-Cl1reservoir
61 %PEG6001reservoir
71
81

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1996 / Details: TOROIDAL MIRROR
RadiationMonochromator: DOUBLE SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.38→25.9 Å / Num. obs: 32587 / % possible obs: 94.7 % / Observed criterion σ(I): 6 / Redundancy: 4.2 % / Biso Wilson estimate: 59 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 8.3
Reflection shellResolution: 2.38→2.51 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.236 / Mean I/σ(I) obs: 3 / Rsym value: 0.236 / % possible all: 95
Reflection shell
*PLUS
% possible obs: 74 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SIR / Resolution: 2.38→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.328 1647 5 %RANDOM
Rwork0.282 ---
all-32138 --
obs-32138 95.8 %-
Displacement parametersBiso mean: 55 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2---3.2 Å20 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.38→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4182 1006 0 0 5188
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0330.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0330.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.63
X-RAY DIFFRACTIONp_mcangle_it3.96
X-RAY DIFFRACTIONp_scbond_it3.44
X-RAY DIFFRACTIONp_scangle_it4.96
X-RAY DIFFRACTIONp_plane_restr0.00180.01
X-RAY DIFFRACTIONp_chiral_restr0.1130.15
X-RAY DIFFRACTIONp_singtor_nbd0.1890.3
X-RAY DIFFRACTIONp_multtor_nbd0.2530.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor1.27
X-RAY DIFFRACTIONp_staggered_tor2015
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor21.920
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.282
Solvent computation
*PLUS
Displacement parameters
*PLUS

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