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- PDB-3siv: Structure of a hPrp31-15.5K-U4atac 5' stem loop complex, dimeric form -

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Basic information

Entry
Database: PDB / ID: 3siv
TitleStructure of a hPrp31-15.5K-U4atac 5' stem loop complex, dimeric form
Components
  • NHP2-like protein 1
  • U4/U6 small nuclear ribonucleoprotein Prp31
  • U4atac snRNA
KeywordsSPLICING/RNA / Major and minor spliceosome / pre-mRNA splicing / RNA-protein complex / U4 snRNP and U4atac snRNP / RNA-binding protein / U4 snRNA / nucleus / SPLICING-RNA complex
Function / homology
Function and homology information


ribonucleoprotein complex localization / U4atac snRNP / U4atac snRNA binding / box C/D sno(s)RNA binding / dense fibrillar component / box C/D methylation guide snoRNP complex / snRNP binding / spliceosomal tri-snRNP complex / U4 snRNA binding / U2-type precatalytic spliceosome ...ribonucleoprotein complex localization / U4atac snRNP / U4atac snRNA binding / box C/D sno(s)RNA binding / dense fibrillar component / box C/D methylation guide snoRNP complex / snRNP binding / spliceosomal tri-snRNP complex / U4 snRNA binding / U2-type precatalytic spliceosome / U2-type spliceosomal complex / box C/D snoRNP assembly / U4 snRNP / rRNA modification in the nucleus and cytosol / U3 snoRNA binding / precatalytic spliceosome / MLL1 complex / spliceosomal tri-snRNP complex assembly / single fertilization / Major pathway of rRNA processing in the nucleolus and cytosol / ribonucleoprotein complex binding / Cajal body / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / maturation of SSU-rRNA / small-subunit processome / mRNA splicing, via spliceosome / ATPase binding / ribosomal small subunit biogenesis / protein-macromolecule adaptor activity / nuclear speck / nucleolus / protein-containing complex / RNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Helix Hairpins - #4070 / Nop domain / Prp31 C-terminal / U4/U6 small nuclear ribonucleoprotein Prp31 / Prp31 C terminal domain / Ribosomal protein L30/S12 / NOSIC / NOSIC (NUC001) domain / Nop domain / Nop domain superfamily ...Helix Hairpins - #4070 / Nop domain / Prp31 C-terminal / U4/U6 small nuclear ribonucleoprotein Prp31 / Prp31 C terminal domain / Ribosomal protein L30/S12 / NOSIC / NOSIC (NUC001) domain / Nop domain / Nop domain superfamily / Nop, C-terminal domain / snoRNA binding domain, fibrillarin / Nop domain profile. / H/ACA ribonucleoprotein complex, subunit Nhp2-like / Serum Albumin; Chain A, Domain 1 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein L7Ae/L8/Nhp2 family / : / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / RNA / RNA (> 10) / NHP2-like protein 1 / U4/U6 small nuclear ribonucleoprotein Prp31
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.304 Å
AuthorsLiu, S. / Ghalei, H. / Luhrmann, R. / Wahl, M.C.
CitationJournal: Rna / Year: 2011
Title: Structural basis for the dual U4 and U4atac snRNA-binding specificity of spliceosomal protein hPrp31.
Authors: Liu, S. / Ghalei, H. / Luhrmann, R. / Wahl, M.C.
History
DepositionJun 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2011Group: Database references
Revision 1.2Jan 31, 2018Group: Advisory / Experimental preparation / Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / Item: _exptl_crystal_grow.temp
Revision 1.3Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NHP2-like protein 1
B: U4/U6 small nuclear ribonucleoprotein Prp31
C: U4atac snRNA
D: NHP2-like protein 1
E: U4/U6 small nuclear ribonucleoprotein Prp31
F: U4atac snRNA
G: NHP2-like protein 1
H: U4/U6 small nuclear ribonucleoprotein Prp31
I: U4atac snRNA
J: NHP2-like protein 1
K: U4/U6 small nuclear ribonucleoprotein Prp31
L: U4atac snRNA


Theoretical massNumber of molelcules
Total (without water)211,79212
Polymers211,79212
Non-polymers00
Water00
1
A: NHP2-like protein 1
B: U4/U6 small nuclear ribonucleoprotein Prp31
C: U4atac snRNA
D: NHP2-like protein 1
E: U4/U6 small nuclear ribonucleoprotein Prp31
F: U4atac snRNA


Theoretical massNumber of molelcules
Total (without water)105,8966
Polymers105,8966
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: NHP2-like protein 1
H: U4/U6 small nuclear ribonucleoprotein Prp31
I: U4atac snRNA
J: NHP2-like protein 1
K: U4/U6 small nuclear ribonucleoprotein Prp31
L: U4atac snRNA


Theoretical massNumber of molelcules
Total (without water)105,8966
Polymers105,8966
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)255.407, 105.325, 188.644
Angle α, β, γ (deg.)90.00, 127.52, 90.00
Int Tables number5
Space group name H-MC121
DetailsTHE PREDICTED HEXAMERIC COMPLEXES RESEMBLE DUPLICATED TRIMERIC COMPLEXES AS IN PDB ENTRY 3SIU. THE TRIMERIC COMPLEXES REPRESENT THE BIOLOGICALLY RELEVANT OLIGOMERIZATION STATE.

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Components

#1: Protein
NHP2-like protein 1 / U4/U6.U5 tri-snRNP 15.5 kDa protein / High mobility group-like nuclear protein 2 homolog 1 / OTK27 ...U4/U6.U5 tri-snRNP 15.5 kDa protein / High mobility group-like nuclear protein 2 homolog 1 / OTK27 / SNU13 homolog / hSNU13


Mass: 14335.656 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NHP2L1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: P55769
#2: Protein
U4/U6 small nuclear ribonucleoprotein Prp31 / Pre-mRNA-processing factor 31 / Serologically defined breast cancer antigen NY-BR-99 / U4/U6 snRNP ...Pre-mRNA-processing factor 31 / Serologically defined breast cancer antigen NY-BR-99 / U4/U6 snRNP 61 kDa protein / Protein 61K / hPrp31


Mass: 28268.225 Da / Num. of mol.: 4 / Fragment: UNP residues 85-333
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRP31, PRPF31 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q8WWY3
#3: RNA chain
U4atac snRNA / U4atac small nuclear RNA (U12-dependent splicing) / RNU4ATAC


Mass: 10344.204 Da / Num. of mol.: 4 / Fragment: GB bases 28-55 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: NR_023343.1

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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: 4.75 Å3/Da / Density % sol: 74.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 0.1 M sodium cacodylate, pH 6.4, 20% v/v PEG550 MME, VAPOR DIFFUSION, SITTING DROP, temperature 393K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 10, 2007 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9841 Å / Relative weight: 1
ReflectionResolution: 3.304→30 Å / Num. all: 59914 / Num. obs: 59255 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 118.9 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 7.9
Reflection shellResolution: 3.3→3.4 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 1.4 / Num. unique all: 4586 / Rsym value: 0.412 / % possible all: 92.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 2OZB

2ozb


Resolution: 3.304→29.923 Å / SU ML: 0.42 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 0 / Phase error: 26.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2386 2991 5.05 %RANDOM
Rwork0.1975 ---
obs0.1995 59249 99.26 %-
all-59691 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 87.754 Å2 / ksol: 0.274 e/Å3
Displacement parametersBiso mean: 138.5 Å2
Baniso -1Baniso -2Baniso -3
1-16.1684 Å20 Å221.5866 Å2
2---10.2996 Å20 Å2
3----5.8688 Å2
Refinement stepCycle: LAST / Resolution: 3.304→29.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11374 2740 0 0 14114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914594
X-RAY DIFFRACTIONf_angle_d1.23220352
X-RAY DIFFRACTIONf_dihedral_angle_d19.385934
X-RAY DIFFRACTIONf_chiral_restr0.0742471
X-RAY DIFFRACTIONf_plane_restr0.0052135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.304-3.35810.38991160.36252519X-RAY DIFFRACTION95
3.3581-3.41590.41151570.3282670X-RAY DIFFRACTION100
3.4159-3.47790.33571460.30272672X-RAY DIFFRACTION100
3.4779-3.54470.36291460.2942723X-RAY DIFFRACTION100
3.5447-3.61690.33471520.27892663X-RAY DIFFRACTION100
3.6169-3.69540.34791340.2772664X-RAY DIFFRACTION100
3.6954-3.78130.27121470.24112703X-RAY DIFFRACTION100
3.7813-3.87560.2751290.21572691X-RAY DIFFRACTION100
3.8756-3.98020.27961320.19892695X-RAY DIFFRACTION100
3.9802-4.0970.24681360.1912668X-RAY DIFFRACTION100
4.097-4.22890.24561480.17822674X-RAY DIFFRACTION100
4.2289-4.37960.19341450.16852689X-RAY DIFFRACTION100
4.3796-4.55440.24751560.16322674X-RAY DIFFRACTION100
4.5544-4.76090.23441270.1782689X-RAY DIFFRACTION99
4.7609-5.01080.22281510.17412688X-RAY DIFFRACTION99
5.0108-5.32310.24061280.20262717X-RAY DIFFRACTION100
5.3231-5.73140.23291450.20332680X-RAY DIFFRACTION99
5.7314-6.30330.21241560.19942675X-RAY DIFFRACTION99
6.3033-7.20430.21731450.17282700X-RAY DIFFRACTION99
7.2043-9.0350.19181490.14082678X-RAY DIFFRACTION98
9.035-29.92430.20931460.19672726X-RAY DIFFRACTION97

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