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- PDB-3siu: Structure of a hPrp31-15.5K-U4atac 5' stem loop complex, monomeri... -

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Basic information

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


ribonucleoprotein complex localization / snRNP binding / U4atac snRNP / U4atac snRNA binding / box C/D sno(s)RNA binding / dense fibrillar component / spliceosomal tri-snRNP complex / U4 snRNA binding / box C/D methylation guide snoRNP complex / U2-type spliceosomal complex ...ribonucleoprotein complex localization / snRNP binding / U4atac snRNP / U4atac snRNA binding / box C/D sno(s)RNA binding / dense fibrillar component / spliceosomal tri-snRNP complex / U4 snRNA binding / box C/D methylation guide snoRNP complex / U2-type spliceosomal complex / U2-type precatalytic spliceosome / U4 snRNP / box C/D snoRNP assembly / 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 LSU-rRNA / maturation of SSU-rRNA / small-subunit processome / mRNA splicing, via spliceosome / protein-macromolecule adaptor activity / ribosomal small subunit biogenesis / ATPase binding / cytosolic large ribosomal subunit / 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 / H/ACA ribonucleoprotein complex, subunit Nhp2-like / 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 / H/ACA ribonucleoprotein complex, subunit Nhp2-like / NOSIC / NOSIC (NUC001) domain / Nop domain / Nop domain superfamily / Nop, C-terminal domain / snoRNA binding domain, fibrillarin / Nop domain profile. / Ribosomal protein L30/S12 / 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: 2.626 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: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,5478
Polymers103,3556
Non-polymers1922
Water1,02757
1
A: NHP2-like protein 1
B: U4/U6 small nuclear ribonucleoprotein Prp31
C: U4atac snRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7734
Polymers51,6773
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-36 kcal/mol
Surface area21290 Å2
MethodPISA
2
D: NHP2-like protein 1
E: U4/U6 small nuclear ribonucleoprotein Prp31
F: U4atac snRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7734
Polymers51,6773
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-44 kcal/mol
Surface area21610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.499, 111.263, 110.858
Angle α, β, γ (deg.)90.00, 101.81, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 2
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.: 2 / 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: 9073.462 Da / Num. of mol.: 2 / Fragment: GB bases 28-55 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: NR_023343.1
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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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: 2.89 Å3/Da / Density % sol: 57.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M lithium sulfate, 0.1 M Bis-Tris, pH 7.0, 20% w/v PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 393K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98
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: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 34765 / Num. obs: 34765 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 66.9 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 19.5
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 1.5 / Num. unique all: 3849 / Rsym value: 0.652 / % possible all: 99.7

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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: 2.626→29.45 Å / SU ML: 0.41 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.35 / σ(I): 0 / Phase error: 30.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2413 1750 5.04 %RANDOM
Rwork0.1982 ---
obs0.2004 34700 98.76 %-
all-35136 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.641 Å2 / ksol: 0.329 e/Å3
Displacement parametersBiso mean: 80.4 Å2
Baniso -1Baniso -2Baniso -3
1-8.6714 Å20 Å21.5191 Å2
2--15.6206 Å20 Å2
3----24.292 Å2
Refinement stepCycle: LAST / Resolution: 2.626→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5627 1202 10 57 6896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087057
X-RAY DIFFRACTIONf_angle_d1.0989816
X-RAY DIFFRACTIONf_dihedral_angle_d17.8222845
X-RAY DIFFRACTIONf_chiral_restr0.0691186
X-RAY DIFFRACTIONf_plane_restr0.0041049
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6261-2.69710.41751130.35182179X-RAY DIFFRACTION85
2.6971-2.77640.3681380.32152560X-RAY DIFFRACTION100
2.7764-2.86590.34481200.28722550X-RAY DIFFRACTION100
2.8659-2.96820.34991540.27172538X-RAY DIFFRACTION100
2.9682-3.0870.3391500.26162562X-RAY DIFFRACTION100
3.087-3.22730.34681200.24962517X-RAY DIFFRACTION100
3.2273-3.39720.28211480.2332563X-RAY DIFFRACTION100
3.3972-3.60970.2361210.21912572X-RAY DIFFRACTION100
3.6097-3.88780.26311220.19122573X-RAY DIFFRACTION100
3.8878-4.2780.20781340.15592582X-RAY DIFFRACTION100
4.278-4.89460.1711260.15112591X-RAY DIFFRACTION100
4.8946-6.15740.25291340.20312589X-RAY DIFFRACTION100
6.1574-29.45190.1911700.16432574X-RAY DIFFRACTION100

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