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- PDB-2ozb: Structure of a human Prp31-15.5K-U4 snRNA complex -

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Basic information

Entry
Database: PDB / ID: 2ozb
TitleStructure of a human Prp31-15.5K-U4 snRNA complex
Components
  • RNA comprising the 5' Stem-Loop RNA of U4snRNA
  • U4/U6 small nuclear ribonucleoprotein Prp31
  • U4/U6.U5 tri-snRNP 15.5 kDa protein
KeywordsRNA BINDING PROTEIN/RNA / RNA-protein complex / ribonucleoprotein particle (RNP) / pre-mRNA splicing / U4/U6 di-snRNA / U4/U6 di-snRNP / hierarchical assembly / Nop domain / RNP-binding domain / RNA BINDING PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


ribonucleoprotein complex localization / U4atac snRNA binding / box C/D sno(s)RNA binding / rRNA 2'-O-methylation / dense fibrillar component / U4atac snRNP / U4atac/U6atac snRNP / box C/D methylation guide snoRNP complex / U4atac/U6atac x U5 tri-snRNP complex / snRNP binding ...ribonucleoprotein complex localization / U4atac snRNA binding / box C/D sno(s)RNA binding / rRNA 2'-O-methylation / dense fibrillar component / U4atac snRNP / U4atac/U6atac snRNP / box C/D methylation guide snoRNP complex / U4atac/U6atac x U5 tri-snRNP complex / snRNP binding / U4 snRNA binding / spliceosomal tri-snRNP complex / U12-type precatalytic spliceosome / U2-type precatalytic spliceosome / U2-type spliceosomal complex / U4/U6 snRNP / box C/D snoRNP assembly / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U3 snoRNA binding / U4 snRNP / mRNA modification / rRNA modification in the nucleus and cytosol / spliceosomal complex assembly / precatalytic spliceosome / MLL1 complex / spliceosomal tri-snRNP complex assembly / U4/U6 x U5 tri-snRNP complex / ribonucleoprotein complex binding / Cajal body / Major pathway of rRNA processing in the nucleolus and cytosol / spliceosomal snRNP assembly / mRNA Splicing - Major Pathway / spliceosomal complex / maturation of SSU-rRNA / small-subunit processome / mRNA splicing, via spliceosome / neuron differentiation / ATPase binding / ribosomal small subunit biogenesis / nuclear speck / protein-macromolecule adaptor activity / 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: 2.6 Å
AuthorsLiu, S. / Luehrmann, R. / Wahl, M.C.
CitationJournal: Science / Year: 2007
Title: Binding of the human Prp31 Nop domain to a composite RNA-protein platform in U4 snRNP.
Authors: Liu, S. / Li, P. / Dybkov, O. / Nottrott, S. / Hartmuth, K. / Luhrmann, R. / Carlomagno, T. / Wahl, M.C.
History
DepositionFeb 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 24, 2018Group: Data collection / Category: diffrn_radiation / Item: _diffrn_radiation.monochromator
Revision 1.5Aug 30, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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
C: RNA comprising the 5' Stem-Loop RNA of U4snRNA
F: RNA comprising the 5' Stem-Loop RNA of U4snRNA
A: U4/U6.U5 tri-snRNP 15.5 kDa protein
B: U4/U6 small nuclear ribonucleoprotein Prp31
D: U4/U6.U5 tri-snRNP 15.5 kDa protein
E: U4/U6 small nuclear ribonucleoprotein Prp31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,8069
Polymers107,6866
Non-polymers1203
Water4,107228
1
C: RNA comprising the 5' Stem-Loop RNA of U4snRNA
A: U4/U6.U5 tri-snRNP 15.5 kDa protein
B: U4/U6 small nuclear ribonucleoprotein Prp31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9235
Polymers53,8433
Non-polymers802
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: RNA comprising the 5' Stem-Loop RNA of U4snRNA
D: U4/U6.U5 tri-snRNP 15.5 kDa protein
E: U4/U6 small nuclear ribonucleoprotein Prp31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8834
Polymers53,8433
Non-polymers401
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.555, 99.896, 169.645
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: RNA chain RNA comprising the 5' Stem-Loop RNA of U4snRNA


Mass: 10626.346 Da / Num. of mol.: 2 / Fragment: U4 5'-SL, residues 20-52 / Source method: obtained synthetically
Details: RNA was chemically synthesized according to gene RNU4A (residues 20-52)
References: GenBank: 36174
#2: Protein U4/U6.U5 tri-snRNP 15.5 kDa protein / High mobility group-like nuclear protein 2 homolog 1 / NHP2-like protein 1 / OTK27 / hSNU13


Mass: 14335.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: HeLa cells / Gene: NHP2L1 / Plasmid: pGEX-4T-2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P55769
#3: Protein U4/U6 small nuclear ribonucleoprotein Prp31 / Pre-mRNA-processing factor 31 / U4/U6 snRNP 61 kDa protein / hPrp31 / Protein 61K / Serologically ...Pre-mRNA-processing factor 31 / U4/U6 snRNP 61 kDa protein / hPrp31 / Protein 61K / Serologically defined breast cancer antigen NY-BR-99


Mass: 28880.961 Da / Num. of mol.: 2 / Fragment: Prp31, residues 78-333
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: HeLa cells / Gene: PRPF31, PRP31 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: Q8WWY3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M calcium acetate, 0.1 M HEPES-NaOH, pH 7.0, 6 % PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1calcium acetate11
2HEPES-NaOH11
3PEG 600011
4H2O11
5calcium acetate12
6PEG 600012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 3, 2006 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL, mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 42155 / Num. obs: 42029 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10.8 % / Rmerge(I) obs: 0.107 / Rsym value: 0.076 / Net I/σ(I): 13.7
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.663 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.663 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345345DTBdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E7K

1e7k


Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.925 / SU B: 18.393 / SU ML: 0.199 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.418 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24756 2227 5 %RANDOM
Rwork0.20569 ---
obs0.20784 42029 99.67 %-
all-42155 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.782 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å20 Å2
2--0.35 Å20 Å2
3----1.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.261 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5707 1406 3 228 7344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227376
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5012.22410291
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4115727
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.29325.039258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.839151096
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1151538
X-RAY DIFFRACTIONr_chiral_restr0.10.21248
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024958
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.23289
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.25011
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2309
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0030.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6611.53742
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1925909
X-RAY DIFFRACTIONr_scbond_it1.56334497
X-RAY DIFFRACTIONr_scangle_it2.6224.54382
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.436 176 -
Rwork0.35 2964 -
obs--97.39 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.1261-0.250.52033.5634-1.87916.1158-0.01360.4741-0.1247-0.28820.0205-0.03150.20820.0273-0.0069-0.14270.0069-0.0054-0.08630.0259-0.1957-0.0671-29.3315-4.733
26.3714-0.59991.01632.89390.45194.19840.1241-0.3297-0.008-0.075-0.22010.5720.1248-0.79960.096-0.2127-0.0194-0.04550.015-0.0948-0.09-41.1798-81.400450.6582
30.72240.1615-0.45050.9529-1.16772.90180.0154-0.04580.09340.1939-0.01140.2297-0.0739-0.0616-0.004-0.08090.00190.0168-0.1098-0.02250.0046-3.7723-40.341737.7118
41.32750.7834-0.88751.2237-0.10361.1160.06710.0580.0848-0.1271-0.0696-0.12150.10840.00430.0025-0.02160.1249-0.0354-0.07640.036-0.0464-1.7627-69.192536.0269
53.561-2.0943-0.55233.1024-0.18081.68460.2094-0.53020.9183-0.02060.07270.214-0.4948-0.4306-0.2821-0.02940.15470.01420.0549-0.07170.0859-13.6413-15.821413.0272
61.9818-0.9271-0.70425.63843.72392.9167-0.11280.7391-0.4501-0.3188-0.20450.10660.6321-0.00580.31720.12850.0354-0.03510.0742-0.1974-0.0546-27.2997-94.566632.5228
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC3 - 1285 - 130
2X-RAY DIFFRACTION2DE4 - 1286 - 130
3X-RAY DIFFRACTION3BD85 - 33312 - 260
4X-RAY DIFFRACTION4EF85 - 33312 - 260
5X-RAY DIFFRACTION5CA20 - 521 - 33
6X-RAY DIFFRACTION6FB20 - 521 - 33

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