[English] 日本語
Yorodumi
- PDB-2ozb: Structure of a human Prp31-15.5K-U4 snRNA complex -

+
Open data


ID or keywords:

Loading...

-
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 snRNP / U4atac snRNA binding / box C/D sno(s)RNA binding / snRNP binding / dense fibrillar component / box C/D methylation guide snoRNP complex / spliceosomal tri-snRNP complex / U4 snRNA binding / U2-type spliceosomal complex ...ribonucleoprotein complex localization / U4atac snRNP / U4atac snRNA binding / box C/D sno(s)RNA binding / snRNP binding / dense fibrillar component / box C/D methylation guide snoRNP complex / spliceosomal tri-snRNP complex / U4 snRNA binding / U2-type spliceosomal complex / U2-type precatalytic spliceosome / box C/D snoRNP assembly / U4 snRNP / rRNA modification in the nucleus and cytosol / U3 snoRNA binding / precatalytic spliceosome / single fertilization / MLL1 complex / spliceosomal tri-snRNP complex assembly / Major pathway of rRNA processing in the nucleolus and cytosol / Cajal body / ribonucleoprotein complex binding / maturation of SSU-rRNA / maturation of LSU-rRNA / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / small-subunit processome / ribosomal small subunit biogenesis / mRNA splicing, via spliceosome / cytosolic large ribosomal subunit / ATPase binding / 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 / NOSIC / NOSIC (NUC001) domain / Nop domain / Nop domain superfamily / Nop, C-terminal domain ...Helix Hairpins - #4070 / Nop domain / Prp31 C-terminal / U4/U6 small nuclear ribonucleoprotein Prp31 / Prp31 C terminal domain / 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 / 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: 2.6 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 cellsHeLa / 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 cellsHeLa / 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 / Water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more