[English] 日本語
Yorodumi
- PDB-4n0t: Core structure of the U6 small nuclear ribonucleoprotein at 1.7 A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4n0t
TitleCore structure of the U6 small nuclear ribonucleoprotein at 1.7 Angstrom resolution
Components
  • U4/U6 snRNA-associated-splicing factor PRP24
  • U6 snRNA
KeywordsRNA BINDING PROTEIN/RNA / spliceosomal ribonucleoprotein complex / annealing U6 and U4 snRNA / nucleus / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


U6 snRNP / snRNA binding / spliceosomal complex assembly / spliceosomal tri-snRNP complex assembly / U6 snRNA binding / spliceosomal complex / mRNA splicing, via spliceosome / ribonucleoprotein complex / RNA binding / nucleus
Similarity search - Function
Occluded RNA-recognition motif / Prp24, RNA recognition motif1 / Prp24, RNA recognition motif2 / : / Occluded RNA-recognition motif / LSM-interacting domain / Lsm interaction motif / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif ...Occluded RNA-recognition motif / Prp24, RNA recognition motif1 / Prp24, RNA recognition motif2 / : / Occluded RNA-recognition motif / LSM-interacting domain / Lsm interaction motif / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / RNA / RNA (> 10) / U4/U6 snRNA-associated-splicing factor PRP24
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMontemayor, E.J. / Curran, E.C. / Liao, H. / Andrews, K.L. / Treba, C.N. / Butcher, S.E. / Brow, D.A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Core structure of the U6 small nuclear ribonucleoprotein at 1.7- angstrom resolution.
Authors: Montemayor, E.J. / Curran, E.C. / Liao, H.H. / Andrews, K.L. / Treba, C.N. / Butcher, S.E. / Brow, D.A.
History
DepositionOct 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Sep 20, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: U4/U6 snRNA-associated-splicing factor PRP24
B: U6 snRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5283
Polymers66,4322
Non-polymers961
Water12,538696
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-30 kcal/mol
Surface area28170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.782, 71.370, 82.081
Angle α, β, γ (deg.)90.00, 109.62, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein U4/U6 snRNA-associated-splicing factor PRP24 / U4/U6 snRNP protein


Mass: 43246.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: PRP24, YM8156.10C, YMR268C / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) STAR pLysS / References: UniProt: P49960
#2: RNA chain U6 snRNA


Mass: 23184.857 Da / Num. of mol.: 1 / Mutation: A62G, U100C, U101C / Source method: obtained synthetically
Details: In vitro transcription using a cloned plasmid template
References: GenBank: BK006945.2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 696 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.06 %
Crystal growTemperature: 274 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100 mM lithium sulfate, 100 mM sodium citrate, pH 5.5, 20 % PEG 1,000, VAPOR DIFFUSION, SITTING DROP, temperature 274K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 15, 2013
RadiationMonochromator: diamond laue monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Net I/σ(I): 15.3
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.9 / % possible all: 97

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GHP

2ghp


Resolution: 1.7→26.25 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2109 4690 3.22 %random
Rwork0.1836 ---
obs0.1845 145765 99.6 %-
all-146350 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→26.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2934 1389 5 696 5024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064547
X-RAY DIFFRACTIONf_angle_d1.0256444
X-RAY DIFFRACTIONf_dihedral_angle_d14.6731932
X-RAY DIFFRACTIONf_chiral_restr0.066780
X-RAY DIFFRACTIONf_plane_restr0.005583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6961-1.71530.35741250.28764407X-RAY DIFFRACTION91
1.7153-1.73550.26391600.26684644X-RAY DIFFRACTION100
1.7355-1.75670.2991740.25754744X-RAY DIFFRACTION100
1.7567-1.77890.29341630.25734679X-RAY DIFFRACTION100
1.7789-1.80230.29541430.24864673X-RAY DIFFRACTION100
1.8023-1.8270.31311640.2364761X-RAY DIFFRACTION100
1.827-1.85310.28011520.23614693X-RAY DIFFRACTION100
1.8531-1.88070.23541660.22974772X-RAY DIFFRACTION100
1.8807-1.91010.29241490.22254708X-RAY DIFFRACTION100
1.9101-1.94140.30111540.22214704X-RAY DIFFRACTION100
1.9414-1.97490.27911460.22284754X-RAY DIFFRACTION100
1.9749-2.01080.22861390.20784779X-RAY DIFFRACTION100
2.0108-2.04950.28391720.20114687X-RAY DIFFRACTION100
2.0495-2.09130.21711500.20224707X-RAY DIFFRACTION100
2.0913-2.13670.23291700.19944700X-RAY DIFFRACTION100
2.1367-2.18640.23391530.19434698X-RAY DIFFRACTION100
2.1864-2.24110.20641430.19764730X-RAY DIFFRACTION100
2.2411-2.30160.27611670.19824769X-RAY DIFFRACTION100
2.3016-2.36930.25021710.19824687X-RAY DIFFRACTION100
2.3693-2.44570.27571480.19314660X-RAY DIFFRACTION100
2.4457-2.53310.22631670.19444725X-RAY DIFFRACTION100
2.5331-2.63440.22031540.18774777X-RAY DIFFRACTION100
2.6344-2.75420.26211550.19544686X-RAY DIFFRACTION100
2.7542-2.89920.22141560.18854719X-RAY DIFFRACTION100
2.8992-3.08060.21831560.18964732X-RAY DIFFRACTION100
3.0806-3.3180.18731670.17824694X-RAY DIFFRACTION100
3.318-3.65110.17691480.15984758X-RAY DIFFRACTION100
3.6511-4.17760.15561630.14634703X-RAY DIFFRACTION100
4.1776-5.25640.14561540.14224737X-RAY DIFFRACTION100
5.2564-26.25360.18871610.174588X-RAY DIFFRACTION98
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)
11.21580.30340.60612.1167-0.09091.0197-1.187-0.5455-1.11910.3563-0.53820.55912.4537-0.4932-0.51582.5628-0.8308-0.02981.0351.08941.279610.9912-17.697477.8594
23.84660.20372.62784.8488-1.76312.19090.47050.05430.46280.3073-0.87350.93411.0874-0.4980.35061.1673-0.21990.41050.83-0.2791.1203-2.1565-31.291449.5011
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'B' and ((resseq 30:36))) or (chain 'B' and ((resseq 97:100)))
2X-RAY DIFFRACTION2(chain 'B' and ((resseq 63:70))) or (chain 'B' and ((resseq 77:86)))

+
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://pdbjlvh1.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