[English] 日本語
Yorodumi
- PDB-5m89: Spliceosome component -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5m89
TitleSpliceosome component
ComponentsSpliceosome WD40 Sc
KeywordsSPLICING / Spliceosome
Function / homology
Function and homology information


Prp19 complex / protein K63-linked ubiquitination / spliceosomal complex / RING-type E3 ubiquitin transferase / mRNA splicing, via spliceosome / ubiquitin protein ligase activity / DNA repair
Similarity search - Function
Pre-mRNA-splicing factor 19 / Pre-mRNA-processing factor 19 / Prp19/Pso4-like / U-box domain profile. / Modified RING finger domain / U-box domain / Zinc finger, RING/FYVE/PHD-type / WD domain, G-beta repeat / WD40 repeats / WD40 repeat ...Pre-mRNA-splicing factor 19 / Pre-mRNA-processing factor 19 / Prp19/Pso4-like / U-box domain profile. / Modified RING finger domain / U-box domain / Zinc finger, RING/FYVE/PHD-type / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Pre-mRNA-processing factor 19
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.605 Å
AuthorsMoura, T.R. / Pena, V.
CitationJournal: Mol. Cell / Year: 2018
Title: Prp19/Pso4 Is an Autoinhibited Ubiquitin Ligase Activated by Stepwise Assembly of Three Splicing Factors.
Authors: de Moura, T.R. / Mozaffari-Jovin, S. / Szabo, C.Z.K. / Schmitzova, J. / Dybkov, O. / Cretu, C. / Kachala, M. / Svergun, D. / Urlaub, H. / Luhrmann, R. / Pena, V.
History
DepositionOct 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Spliceosome WD40 Sc
B: Spliceosome WD40 Sc


Theoretical massNumber of molelcules
Total (without water)69,8382
Polymers69,8382
Non-polymers00
Water13,295738
1
A: Spliceosome WD40 Sc


Theoretical massNumber of molelcules
Total (without water)34,9191
Polymers34,9191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Spliceosome WD40 Sc


Theoretical massNumber of molelcules
Total (without water)34,9191
Polymers34,9191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.229, 103.715, 74.389
Angle α, β, γ (deg.)90.000, 101.770, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Spliceosome WD40 Sc


Mass: 34919.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0072540 / Production host: Chaetomium thermophilum (fungus) / References: UniProt: G0SFY0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 738 / 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: 2.4 Å3/Da / Density % sol: 48.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 0.1 M Citric Acid Anhydrous pH 4.0 20% PEG 6000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 176701 / % possible obs: 99.5 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 15.6
Reflection shellResolution: 1.6→1.61 Å

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M8C

5m8c


Resolution: 1.605→43.299 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.08 / Phase error: 19.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1857 8411 5.01 %
Rwork0.1651 159455 -
obs0.1662 167866 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.64 Å2 / Biso mean: 26.481 Å2 / Biso min: 9.39 Å2
Refinement stepCycle: final / Resolution: 1.605→43.299 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4896 0 0 738 5634
Biso mean---38.11 -
Num. residues----655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065036
X-RAY DIFFRACTIONf_angle_d0.8236867
X-RAY DIFFRACTIONf_chiral_restr0.057804
X-RAY DIFFRACTIONf_plane_restr0.005880
X-RAY DIFFRACTIONf_dihedral_angle_d2.8773980
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6054-1.62360.34042400.30354419465983
1.6236-1.64270.3112880.300654305718100
1.6427-1.66280.31232770.284752655542100
1.6628-1.68380.25142860.275354045690100
1.6838-1.7060.28432820.264953685650100
1.706-1.72930.30042780.245253115589100
1.7293-1.7540.27042790.227453125591100
1.754-1.78020.25122850.217853905675100
1.7802-1.8080.23612780.206152875565100
1.808-1.83770.23352830.196453745657100
1.8377-1.86940.23972790.188453275606100
1.8694-1.90340.2062820.183453685650100
1.9034-1.940.21142840.177853075591100
1.94-1.97960.20092810.179453905671100
1.9796-2.02260.20572820.178653475629100
2.0226-2.06970.20442790.16953105589100
2.0697-2.12140.21512850.166554195704100
2.1214-2.17880.17482810.165353045585100
2.1788-2.24290.18032860.163853535639100
2.2429-2.31530.20812800.167853515631100
2.3153-2.3980.18222820.165453445626100
2.398-2.4940.17452810.159752985579100
2.494-2.60750.17252830.160453925675100
2.6075-2.7450.16912810.160553295610100
2.745-2.91690.1682820.164953125594100
2.9169-3.14210.19382880.167554165704100
3.1421-3.45820.16662800.146952805560100
3.4582-3.95830.16852810.144653735654100
3.9583-4.98580.13382790.114653415620100
4.9858-43.31460.15352790.151553345613100
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)
10.65470.0476-0.1221.5942-0.13851.14960.0235-0.0286-0.0535-0.0982-0.03260.12130.12820.0797-0.00190.07550.0394-0.01270.11990.01650.1146-7.165617.088-35.2026
20.40020.11340.00391.6098-0.12031.4532-0.0172-0.00740.04580.01480.017-0.0145-0.07580.0022-0.00070.10250.02020.01440.1244-0.00710.1218-0.896344.8409-71.0132
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 156:479)A156 - 479
2X-RAY DIFFRACTION2(chain B and resseq 152:479)B152 - 479

+
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