[English] 日本語
Yorodumi
- PDB-6q8f: Nterminal domain of human SMU1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6q8f
TitleNterminal domain of human SMU1
ComponentsWD40 repeat-containing protein SMU1
KeywordsSPLICING / Splicing factor
Function / homology
Function and homology information


U2-type precatalytic spliceosome / precatalytic spliceosome / regulation of alternative mRNA splicing, via spliceosome / mRNA Splicing - Major Pathway / RNA splicing / mRNA splicing, via spliceosome / nuclear speck / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
WD40 repeat-containing protein SMU1 / LisH-like dimerisation domain / C-terminal to LisH motif. / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / G-protein beta WD-40 repeat / WD40 repeat, conserved site ...WD40 repeat-containing protein SMU1 / LisH-like dimerisation domain / C-terminal to LisH motif. / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
WD40 repeat-containing protein SMU1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsTengo, L. / Le Corre, L. / Fournier, G. / Ashraf, U. / Busca, P. / Rameix-Welti, M.-A. / Gravier-Pelletier, C. / Ruigrok, R.W.H. / Jacob, Y. / Vidalain, P.-O. ...Tengo, L. / Le Corre, L. / Fournier, G. / Ashraf, U. / Busca, P. / Rameix-Welti, M.-A. / Gravier-Pelletier, C. / Ruigrok, R.W.H. / Jacob, Y. / Vidalain, P.-O. / Pietrancosta, N. / Naffakh, N. / McCarthy, A.A. / Crepin, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Destabilization of the human RED-SMU1 splicing complex as a basis for host-directed antiinfluenza strategy.
Authors: Ashraf, U. / Tengo, L. / Le Corre, L. / Fournier, G. / Busca, P. / McCarthy, A.A. / Rameix-Welti, M.A. / Gravier-Pelletier, C. / Ruigrok, R.W.H. / Jacob, Y. / Vidalain, P.O. / Pietrancosta, ...Authors: Ashraf, U. / Tengo, L. / Le Corre, L. / Fournier, G. / Busca, P. / McCarthy, A.A. / Rameix-Welti, M.A. / Gravier-Pelletier, C. / Ruigrok, R.W.H. / Jacob, Y. / Vidalain, P.O. / Pietrancosta, N. / Crepin, T. / Naffakh, N.
History
DepositionDec 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: WD40 repeat-containing protein SMU1
B: WD40 repeat-containing protein SMU1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,5924
Polymers115,3482
Non-polymers2452
Water3,909217
1
B: WD40 repeat-containing protein SMU1
hetero molecules

A: WD40 repeat-containing protein SMU1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,5924
Polymers115,3482
Non-polymers2452
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area4880 Å2
ΔGint-40 kcal/mol
Surface area21380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.183, 41.225, 123.599
Angle α, β, γ (deg.)90.00, 91.48, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein WD40 repeat-containing protein SMU1 / Smu-1 suppressor of mec-8 and unc-52 protein homolog


Mass: 57673.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMU1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2TAY7
#2: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-Tris pH 5.5, 16-20 % PEG 10K, 0.1 M ammonium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95373 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 31423 / % possible obs: 97.2 % / Redundancy: 5.6 % / Rrim(I) all: 0.064 / Net I/σ(I): 22.3
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.36 / Num. unique obs: 1956 / Rrim(I) all: 0.536 / % possible all: 81.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
XSCALEdata scaling
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→39.14 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.483 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.138 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21375 1610 5.1 %RANDOM
Rwork0.17442 ---
obs0.17644 29818 97.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.692 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å2-0 Å21.19 Å2
2---0.55 Å2-0 Å2
3----0.48 Å2
Refinement stepCycle: 1 / Resolution: 1.9→39.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3024 0 15 217 3256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133089
X-RAY DIFFRACTIONr_bond_other_d00.0173001
X-RAY DIFFRACTIONr_angle_refined_deg1.491.644183
X-RAY DIFFRACTIONr_angle_other_deg1.3471.5716964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9265378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.00622.284162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02515573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6351524
X-RAY DIFFRACTIONr_chiral_restr0.0690.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023359
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02593
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5142.5081521
X-RAY DIFFRACTIONr_mcbond_other3.5142.5051519
X-RAY DIFFRACTIONr_mcangle_it5.0593.7341893
X-RAY DIFFRACTIONr_mcangle_other5.0583.7341893
X-RAY DIFFRACTIONr_scbond_it4.2552.8941568
X-RAY DIFFRACTIONr_scbond_other4.2542.8941569
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4164.22290
X-RAY DIFFRACTIONr_long_range_B_refined9.08129.8873545
X-RAY DIFFRACTIONr_long_range_B_other9.09929.8363508
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 108 -
Rwork0.258 1826 -
obs--81.36 %

+
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