[English] 日本語
Yorodumi
- PDB-5en7: Crystal structure of the Smu1-RED complex (native) of Caenorhabdi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5en7
TitleCrystal structure of the Smu1-RED complex (native) of Caenorhabditis elegans.
Components
  • SMU-1
  • Suppressor of Mec and Unc defects
KeywordsSPLICING / LisH motif / CTLH / dimer / heterotetramer
Function / homology
Function and homology information


nematode larval development / muscle organ morphogenesis / mechanosensory behavior / locomotion / U2-type precatalytic spliceosome / embryo development ending in birth or egg hatching / regulation of alternative mRNA splicing, via spliceosome / precatalytic spliceosome / neuron development / RNA splicing ...nematode larval development / muscle organ morphogenesis / mechanosensory behavior / locomotion / U2-type precatalytic spliceosome / embryo development ending in birth or egg hatching / regulation of alternative mRNA splicing, via spliceosome / precatalytic spliceosome / neuron development / RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / nucleolus / protein homodimerization activity / identical protein binding / nucleus
Similarity search - Function
Protein RED, C-terminal / RED-like, N-terminal / Protein Red-like / RED-like protein C-terminal region / RED-like protein N-terminal region / WD40 repeat-containing protein SMU1 / : / LisH-like dimerisation domain / C-terminal to LisH motif. / CTLH, C-terminal LisH motif ...Protein RED, C-terminal / RED-like, N-terminal / Protein Red-like / RED-like protein C-terminal region / RED-like protein N-terminal region / 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 / 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
Smu-1 suppressor of mec-8 and unc-52 protein / Smu-2 suppressor of mec-8 and unc-52 protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.936 Å
AuthorsUlrich, A.K.C. / Wahl, M.C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationWA1126/7-1 Germany
CitationJournal: to be published
Title: splicing factor
Authors: Ulrich, A.K.C. / Schulz, J.F. / Kamprad, A. / Schuetze, T. / Wahl, M.C.
History
DepositionNov 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SMU-1
B: Suppressor of Mec and Unc defects
C: SMU-1
D: Suppressor of Mec and Unc defects
E: SMU-1
F: Suppressor of Mec and Unc defects
G: SMU-1
H: Suppressor of Mec and Unc defects


Theoretical massNumber of molelcules
Total (without water)110,6928
Polymers110,6928
Non-polymers00
Water2,540141
1
A: SMU-1
B: Suppressor of Mec and Unc defects
C: SMU-1
D: Suppressor of Mec and Unc defects


Theoretical massNumber of molelcules
Total (without water)55,3464
Polymers55,3464
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-46 kcal/mol
Surface area22140 Å2
MethodPISA
2
E: SMU-1
F: Suppressor of Mec and Unc defects
G: SMU-1
H: Suppressor of Mec and Unc defects


Theoretical massNumber of molelcules
Total (without water)55,3464
Polymers55,3464
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-51 kcal/mol
Surface area22030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.322, 41.036, 126.382
Angle α, β, γ (deg.)90.000, 95.920, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid A
21chain C and segid C
31chain E and segid E
41chain G and segid G
12chain B and segid B
22chain D and segid D
32chain F and segid F

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain C and segid CC0
311chain E and segid EE0
411chain G and segid GG0
112chain B and segid BB0
212chain D and segid DD0
312chain F and segid FF0

NCS ensembles :
ID
1
2

-
Components

#1: Protein
SMU-1 / Suppressor of Mec and Unc defects


Mass: 20708.719 Da / Num. of mol.: 4 / Fragment: NTR, UNP residues 2-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: smu-1, CC4.3, CELE_CC4.3 / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: G5EEG7
#2: Protein
Suppressor of Mec and Unc defects


Mass: 6964.369 Da / Num. of mol.: 4 / Fragment: UNP residues 163-223
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: smu-2, CELE_Y49F6B.4, Y49F6B.4 / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: Q9N4U5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.84 Å3/Da / Density % sol: 56.72 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion
Details: 0.1 M HEPES, pH 7.5, 0.02 M MgCl2, 22 % [w/v] polyacrilic acid 5,100
PH range: 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.936→46.16 Å / Num. obs: 26994 / % possible obs: 98.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 62.7 Å2 / CC1/2: 0.995 / Rsym value: 0.124 / Net I/σ(I): 10.6
Reflection shellResolution: 2.94→3.11 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.4 / % possible all: 92.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5en6

5en6


Resolution: 2.936→46.156 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2686 1350 5 %Random selection
Rwork0.2215 25634 --
obs0.2239 26984 98.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 167.65 Å2 / Biso mean: 67.6457 Å2 / Biso min: 17.2 Å2
Refinement stepCycle: final / Resolution: 2.936→46.156 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6320 0 0 141 6461
Biso mean---53.71 -
Num. residues----785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056411
X-RAY DIFFRACTIONf_angle_d0.8988670
X-RAY DIFFRACTIONf_chiral_restr0.0381034
X-RAY DIFFRACTIONf_plane_restr0.0041106
X-RAY DIFFRACTIONf_dihedral_angle_d14.5612457
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3414X-RAY DIFFRACTION12.234TORSIONAL
12C3414X-RAY DIFFRACTION12.234TORSIONAL
13E3414X-RAY DIFFRACTION12.234TORSIONAL
14G3414X-RAY DIFFRACTION12.234TORSIONAL
21B217X-RAY DIFFRACTION12.234TORSIONAL
22D217X-RAY DIFFRACTION12.234TORSIONAL
23F217X-RAY DIFFRACTION12.234TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9361-3.0410.38961170.34742216233388
3.041-3.16280.3371370.30126022739100
3.1628-3.30670.36571320.26762521265399
3.3067-3.4810.32311360.260625822718100
3.481-3.6990.26161380.223826102748100
3.699-3.98440.281340.20642540267499
3.9844-4.38510.26361350.1852568270399
4.3851-5.0190.20541380.183326252763100
5.019-6.32080.26361380.230426342772100
6.3208-46.16180.23711450.2042736288199

+
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