[English] 日本語
Yorodumi
- PDB-3gs3: Structure of the N-terminal HEAT Domain of Symplekin from D. mela... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3gs3
TitleStructure of the N-terminal HEAT Domain of Symplekin from D. melanogaster
ComponentsSymplekin
KeywordsTranscription / Protein Binding / helix-turn-helix HEAT repeat extended loop
Function / homology
Function and homology information


Processing of Intronless Pre-mRNAs / histone locus body / mRNA 3'-end processing / Processing of Capped Intron-Containing Pre-mRNA / tricellular tight junction / RNA Polymerase II Transcription Termination / Transport of Mature mRNA Derived from an Intronless Transcript / mRNA 3'-end processing by stem-loop binding and cleavage / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / mRNA cleavage and polyadenylation specificity factor complex ...Processing of Intronless Pre-mRNAs / histone locus body / mRNA 3'-end processing / Processing of Capped Intron-Containing Pre-mRNA / tricellular tight junction / RNA Polymerase II Transcription Termination / Transport of Mature mRNA Derived from an Intronless Transcript / mRNA 3'-end processing by stem-loop binding and cleavage / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / mRNA cleavage and polyadenylation specificity factor complex / RNA binding / nucleus
Similarity search - Function
Symplekin/Pta1 / Symplekin C-terminal / Symplekin/Pta1, N-terminal / Symplekin/PTA1 N-terminal / Symplekin tight junction protein C terminal / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsKennedy, S.A. / Redinbo, M.R.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structure of the HEAT domain from the Pre-mRNA processing factor Symplekin.
Authors: Kennedy, S.A. / Frazier, M.L. / Steiniger, M. / Mast, A.M. / Marzluff, W.F. / Redinbo, M.R.
History
DepositionMar 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Symplekin


Theoretical massNumber of molelcules
Total (without water)28,3151
Polymers28,3151
Non-polymers00
Water2,468137
1
A: Symplekin

A: Symplekin


Theoretical massNumber of molelcules
Total (without water)56,6292
Polymers56,6292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area1260 Å2
ΔGint-17 kcal/mol
Surface area23700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.336, 68.336, 139.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Symplekin / LD45768p


Mass: 28314.590 Da / Num. of mol.: 1 / Fragment: residues 19-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG2097, Dmel_CG2097 / Plasmid: pMCGS9 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 GOLD / References: UniProt: Q8MSU4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 27% PEG 3350 0.425 M sodium citrate 10 mM HEPES 1 mM DTT 0.01% sodium azide , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97190, 0.97958
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 18, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97191
20.979581
ReflectionResolution: 2.4→50 Å / Num. all: 13568 / Num. obs: 12295 / % possible obs: 90.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Net I/σ(I): 24.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.9 / % possible all: 79.6

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.4→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2653 876 -Random
Rwork0.2068 ---
all0.2068 13568 --
obs0.2068 12295 90.6 %-
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1922 0 0 137 2059

+
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