[English] 日本語
Yorodumi
- PDB-8pnk: Crystal structure of the Ded1p RecA1 domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8pnk
TitleCrystal structure of the Ded1p RecA1 domain
ComponentsATP-dependent RNA helicase DED1
KeywordsRNA BINDING PROTEIN / Ded1p / helicase / RecA
Function / homology
Function and homology information


positive regulation of formation of translation preinitiation complex / spliceosomal complex disassembly / eukaryotic initiation factor 4G binding / RNA strand annealing activity / Neutrophil degranulation / translation initiation factor activity / translational initiation / cytoplasmic stress granule / RNA helicase activity / RNA helicase ...positive regulation of formation of translation preinitiation complex / spliceosomal complex disassembly / eukaryotic initiation factor 4G binding / RNA strand annealing activity / Neutrophil degranulation / translation initiation factor activity / translational initiation / cytoplasmic stress granule / RNA helicase activity / RNA helicase / mRNA binding / ATP hydrolysis activity / RNA binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
Ded1/Dbp1, DEAD-box helicase domain / DEAD-box subfamily ATP-dependent helicases signature. / RNA helicase, DEAD-box type, Q motif / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. ...Ded1/Dbp1, DEAD-box helicase domain / DEAD-box subfamily ATP-dependent helicases signature. / RNA helicase, DEAD-box type, Q motif / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP-dependent RNA helicase DED1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHuebner, J. / Sprangers, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)418960343 Germany
CitationJournal: To Be Published
Title: Crystal structure of the Ded1p RecA1 domain
Authors: Huebner, J. / Sprangers, R.
History
DepositionJun 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP-dependent RNA helicase DED1


Theoretical massNumber of molelcules
Total (without water)31,7981
Polymers31,7981
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.000, 110.000, 52.200
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

-
Components

#1: Protein ATP-dependent RNA helicase DED1 / DEAD box protein 1 / Defines essential domain protein 1


Mass: 31798.037 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DED1, SPP81, YOR204W / Production host: Escherichia coli (E. coli) / References: UniProt: P06634, RNA helicase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.87 Å3/Da / Density % sol: 57.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.0, 30% Jeffamine ED-2001 pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.000036 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000036 Å / Relative weight: 1
ReflectionResolution: 2.2→47.63 Å / Num. obs: 18435 / % possible obs: 99.66 % / Redundancy: 6.6 % / Biso Wilson estimate: 47.87 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.04857 / Rpim(I) all: 0.02025 / Rrim(I) all: 0.0527 / Net I/σ(I): 21.69
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.7115 / Mean I/σ(I) obs: 2.48 / Num. unique obs: 1764 / CC1/2: 0.778 / CC star: 0.936 / Rpim(I) all: 0.3181 / Rrim(I) all: 0.7811 / % possible all: 97.4

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→47.63 Å / SU ML: 0.2058 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.5117
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2246 922 5 %
Rwork0.1891 17509 -
obs0.1908 18431 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.99 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1981 0 0 45 2026
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00252025
X-RAY DIFFRACTIONf_angle_d0.54072745
X-RAY DIFFRACTIONf_chiral_restr0.0433306
X-RAY DIFFRACTIONf_plane_restr0.0049360
X-RAY DIFFRACTIONf_dihedral_angle_d4.514274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.320.25281270.22922423X-RAY DIFFRACTION98.11
2.32-2.460.28021310.2112492X-RAY DIFFRACTION99.96
2.46-2.650.24011320.20692513X-RAY DIFFRACTION100
2.65-2.920.25231310.21292492X-RAY DIFFRACTION100
2.92-3.340.30811320.21772504X-RAY DIFFRACTION99.96
3.34-4.210.22091330.18682514X-RAY DIFFRACTION99.96
4.21-47.630.1831360.16612571X-RAY DIFFRACTION99.74

+
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