[English] 日本語
Yorodumi
- PDB-4tyn: DEAD-box helicase Mss116 bound to ssDNA and ADP-BeF -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4tyn
TitleDEAD-box helicase Mss116 bound to ssDNA and ADP-BeF
Components
  • ATP-dependent RNA helicase MSS116, mitochondrial
  • DNA (5'-D(P*AP*AP*AP*AP*AP*AP*A)-3')
KeywordsHYDROLASE/DNA / DEAD-box / RNA helicase / hydrolase / RNA BINDING PROTEIN-DNA complex / HYDROLASE-DNA complex
Function / homology
Function and homology information


Group II intron splicing / transcription elongation by mitochondrial RNA polymerase / mitochondrial RNA processing / mitochondrial translational initiation / RNA strand annealing activity / G-quadruplex DNA binding / mitochondrial translational elongation / mitochondrial ribosome / Group I intron splicing / RNA folding ...Group II intron splicing / transcription elongation by mitochondrial RNA polymerase / mitochondrial RNA processing / mitochondrial translational initiation / RNA strand annealing activity / G-quadruplex DNA binding / mitochondrial translational elongation / mitochondrial ribosome / Group I intron splicing / RNA folding / mRNA processing / regulation of translation / G-quadruplex RNA binding / RNA helicase activity / RNA helicase / mitochondrial matrix / mRNA binding / ATP hydrolysis activity / mitochondrion / RNA binding / ATP binding
Similarity search - Function
DEAD-box subfamily ATP-dependent helicases signature. / 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 ...DEAD-box subfamily ATP-dependent helicases signature. / 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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA / ATP-dependent RNA helicase MSS116, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.959 Å
AuthorsMallam, A.L. / Sidote, D.J. / Lambowitz, A.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Elife / Year: 2014
Title: Molecular insights into RNA and DNA helicase evolution from the determinants of specificity for a DEAD-box RNA helicase.
Authors: Mallam, A.L. / Sidote, D.J. / Lambowitz, A.M.
History
DepositionJul 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 1.2Mar 4, 2015Group: Database references
Revision 1.3Mar 30, 2022Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: database_2 / entity_src_gen ...database_2 / entity_src_gen / pdbx_audit_support / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*A)-3')
A: ATP-dependent RNA helicase MSS116, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5095
Polymers59,9912
Non-polymers5183
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-14 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.389, 126.189, 55.231
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: DNA chain DNA (5'-D(P*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 2147.490 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#2: Protein ATP-dependent RNA helicase MSS116, mitochondrial


Mass: 57843.730 Da / Num. of mol.: 1 / Fragment: UNP residues 88-596
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: MSS116, YDR194C, YD9346.05C / Plasmid: pMAL-c2t / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta 2 / References: UniProt: P15424, RNA helicase
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M ammonium acetate, 20 % PEG 3350

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.959→44.15 Å / Num. obs: 13129 / % possible obs: 94.64 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.198 / Net I/σ(I): 8.55
Reflection shellResolution: 3→3.05 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 1.46 / Rsym value: 0.491 / % possible all: 88

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_1583) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I5X

3i5x


Resolution: 2.959→44.15 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2444 659 5.03 %Random selection
Rwork0.1962 ---
obs0.1986 13111 95.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.959→44.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3910 147 32 0 4089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034181
X-RAY DIFFRACTIONf_angle_d0.7515699
X-RAY DIFFRACTIONf_dihedral_angle_d15.2181548
X-RAY DIFFRACTIONf_chiral_restr0.03673
X-RAY DIFFRACTIONf_plane_restr0.003703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9594-3.18780.34051220.24762105X-RAY DIFFRACTION83
3.1878-3.50850.27591170.22812506X-RAY DIFFRACTION97
3.5085-4.01590.23571400.20562556X-RAY DIFFRACTION99
4.0159-5.05840.21281420.16642600X-RAY DIFFRACTION99
5.0584-44.15530.23271380.18432685X-RAY DIFFRACTION98

+
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