[English] 日本語
Yorodumi
- PDB-6m6s: Crystal structure of Caenorhabditis elegans Dicer-related helicas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6m6s
TitleCrystal structure of Caenorhabditis elegans Dicer-related helicase 3 (DRH-3) C-terminal domain with 5'-ppp 12-mer dsRNA
Components
  • Dicer Related Helicase
  • RNA (5'-R(*(GTP)P*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')
KeywordsRNA BINDING PROTEIN/RNA / RNA Interference (RNAi) / RNA Helicase / HYDROLASE / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


Negative regulators of DDX58/IFIH1 signaling / ISG15 antiviral mechanism / metaphase plate / Ub-specific processing proteases / P granule assembly / regulatory ncRNA-mediated post-transcriptional gene silencing / siRNA processing / ATP-dependent activity, acting on RNA / P granule / RNA polymerase binding ...Negative regulators of DDX58/IFIH1 signaling / ISG15 antiviral mechanism / metaphase plate / Ub-specific processing proteases / P granule assembly / regulatory ncRNA-mediated post-transcriptional gene silencing / siRNA processing / ATP-dependent activity, acting on RNA / P granule / RNA polymerase binding / antiviral innate immune response / helicase activity / condensed nuclear chromosome / double-stranded RNA binding / single-stranded RNA binding / ATP hydrolysis activity / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
RIG-I-like receptor, C-terminal regulatory domain / RIG-I-like receptor, C-terminal domain superfamily / C-terminal domain of RIG-I / RIG-I-like receptor (RLR) C-terminal regulatory (CTR) domain profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / 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. ...RIG-I-like receptor, C-terminal regulatory domain / RIG-I-like receptor, C-terminal domain superfamily / C-terminal domain of RIG-I / RIG-I-like receptor (RLR) C-terminal regulatory (CTR) domain profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / 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
RNA / RNA (> 10) / Helicase ATP-binding domain-containing protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLi, K. / Zheng, J. / Wirawan, M. / Xiong, Z. / Fedorova, O. / Griffin, P. / Plyle, A. / Luo, D.
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Insights into the structure and RNA-binding specificity of Caenorhabditis elegans Dicer-related helicase 3 (DRH-3).
Authors: Li, K. / Zheng, J. / Wirawan, M. / Trinh, N.M. / Fedorova, O. / Griffin, P.R. / Pyle, A.M. / Luo, D.
History
DepositionMar 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 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
A: Dicer Related Helicase
B: Dicer Related Helicase
C: RNA (5'-R(*(GTP)P*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')
D: RNA (5'-R(*(GTP)P*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8566
Polymers48,7264
Non-polymers1312
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-16 kcal/mol
Surface area19680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.775, 93.090, 133.823
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

-
Components

#1: Protein Dicer Related Helicase


Mass: 20345.457 Da / Num. of mol.: 2 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: drh-3, CELE_D2005.5, D2005.5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q93413
#2: RNA chain RNA (5'-R(*(GTP)P*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')


Mass: 4017.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.02 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Tris pH 7.5, 30% w/v polyethylene glycol 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.6→43.96 Å / Num. obs: 56358 / % possible obs: 99.4 % / Redundancy: 3.1 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.042 / Rrim(I) all: 0.064 / Χ2: 0.88 / Net I/σ(I): 14.9
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.761 / Num. unique obs: 2845 / CC1/2: 0.586 / Rrim(I) all: 1.021 / Χ2: 0.75 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIXdev_1137refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M6R

6m6r


Resolution: 1.6→23.03 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 19.74
RfactorNum. reflection% reflection
Rfree0.1988 2858 5.08 %
Rwork0.1692 --
obs0.1707 56281 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→23.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2661 534 2 332 3529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0173452
X-RAY DIFFRACTIONf_angle_d1.8814775
X-RAY DIFFRACTIONf_dihedral_angle_d20.0011399
X-RAY DIFFRACTIONf_chiral_restr0.125532
X-RAY DIFFRACTIONf_plane_restr0.009499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.62760.2941360.26072639X-RAY DIFFRACTION100
1.6276-1.65720.27441390.24032636X-RAY DIFFRACTION100
1.6572-1.6890.27391450.22662678X-RAY DIFFRACTION100
1.689-1.72350.25261340.21952632X-RAY DIFFRACTION100
1.7235-1.7610.26031470.20372663X-RAY DIFFRACTION100
1.761-1.80190.22731450.19992640X-RAY DIFFRACTION100
1.8019-1.8470.21961570.18792631X-RAY DIFFRACTION100
1.847-1.89690.22331300.18252698X-RAY DIFFRACTION100
1.8969-1.95270.22321330.17962655X-RAY DIFFRACTION100
1.9527-2.01570.19961410.17412691X-RAY DIFFRACTION100
2.0157-2.08760.21121540.17272658X-RAY DIFFRACTION100
2.0876-2.17120.20461440.16672655X-RAY DIFFRACTION100
2.1712-2.26990.19951520.16382701X-RAY DIFFRACTION100
2.2699-2.38950.19751580.16712660X-RAY DIFFRACTION100
2.3895-2.5390.19171310.16592678X-RAY DIFFRACTION99
2.539-2.73470.21251330.17742704X-RAY DIFFRACTION99
2.7347-3.00940.21871470.1782714X-RAY DIFFRACTION99
3.0094-3.44360.15971330.15492708X-RAY DIFFRACTION98
3.4436-4.33390.16521460.13892683X-RAY DIFFRACTION97
4.3339-23.030.18481530.15882699X-RAY DIFFRACTION92
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.79570.5947-0.05641.8271-0.38941.9842-0.04220.2065-0.0858-0.13570.0904-0.00020.0437-0.0776-0.04530.13040.0002-0.00780.0862-0.00060.072-11.9244-14.7492-1.2914
21.44050.1691-0.23692.1788-0.58312.5555-0.0254-0.0897-0.1585-0.056-0.02390.05360.12860.24160.02310.1626-0.014-0.03940.20640.06610.1212-7.6694-33.645632.6755
30.332-0.58950.42361.0338-0.76830.5337-0.0025-0.2722-0.2982-0.21070.06260.09410.90980.1667-0.08640.54580.10690.01930.29130.06310.2546-8.3833-37.35678.1379
41.5383-0.1622-0.91390.2817-1.00285.0269-0.0332-0.2563-0.2735-0.6842-0.12840.09281.12621.0041-0.07760.6305-0.0486-0.02550.38250.02440.2454-9.6433-39.031410.3231
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'D'

+
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