[English] 日本語
Yorodumi
- PDB-5vhe: DHX36 in complex with the c-Myc G-quadruplex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vhe
TitleDHX36 in complex with the c-Myc G-quadruplex
Components
  • DEAH (Asp-Glu-Ala-His) box polypeptide 36
  • DNA (5'-D(*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*TP*TP*TP*TP*TP*T)-3')
KeywordsHYDROLASE
Function / homology
Function and homology information


DEx/H-box helicases activate type I IFN and inflammatory cytokines production / positive regulation of intracellular mRNA localization / positive regulation of hematopoietic progenitor cell differentiation / positive regulation of cardioblast differentiation / positive regulation of mRNA 3'-end processing / positive regulation of telomere maintenance via telomere lengthening / pre-miRNA binding / G-quadruplex DNA unwinding / RNA secondary structure unwinding / G-quadruplex DNA binding ...DEx/H-box helicases activate type I IFN and inflammatory cytokines production / positive regulation of intracellular mRNA localization / positive regulation of hematopoietic progenitor cell differentiation / positive regulation of cardioblast differentiation / positive regulation of mRNA 3'-end processing / positive regulation of telomere maintenance via telomere lengthening / pre-miRNA binding / G-quadruplex DNA unwinding / RNA secondary structure unwinding / G-quadruplex DNA binding / positive regulation of dendritic spine morphogenesis / regulation of transcription by RNA polymerase III / 3'-UTR-mediated mRNA destabilization / mRNA 3'-UTR AU-rich region binding / positive regulation of cytoplasmic translation / cellular response to arsenite ion / telomerase RNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / regulation of embryonic development / positive regulation of transcription initiation by RNA polymerase II / regulation of mRNA stability / DNA helicase activity / mRNA 3'-UTR binding / mRNA 5'-UTR binding / cytoplasmic stress granule / cellular response to UV / cellular response to heat / perikaryon / G-quadruplex RNA binding / spermatogenesis / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / DNA helicase / negative regulation of translation / RNA helicase activity / chromosome, telomeric region / cell differentiation / RNA helicase / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / axon / innate immune response / dendrite / positive regulation of gene expression / magnesium ion binding / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / mitochondrion / RNA binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / DEAD/DEAH box helicase ...: / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / 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
: / DNA / DNA (> 10) / ATP-dependent DNA/RNA helicase DHX36
Similarity search - Component
Biological speciesBos taurus (cattle)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.793 Å
AuthorsChen, M. / Ferre-D'Amare, A.
CitationJournal: Nature / Year: 2018
Title: Structural basis of G-quadruplex unfolding by the DEAH/RHA helicase DHX36.
Authors: Chen, M.C. / Tippana, R. / Demeshkina, N.A. / Murat, P. / Balasubramanian, S. / Myong, S. / Ferre-D'Amare, A.R.
History
DepositionApr 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DEAH (Asp-Glu-Ala-His) box polypeptide 36
B: DNA (5'-D(*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,8344
Polymers114,7562
Non-polymers782
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-35 kcal/mol
Surface area41980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.526, 79.282, 212.077
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein DEAH (Asp-Glu-Ala-His) box polypeptide 36


Mass: 107181.789 Da / Num. of mol.: 1 / Fragment: residues 56-1010
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: Q05B79
#2: DNA chain DNA (5'-D(*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*TP*TP*TP*TP*TP*T)-3')


Mass: 7573.854 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.59 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 200 mM sodium malonate (pH 7.0) and 25% w/v PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.793→39.641 Å / Num. obs: 12615 / % possible obs: 99.24 % / Redundancy: 9.6 % / Biso Wilson estimate: 115.04 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.2745 / Rpim(I) all: 0.09196 / Net I/σ(I): 7.81

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VHA

5vha


Resolution: 3.793→39.641 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.28 1261 10 %
Rwork0.2384 --
obs0.2427 12607 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.793→39.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6697 503 2 0 7202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027392
X-RAY DIFFRACTIONf_angle_d0.49610151
X-RAY DIFFRACTIONf_dihedral_angle_d16.4284375
X-RAY DIFFRACTIONf_chiral_restr0.0391172
X-RAY DIFFRACTIONf_plane_restr0.0031215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7927-3.94440.33261280.30931155X-RAY DIFFRACTION94
3.9444-4.12380.33991380.28261245X-RAY DIFFRACTION100
4.1238-4.34090.30091400.26631247X-RAY DIFFRACTION100
4.3409-4.61250.27691380.23861242X-RAY DIFFRACTION100
4.6125-4.9680.24471400.23651267X-RAY DIFFRACTION100
4.968-5.46680.32751400.23911256X-RAY DIFFRACTION100
5.4668-6.25520.33541420.26241278X-RAY DIFFRACTION100
6.2552-7.87080.29741430.25371288X-RAY DIFFRACTION100
7.8708-39.64310.22261520.19121368X-RAY DIFFRACTION100
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)
10.3405-0.0993-0.73820.6885-0.03711.0772-0.03810.18720.52670.2007-0.0996-0.2689-0.3976-0.13860.17531.8875-0.1047-0.05821.26930.05051.50446.447512.2642-18.2557
21.5917-0.7336-1.70641.51951.52844.7968-0.0169-0.1296-0.23920.3990.01840.13140.7477-0.62260.02520.9414-0.1411-0.06310.87290.13310.897820.8609-25.1536-20.342
30.84410.38580.82022.26711.87337.14120.0429-0.1288-0.17720.26920.1413-0.36610.1134-0.0347-0.15950.64280.0157-0.05660.7138-0.07370.886635.7325-21.2749-36.0605
42.5988-0.27860.71661.1431-0.55863.9388-0.0371-0.33150.44610.13350.0735-0.0421-0.60640.4601-0.06350.9836-0.0581-0.040.6932-0.06780.9638.174510.78-23.1871
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 58 through 179 )
2X-RAY DIFFRACTION2chain 'A' and (resid 180 through 454 )
3X-RAY DIFFRACTION3chain 'A' and (resid 455 through 665 )
4X-RAY DIFFRACTION4chain 'A' and (resid 666 through 991 )

+
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