[English] 日本語
Yorodumi
- EMDB-43547: Cryo-EM Structure of DHX36 bound to a RNA G-quadruplex derived fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-43547
TitleCryo-EM Structure of DHX36 bound to a RNA G-quadruplex derived from the cMyc G-quadruplex, Class 1
Map dataMap of the Entire DHX36-RNA Complex
Sample
  • Complex: Binary Complex of Bos taurus DHX36 bound to a RNA construct derived from the cMyc G-quadruplex
    • Protein or peptide: ATP-dependent DNA/RNA helicase DHX36
    • RNA: RNA (27-MER)
  • Ligand: water
KeywordsDEAH-Box Helicase / Helicase / G-quadruplex / RNA / Hydrolase-RNA complex
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 / catalytic activity, acting on a nucleic acid / positive regulation of cardioblast differentiation / telomerase RNA stabilization / positive regulation of mRNA 3'-end processing / pre-miRNA binding / positive regulation of telomere maintenance via telomere lengthening / positive regulation of myeloid dendritic cell cytokine production ...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 / catalytic activity, acting on a nucleic acid / positive regulation of cardioblast differentiation / telomerase RNA stabilization / positive regulation of mRNA 3'-end processing / pre-miRNA binding / positive regulation of telomere maintenance via telomere lengthening / positive regulation of myeloid dendritic cell cytokine production / 3'-UTR-mediated mRNA destabilization / G-quadruplex DNA binding / regulation of transcription by RNA polymerase III / positive regulation of dendritic spine morphogenesis / cellular response to arsenite ion / mRNA 3'-UTR AU-rich region binding / positive regulation of cytoplasmic translation / telomerase RNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / response to exogenous dsRNA / positive regulation of interferon-alpha production / regulation of embryonic development / positive regulation of transcription initiation by RNA polymerase II / regulation of mRNA stability / DNA helicase activity / ossification / mRNA 3'-UTR binding / mRNA 5'-UTR binding / histone deacetylase binding / cytoplasmic stress granule / cellular response to UV / single-stranded DNA binding / double-stranded RNA binding / cellular response to heat / G-quadruplex RNA binding / perikaryon / spermatogenesis / DNA helicase / defense response to virus / cell differentiation / chromosome, telomeric region / positive regulation of canonical NF-kappaB signal transduction / RNA helicase activity / negative regulation of translation / nuclear speck / RNA helicase / RNA polymerase II cis-regulatory region sequence-specific DNA binding / axon / innate immune response / dendrite / positive regulation of gene expression / magnesium ion binding / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / 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 (HA2), winged-helix / Helicase-associated domain / 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 domain ...: / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase associated domain (HA2), winged-helix / Helicase-associated domain / 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 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 DNA/RNA helicase DHX36
Similarity search - Component
Biological speciesBos taurus (domestic cattle) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsBanco MT / Ferre-D'Amare AR
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
CitationJournal: To Be Published
Title: Inter-domain synergy enables both DNA and RNA G-quadruplex unwinding by the DEAH-box helicase DHX36
Authors: Banco MT / Paul T / Jiang J / Myong S / Ferre-D'Amare AR
History
DepositionJan 30, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_43547.png

Downloads & links

-
Map

FileDownload / File: emd_43547.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of the Entire DHX36-RNA Complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.155
Minimum - Maximum-0.3264396 - 0.9478814
Average (Standard dev.)0.0015387624 (±0.02123063)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.0 Å
α=β=γ: 90.0 °

-
Supplemental data

+
Mask #1

Fileemd_43547_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Locally Refined half map A of the DSM...

Fileemd_43547_additional_1.map
AnnotationLocally Refined half map A of the DSM domain and RNA G-quadruplex bound to DHX36
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Locally Refined half map A of the helicase core of DHX36

Fileemd_43547_additional_10.map
AnnotationLocally Refined half map A of the helicase core of DHX36
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Locally Refined unsharpened map of the DSM domain...

Fileemd_43547_additional_11.map
AnnotationLocally Refined unsharpened map of the DSM domain and RNA G-quadruplex bound to DHX36. This map was used for rigid body fitting the DSM alpha helix and RNA G-quadruplex core.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Locally Refined unsharpened map of the RecA domains...

Fileemd_43547_additional_12.map
AnnotationLocally Refined unsharpened map of the RecA domains of DHX36. This map was used for modeling the RecA2-G4 loop.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Locally Refined mask of the RecA domains of DHX36

Fileemd_43547_additional_2.map
AnnotationLocally Refined mask of the RecA domains of DHX36
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Locally Refined unsharpened map of the helicase core...

Fileemd_43547_additional_3.map
AnnotationLocally Refined unsharpened map of the helicase core of DHX36. This map was used for modeling in water molecules.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Locally Refined half map B of the DSM...

Fileemd_43547_additional_4.map
AnnotationLocally Refined half map B of the DSM domain and RNA G-quadruplex bound to DHX36
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Locally Refined mask of the helicase core of DHX36

Fileemd_43547_additional_5.map
AnnotationLocally Refined mask of the helicase core of DHX36
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Locally Refined half map B of the RecA domains of DHX36

Fileemd_43547_additional_6.map
AnnotationLocally Refined half map B of the RecA domains of DHX36
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Locally Refined half map A of the RecA domains of DHX36

Fileemd_43547_additional_7.map
AnnotationLocally Refined half map A of the RecA domains of DHX36
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Locally Refined mask of the DSM domain and...

Fileemd_43547_additional_8.map
AnnotationLocally Refined mask of the DSM domain and RNA G-quadruplex bound to DHX36
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Locally Refined half map B of the helicase core of DHX36

Fileemd_43547_additional_9.map
AnnotationLocally Refined half map B of the helicase core of DHX36
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Half map: Half map B for refinements of the entire DHX36-RNA complex

Fileemd_43547_half_map_1.map
AnnotationHalf map B for refinements of the entire DHX36-RNA complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Half map: Half map A for refinements of the entire DHX36-RNA complex

Fileemd_43547_half_map_2.map
AnnotationHalf map A for refinements of the entire DHX36-RNA complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Binary Complex of Bos taurus DHX36 bound to a RNA construct deriv...

EntireName: Binary Complex of Bos taurus DHX36 bound to a RNA construct derived from the cMyc G-quadruplex
Components
  • Complex: Binary Complex of Bos taurus DHX36 bound to a RNA construct derived from the cMyc G-quadruplex
    • Protein or peptide: ATP-dependent DNA/RNA helicase DHX36
    • RNA: RNA (27-MER)
  • Ligand: water

-
Supramolecule #1: Binary Complex of Bos taurus DHX36 bound to a RNA construct deriv...

SupramoleculeName: Binary Complex of Bos taurus DHX36 bound to a RNA construct derived from the cMyc G-quadruplex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Bos taurus (domestic cattle)

-
Macromolecule #1: ATP-dependent DNA/RNA helicase DHX36

MacromoleculeName: ATP-dependent DNA/RNA helicase DHX36 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 111.646938 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GGRGGRGRHP GHLKGREIGL WYAKKQGQKN KEAERQERAV VHMDERREEQ IVQLLHSVQT KNDKDEEAQI SWFAPEDHGY GTEAPAENK PNSVKNVEHQ AAAMINQEKR PFRIRDKYID RDSEYLLQEN EPDATLDQQL LEDLQKKKTD LRYIEMQRFR E KLPSYGMQ ...String:
GGRGGRGRHP GHLKGREIGL WYAKKQGQKN KEAERQERAV VHMDERREEQ IVQLLHSVQT KNDKDEEAQI SWFAPEDHGY GTEAPAENK PNSVKNVEHQ AAAMINQEKR PFRIRDKYID RDSEYLLQEN EPDATLDQQL LEDLQKKKTD LRYIEMQRFR E KLPSYGMQ KELVNMIDNH QVTVISGETG CGKTTQVTQF ILDNYIERGK GSACRIVCTQ PRRISAISVA ERVAAERAES CG NGNSTGY QIRLQSRLPR KQGSILYCTT GIILQWLQSD PHLSSVSHIV LDEIHERNLQ SDVLMTVVKD LLSYRPDLKV VLM SATLNA EKFSEYFGNC PMIHIPGFTF PVVEYLLEDI IEKIRYVPEQ KEHRSQFKKG FMQGHVNRQE KEEKEAIYKE RWPG YLREL RQRYSASTVD VVEMMDDEKV DLNLIAALIR YIVLEEEDGA ILVFLPGWDN ISTLHDLLMS QVMFKSDKFI IIPLH SLMP TVNQTQVFKR TPPGVRKIVI ATNIAETSIT IDDVVYVIDG GKIKETHFDT QNNISTMSAE WVSKANAKQR KGRAGR VQP GHCYHLYNSL RASLLDDYQL PEILRTPLEE LCLQIKILRL GGIAHFLSRL MDPPSNEAVL LSIKHLMELN ALDKQEE LT PLGVHLARLP VEPHIGKMIL FGALFCCLDP VLTIAASLSF KDPFVIPLGK EKVADARRKE LAKDTKSDHL TVVNAFKG W EKAKQRGFRY EKDYCWEYFL SSNTLQMLHN MKGQFAEHLL GAGFVSSRNP QDPESNINSD NEKIIKAVIC AGLYPKVAK IRLNLGKKRK MVKVYTKTDG VVAIHPKSVN VEQTEFNYNW LIYHLKMRTS SIYLYDCTEV SPYCLLFFGG DISIQKDNDQ ETIAVDEWI IFQSPARIAH LVKELRKELD ILLQEKIESP HPVDWKDTKS RDCAVLSAII DLIKTQEKAT PRNLPPRFQD G YYSPHHHH HHHH

UniProtKB: ATP-dependent DNA/RNA helicase DHX36

-
Macromolecule #2: RNA (27-MER)

MacromoleculeName: RNA (27-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.775119 KDa
SequenceString:
AGGGUGGGUA GGGUGGGUUG UUUUUUU

-
Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 30 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
Component:
ConcentrationName
0.8 (V/v) %Glycerol
25.0 mMHEPES-KOH
150.0 mMPotassium Chloride
0.5 mMTCEP
2.5 mMMagnesium Chloride
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: RELION / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 222832
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

5vhe


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL
Output model

PDB-8vv2:
Cryo-EM Structure of DHX36 bound to a RNA G-quadruplex derived from the cMyc G-quadruplex, Class 1

+
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