[English] 日本語
Yorodumi
- PDB-9oh4: Cryo-EM structure of cGAS tetramer in complex with BuDNA (bubble DNA) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9oh4
TitleCryo-EM structure of cGAS tetramer in complex with BuDNA (bubble DNA)
Components
  • Bubble DNA Forward(41-MER)
  • Bubble DNA Reverse(41-MER)
  • Cyclic GMP-AMP synthase
KeywordsTRANSFERASE/DNA / Complex / Activator / TRANSFERASE-DNA complex
Function / homology
Function and homology information


: / 2',3'-cyclic GMP-AMP synthase activity / cyclic GMP-AMP synthase / regulation of type I interferon production / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / regulation of immunoglobulin production / : / regulation of T cell activation / cGAS/STING signaling pathway ...: / 2',3'-cyclic GMP-AMP synthase activity / cyclic GMP-AMP synthase / regulation of type I interferon production / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / regulation of immunoglobulin production / : / regulation of T cell activation / cGAS/STING signaling pathway / pattern recognition receptor signaling pathway / negative regulation of DNA repair / negative regulation of cGAS/STING signaling pathway / cellular response to exogenous dsRNA / cytoplasmic pattern recognition receptor signaling pathway / regulation of immune response / negative regulation of double-strand break repair via homologous recombination / nucleosome binding / positive regulation of defense response to virus by host / positive regulation of type I interferon production / phosphatidylinositol-4,5-bisphosphate binding / activation of innate immune response / determination of adult lifespan / molecular condensate scaffold activity / positive regulation of cellular senescence / site of double-strand break / double-stranded DNA binding / defense response to virus / nuclear body / innate immune response / DNA repair / DNA damage response / chromatin binding / GTP binding / protein homodimerization activity / DNA binding / nucleoplasm / ATP binding / metal ion binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Mab-21-like, nucleotidyltransferase domain / Mab-21 protein nucleotidyltransferase domain / Mab-21-like / Mab-21-like, HhH/H2TH-like domain / Mab-21 protein HhH/H2TH-like domain / Mab-21
Similarity search - Domain/homology
DNA / DNA (> 10) / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.48 Å
AuthorsWu, S. / Sohn, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM129342 United States
CitationJournal: To Be Published
Title: The Cryo-EM structure of cGAS tetramer in complex with BuDNA (bubble DNA)
Authors: Wu, S. / Sohn, J.
History
DepositionMay 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2026Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cyclic GMP-AMP synthase
B: Cyclic GMP-AMP synthase
C: Cyclic GMP-AMP synthase
D: Cyclic GMP-AMP synthase
E: Bubble DNA Forward(41-MER)
F: Bubble DNA Reverse(41-MER)
G: Bubble DNA Forward(41-MER)
H: Bubble DNA Reverse(41-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,62412
Polymers218,3638
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein
Cyclic GMP-AMP synthase / m-cGAS / 2'3'-cGAMP synthase / Mab-21 domain-containing protein 1


Mass: 41970.508 Da / Num. of mol.: 4 / Fragment: UNP residues 149-505
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mb21d1 / Plasmid: nHMT mcGAS FL
Details (production host): His*6-MBP-Tev-AgeI-mcGAS FL, Kanamycin resistance
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8C6L5, cyclic GMP-AMP synthase
#2: DNA chain Bubble DNA Forward(41-MER)


Mass: 12694.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: ordered from IDT / Source: (synth.) synthetic construct (others)
#3: DNA chain Bubble DNA Reverse(41-MER)


Mass: 12546.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: ordered from IDT / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeDetails (eV)Entity IDParent-IDSource
1The structure of mouse cGAS in complex with a bubble DNACOMPLEXComplex generated by incubating mouse cGAS with a bubble DNA.#1-#30MULTIPLE SOURCES
2mouse cGASCOMPLEX#11RECOMBINANT
3The forward strand of bubble DNACOMPLEXBubble DNA Forward oligo DNA sequence#21NATURAL
4The reverse strand of bubble DNACOMPLEXBubble DNA Reverse oligo DNA sequence#31NATURAL
Molecular weightValue: 0.222 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
32Mus musculus (house mouse)10090
43synthetic construct (others)32630
54synthetic construct (others)32630
Source (recombinant)Organism: Escherichia coli BL21 (DE3) (bacteria)
Buffer solutionpH: 7.5 / Details: 20mM Tris pH 7.5, 150mM NaCl, and 0.5mM TCEP
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMtris(hydroxymethyl)aminomethane1
2150 mMsodium chlorideNaCl1
30.5 mMtris(2-carboxyethyl)phosphine1
SpecimenConc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The complex was prepared using a gel filtration column(HiLoadTM 16/600 SuperdexTM 200pg,Cytiva).
Specimen supportDetails: Glow-discharged with a PELCO easiGlow Cryo-EM Glow Discharge Set (TED PELLA, INC.) with settings as follow: Plasma Current 15 mA, Process Timer 60s, Working Vacuum 0.37mBar, Preprocess Hold ...Details: Glow-discharged with a PELCO easiGlow Cryo-EM Glow Discharge Set (TED PELLA, INC.) with settings as follow: Plasma Current 15 mA, Process Timer 60s, Working Vacuum 0.37mBar, Preprocess Hold Timer 10s, and negative polarity.
Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K
Details: Filter paper blotted with blot force 2 and blot time 2s, and plunge-frozen in liquid ethane using a Vitrobot Mark IV at 4 degree Celsius and 100% humidity.

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9927
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV
Image scansWidth: 4096 / Height: 4096

-
Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARCv4.3.1particle selectionBlob Picker
2EPU1.12 - 3.7image acquisition
4cryoSPARCv4.3.1CTF correction
7UCSF ChimeraXversion 1.9model fitting
9cryoSPARCv4.3.1initial Euler assignment
10cryoSPARCv4.3.1final Euler assignment
11cryoSPARCv4.3.1classification
12cryoSPARCv4.3.13D reconstruction
13PHENIX1.18.2_3874:model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2969717
Details: A total of 2,969,717 particles were auto-picked using Blob Picker in CryoSPARC.
3D reconstructionResolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 62441 / Details: Particles are randomly split into two halves. / Symmetry type: POINT
Atomic model buildingB value: 87.5 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Cross-correlation coefficient
Details: Initial local fitting was done using UCSF ChimeraX, and then COOT was used for manual building.
Atomic model building

3D fitting-ID: 1 / Accession code: 5N6I / PDB-ID: 5N6I

5n6i

/ Source name: PDB / Type: experimental model

IDPdb chain-IDChain-ID
1AA
2BB
3CC
4DD
5GG
6HH
7II
8JJ
RefinementHighest resolution: 3.48 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00315832
ELECTRON MICROSCOPYf_angle_d0.52822002
ELECTRON MICROSCOPYf_dihedral_angle_d25.3863412
ELECTRON MICROSCOPYf_chiral_restr0.0352392
ELECTRON MICROSCOPYf_plane_restr0.0052220

+
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