[English] 日本語
Yorodumi
- PDB-8gin: Structure of Ternary Complex of mouse cGAS with dsDNA and Bound A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8gin
TitleStructure of Ternary Complex of mouse cGAS with dsDNA and Bound ATP: with 10mM Mg2+ and 0.015mM Mn2+
Components
  • Cyclic GMP-AMP synthase
  • Palindromic DNA18
KeywordsIMMUNE SYSTEM/DNA / Transferase-DNA complex / cGAS / ATP and divalent metal / IMMUNE SYSTEM / IMMUNE SYSTEM-DNA complex
Function / homology
Function and homology information


2',3'-cyclic GMP-AMP synthase activity / cyclic GMP-AMP synthase / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / regulation of type I interferon production / regulation of immunoglobulin production / cGAS/STING signaling pathway / regulation of T cell activation / negative regulation of cGAS/STING signaling pathway / negative regulation of DNA repair ...2',3'-cyclic GMP-AMP synthase activity / cyclic GMP-AMP synthase / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / regulation of type I interferon production / regulation of immunoglobulin production / cGAS/STING signaling pathway / regulation of T cell activation / negative regulation of cGAS/STING signaling pathway / negative regulation of DNA repair / cGMP-mediated signaling / cellular response to exogenous dsRNA / positive regulation of type I interferon production / nucleosome binding / regulation of immune response / negative regulation of double-strand break repair via homologous recombination / positive regulation of defense response to virus by host / activation of innate immune response / phosphatidylinositol-4,5-bisphosphate binding / cAMP-mediated signaling / 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 / ATP binding / nucleus / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Mab-21-like, nucleotidyltransferase domain / Mab-21-like / Mab-21-like, HhH/H2TH-like domain / Mab-21 protein HhH/H2TH-like domain / Mab-21 / Mab-21 protein nucleotidyltransferase domain
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / DNA / DNA (> 10) / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsWu, S. / Sohn, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2024
Title: The structural basis for 2'-5'/3'-5'-cGAMP synthesis by cGAS.
Authors: Wu, S. / Gabelli, S.B. / Sohn, J.
History
DepositionMar 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cyclic GMP-AMP synthase
C: Cyclic GMP-AMP synthase
E: Palindromic DNA18
F: Palindromic DNA18
I: Palindromic DNA18
J: Palindromic DNA18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,64314
Polymers107,3396
Non-polymers1,3048
Water37821
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.392, 98.709, 142.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / DNA chain , 2 types, 6 molecules ACEFIJ

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


Mass: 42640.254 Da / Num. of mol.: 2 / Fragment: catalytic domain, residues 147-507
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cgas, Mb21d1 / Plasmid: nHMT mCAT WT
Details (production host): His*6-MBP-Tev-AgeI-mcGAS CAT, Kanamycin resistance
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8C6L5, cyclic GMP-AMP synthase
#2: DNA chain
Palindromic DNA18


Mass: 5514.603 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: ordered from IDT / Source: (synth.) synthetic construct (others)

-
Non-polymers , 5 types, 29 molecules

#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.41 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M ammonium acetate, 32% MPD, with 0.1 M Bis-Tris pH 6.5
PH range: 6.0-7.0 / Temp details: 4-degree Celsius in cold room

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: nitrogen gas stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 1.891 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 1, 2022
RadiationMonochromator: horizontal bounce Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.891 Å / Relative weight: 1
ReflectionResolution: 2.75→29.78 Å / Num. obs: 28710 / % possible obs: 99 % / Redundancy: 6.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.045 / Rrim(I) all: 0.115 / Χ2: 1.02 / Net I/σ(I): 10.8 / Num. measured all: 186375
Reflection shellResolution: 2.75→2.9 Å / % possible obs: 94 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.552 / Num. measured all: 24848 / Num. unique obs: 3913 / CC1/2: 0.867 / Rpim(I) all: 0.233 / Rrim(I) all: 0.6 / Χ2: 1.04 / Net I/σ(I) obs: 3.1

-
Processing

Software
NameVersionClassification
XDS20210205data reduction
Aimless0.7.7data scaling
MOLREP11.7.03phasing
Coot0.9.6model building
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→29.78 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2247 2708 5.03 %
Rwork0.1807 --
obs0.1829 28710 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5830 1464 68 21 7383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_d1.087
X-RAY DIFFRACTIONf_dihedral_angle_d23.881470
X-RAY DIFFRACTIONf_chiral_restr0.0541151
X-RAY DIFFRACTIONf_plane_restr0.0091084
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.80.37431170.31432078X-RAY DIFFRACTION77
2.8-2.860.33491540.28532722X-RAY DIFFRACTION100
2.86-2.910.32051500.26622733X-RAY DIFFRACTION100
2.91-2.980.3031430.25872745X-RAY DIFFRACTION100
2.98-3.050.3251390.26192707X-RAY DIFFRACTION100
3.05-3.120.33161460.25072700X-RAY DIFFRACTION100
3.12-3.210.25451170.22722784X-RAY DIFFRACTION100
3.21-3.30.23791490.19762679X-RAY DIFFRACTION100
3.3-3.410.27471410.20152728X-RAY DIFFRACTION99
3.41-3.530.23281610.1892711X-RAY DIFFRACTION99
3.53-3.670.21811250.1932739X-RAY DIFFRACTION100
3.67-3.840.25521440.18732690X-RAY DIFFRACTION100
3.84-4.040.1991550.17262751X-RAY DIFFRACTION100
4.04-4.290.18921360.15472721X-RAY DIFFRACTION100
4.29-4.620.20251770.152693X-RAY DIFFRACTION100
4.62-5.080.21041390.15292736X-RAY DIFFRACTION100
5.08-5.810.22031230.16542729X-RAY DIFFRACTION100
5.82-7.310.21211480.18292733X-RAY DIFFRACTION100
7.31-29.780.14651440.12022716X-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)
11.4214-0.277-0.34881.8232-0.231.28080.0035-0.0790.1931-0.01820.03710.1245-0.1269-0.0622-0.0460.332-0.0004-0.02770.3316-0.00610.36684.895826.728320.3705
21.7267-1.08060.3592.8714-0.60281.5832-0.1085-0.1742-0.0799-0.07370.0714-0.42060.11540.1520.03330.35340.04450.04830.43440.02780.428933.6039-8.336418.7272
33.2485-0.75311.11992.39881.93782.54290.2098-1.00410.040.64650.1885-0.07010.34530.2904-0.52590.5345-0.14270.0540.8067-0.01230.522128.772222.857631.6025
42.3482-0.75950.71573.5518-0.01212.08570.3393-0.8346-0.19040.646-0.03450.12980.47150.8489-0.34520.8035-0.0717-0.06940.8544-0.02810.493429.516323.42732.5288
53.488-0.8911-1.26782.5891-0.18732.1570.29070.0127-0.4424-0.27640.24830.1720.4568-0.4479-0.47010.6435-0.0677-0.03550.5410.10210.56298.0897-8.668617.7321
63.6118-0.26010.76713.480.04442.14070.20430.2107-0.2844-0.250.26360.233-0.2862-0.588-0.45210.6082-0.03230.08110.63210.14310.51268.4466-6.649218.6173
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 148:506) or (chain A and resseq 602:602)
2X-RAY DIFFRACTION2(chain C and resseq 148:506) or (chain C and resseq 602:602)
3X-RAY DIFFRACTION3(chain E and resseq 1:18)
4X-RAY DIFFRACTION4(chain F and resseq 1:18)
5X-RAY DIFFRACTION5(chain I and resseq 1:18)
6X-RAY DIFFRACTION6(chain J and resseq 1:18)

+
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