7V0W | pdb_00007v0w

Structure of Ternary Complex of cGAS with dsDNA and Bound 5 -pppG(2,5 )pA

PDB DOI: https://doi.org/10.2210/pdb7V0W/pdb
NAKB: 7V0W

Classification: Transferase/DNA
Organism(s): Mus musculus, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-05-11 Released: 2023-05-17
Deposition Author(s): Wu, S., Gabelli, S.B., Sohn, J.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.66 Å
R-Value Free:
0.238 (Depositor), 0.248 (DCC)
R-Value Work:
0.199 (Depositor), 0.207 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

The structural basis for 2'-5'/3'-5'-cGAMP synthesis by cGAS

Wu, S., Gabelli, S.B., Sohn, J.

(2024) Nat Commun 15: 4012

DOI: https://doi.org/10.1038/s41467-024-48365-3

Macromolecule Content

Total Structure Weight: 109.32 kDa
Atom Count: 7,266
Modeled Residue Count: 756
Deposited Residue Count: 800
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic GMP-AMP synthase	A, B [auth C]	364	Mus musculus	Mutation(s): 2 Gene Names: Cgas, Mb21d1 EC: 2.7.7.86
UniProt & NIH Common Fund Data Resources
Find proteins for Q8C6L5 (Mus musculus) Explore Q8C6L5 Go to UniProtKB: Q8C6L5
IMPC: MGI:2442261
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8C6L5
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
Palindromic DNA18	C [auth E], D [auth F], E [auth I], F [auth J]	18	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP (Subject of Investigation/LOI) Query on GTP Download:Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain J [auth A] MOL2 format, chain N [auth C] MOL2 format, chain J [auth A] mmCIF format, chain N [auth C] mmCIF format, chain J [auth A]	J [auth A], N [auth C]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain J [auth A] Focus chain N [auth C] Interactions & Density Focus chain J [auth A] Focus chain N [auth C]
AMP (Subject of Investigation/LOI) Query on AMP Download:Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain I [auth A] MOL2 format, chain M [auth C] MOL2 format, chain I [auth A] mmCIF format, chain M [auth C] mmCIF format, chain I [auth A]	I [auth A], M [auth C]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain I [auth A] Focus chain M [auth C] Interactions & Density Focus chain I [auth A] Focus chain M [auth C]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain G [auth A] MOL2 format, chain K [auth C] MOL2 format, chain G [auth A] mmCIF format, chain K [auth C] mmCIF format, chain G [auth A]	G [auth A], K [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth C] Interactions & Density Focus chain G [auth A] Focus chain K [auth C]
MN (Subject of Investigation/LOI) Query on MN Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain H [auth A] MOL2 format, chain L [auth C] MOL2 format, chain H [auth A] mmCIF format, chain L [auth C] mmCIF format, chain H [auth A]	H [auth A], L [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth C] Interactions & Density Focus chain H [auth A] Focus chain L [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.66 Å
R-Value Free: 0.238 (Depositor), 0.248 (DCC)
R-Value Work: 0.199 (Depositor), 0.207 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.475	α = 90
b = 99.474	β = 90
c = 142.088	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
MOLREP	phasing
REFMAC	refinement
PDB-REDO	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-05-17

Deposition Author(s):

Wu, S.

Gabelli, S.B.

Sohn, J.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2023-05-17
Type: Initial release
Version 1.1: 2023-10-25
Changes: Data collection, Refinement description
Version 1.2: 2024-05-22
Changes: Database references
Version 2.0: 2024-05-29
Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Structure summary