4K98

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

> Summary

Summary for 4K98

Related4K96 4K97 4K8V 4K99 4K9A 4K9B
DescriptorCyclic GMP-AMP synthase (E.C.2.7.7.-)/DNA
Functional Keywordsnucleotidyltransferase fold, transferase-dna complex, transferase/dna
Biological sourceMus musculus (mouse)
More
Cellular locationCytoplasm, cytosol Q8C6L5
Total number of polymer chains3
Total molecular weight53925.81
Authors
Gao, P.,Wu, Y.,Patel, D.J. (deposition date: 2013-04-19, release date: 2013-05-15, modification date: 2013-08-28)
Primary citation
Gao, P.,Ascano, M.,Wu, Y.,Barchet, W.,Gaffney, B.L.,Zillinger, T.,Serganov, A.A.,Liu, Y.,Jones, R.A.,Hartmann, G.,Tuschl, T.,Patel, D.J.
Cyclic [G(2',5')pA(3',5')p] is the metazoan second messenger produced by DNA-activated cyclic GMP-AMP synthase.
Cell(Cambridge,Mass.), 153:1094-1107, 2013
PubMed: 23647843
DOI: 10.1016/j.cell.2013.04.046
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (1.94 Å)
?

Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.196504.3%5.2%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 4k98
no rotation
Molmil generated image of 4k98
rotated about x axis by 90°
Molmil generated image of 4k98
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
ACyclic GMP-AMP synthasepolymer36242512.51
UniProt (Q8C6L5)
Pfam (PF03281)
Mus musculus (mouse)@PDBjcGAMP synthase, cGAS, m-cGAS, Mab-21 domain-containing protein 1
DDNA-Fpolymer175253.51
EDNA-Rpolymer175159.41
ZINC IONnon-polymer65.41
MAGNESIUM IONnon-polymer24.32
GUANOSINE-5'-TRIPHOSPHATEnon-polymer523.21
GUANOSINE-5'-MONOPHOSPHATEnon-polymer363.21
waterwater18.0361

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains3
Total molecular weight52925.4
Non-Polymers*Number of molecules5
Total molecular weight1000.4
All*Total molecular weight53925.8
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.94 Å)

Cell axes85.37597.877133.465
Cell angles90.0090.0090.00
SpacegroupI 2 2 2
Resolution limits39.45 - 1.94
the highest resolution shell value1.988 - 1.940
R-factor0.1593
R-work0.15720
the highest resolution shell value0.291
R-free0.19920
the highest resolution shell value0.334
RMSD bond length0.018
RMSD bond angle2.183

Data Collection Statistics

Resolution limits50.00 - 1.94
the highest resolution shell value -
Number of reflections41225
Completeness98.9
I/sigma(I)2

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, SITTING DROP5293

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

?

Functional Information from GO Data

ChainGOidnamespacecontents
A0005829cellular_componentcytosol
A0005524molecular_functionATP binding
A0061501molecular_functioncyclic-GMP-AMP synthase activity
A0003677molecular_functionDNA binding
A0005525molecular_functionGTP binding
A0046872molecular_functionmetal ion binding
A0002218biological_processactivation of innate immune response
A0071360biological_processcellular response to exogenous dsRNA
A0009190biological_processcyclic nucleotide biosynthetic process
A0051607biological_processdefense response to virus
A0045087biological_processinnate immune response
A0002230biological_processpositive regulation of defense response to virus by host
?

Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC14BINDING SITE FOR RESIDUE ZN A 601
ChainResidue
AHIS233
ACYS239
ACYS240
ACYS247

AC25BINDING SITE FOR RESIDUE MG A 602
ChainResidue
AGLU66
AASP68
AMG
AGTP
AHOH

AC36BINDING SITE FOR RESIDUE MG A 603
ChainResidue
AGLU66
AASP68
AASP162
AMG
AGTP
AG

AC418BINDING SITE FOR RESIDUE GTP A 604
ChainResidue
AGLY53
ASER54
AGLU66
AASP68
AARG219
ALYS257
ACYS274
ASER275
ATYR276
AMG
AMG
AG
AHOH
AHOH
AHOH
AHOH
AHOH
AHOH

AC511BINDING SITE FOR RESIDUE G A 605
ChainResidue
ATHR52
AASP68
AMET70
APRO147
AASP162
AARG219
ASER221
ASER223
AMG
AGTP
AHOH

?

Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
G_4k98_A_60516GUANOSINE-5'-MONOPHOSPHATE binding site
ChainResidueligand
ATHR197G: GUANOSINE-5'-MONOPHOSPHATE
AGLU211G: GUANOSINE-5'-MONOPHOSPHATE
AASP213G: GUANOSINE-5'-MONOPHOSPHATE
AMET215G: GUANOSINE-5'-MONOPHOSPHATE
ASER291-ALA293G: GUANOSINE-5'-MONOPHOSPHATE
AASP307G: GUANOSINE-5'-MONOPHOSPHATE
AILE309G: GUANOSINE-5'-MONOPHOSPHATE
AVAL348G: GUANOSINE-5'-MONOPHOSPHATE
ALYS350G: GUANOSINE-5'-MONOPHOSPHATE
AARG364-SER368G: GUANOSINE-5'-MONOPHOSPHATE

GTP_4k98_A_60414GUANOSINE-5'-TRIPHOSPHATE binding site
ChainResidueligand
AGLY198-SER199GTP: GUANOSINE-5'-TRIPHOSPHATE
AGLU202GTP: GUANOSINE-5'-TRIPHOSPHATE
ALYS205GTP: GUANOSINE-5'-TRIPHOSPHATE
AGLU211GTP: GUANOSINE-5'-TRIPHOSPHATE
AASP213GTP: GUANOSINE-5'-TRIPHOSPHATE
AASP307GTP: GUANOSINE-5'-TRIPHOSPHATE
AARG364GTP: GUANOSINE-5'-TRIPHOSPHATE
ALYS402GTP: GUANOSINE-5'-TRIPHOSPHATE
ACYS419-TYR421GTP: GUANOSINE-5'-TRIPHOSPHATE
ALYS424GTP: GUANOSINE-5'-TRIPHOSPHATE
AHIS467GTP: GUANOSINE-5'-TRIPHOSPHATE

?

Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
?

Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI33ATP.
ChainResidueDetails
ASER54
AGLU226
ALYS257

SWS_FT_FI42GTP.
ChainResidueDetails
ATHR52
AASP162

SWS_FT_FI51ATP.
ChainResidueDetails
ANA*

SWS_FT_FI61GTP.
ChainResidueDetails
ANA*

?

Catalytic Information from CSA

site_idNumber of ResiduesDetails
?

Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

PDBj@FacebookPDBj@TwitterwwPDBwwPDB FoundationEM DataBank

Copyright © 2013-2016 Protein Data Bank Japan