4K99

Structure of Ternary Complex of cGAS with dsDNA and Bound 5 -pppdG(2 ,5 )pdG

> Summary

Summary for 4K99

Related4K96 4K97 4K98 4K8V 4K9A 4K9B
DescriptorCyclic GMP-AMP synthase (E.C.2.7.7.-)/DNA
Functional Keywordsnucleotidyltransferase fold, transferase-dna complex, transferase/dna
Biological sourceMus musculus (mouse)
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Cellular locationCytoplasm, cytosol Q8C6L5
Total number of polymer chains3
Total molecular weight53893.82
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 (1.95 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.209404.3%4.4%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 4k99
no rotation
Molmil generated image of 4k99
rotated about x axis by 90°
Molmil generated image of 4k99
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
3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATEnon-polymer507.21
3'-DEOXY-GUANOSINE 5'-MONOPHOSPHATEnon-polymer347.21
waterwater18.0314

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains3
Total molecular weight52925.4
Non-Polymers*Number of molecules5
Total molecular weight968.4
All*Total molecular weight53893.8
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.95 Å)
Cell axes85.12497.613131.372
Cell angles90.0090.0090.00
SpacegroupI 2 2 2
Resolution limits39.18 - 1.95
the highest resolution shell value2.007 - 1.950
R-factor0.1776
R-work0.17600
the highest resolution shell value0.230
R-free0.21240
the highest resolution shell value0.271
RMSD bond length0.008
RMSD bond angle1.718

Data Collection Statistics

Resolution limits50.00 - 1.95
the highest resolution shell value -
Number of reflections40199
Completeness100.0
I/sigma(I)2

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, SITTING DROP5.2293

Crystallization Reagents

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

> Functional details

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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
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC15BINDING SITE FOR RESIDUE MG A 602
ChainResidue
AGLU66
AASP68
AMG
AGH3
AHOH

AC26BINDING SITE FOR RESIDUE MG A 603
ChainResidue
AGLU66
AASP68
AASP162
AMG
AGH3
AGDO

AC321BINDING SITE FOR RESIDUE GH3 A 604
ChainResidue
AGLY53
ASER54
AGLU66
AASP68
AARG219
ALYS257
ACYS274
ASER275
ATYR276
AMG
AMG
AGDO
AHOH
AHOH
AHOH
AHOH
AHOH
AHOH
AHOH
AHOH
AHOH

AC414BINDING SITE FOR RESIDUE GDO A 605
ChainResidue
ATHR52
AASP68
AMET70
APRO147
AASP162
AILE164
AARG219
ASER221
ASER223
AMG
AGH3
AHOH
AHOH
AHOH

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

site_idNumber of ResiduesDetails
GDO_4k99_A_605163'-DEOXY-GUANOSINE 5'-MONOPHOSPHATE binding site
ChainResidueligand
ATHR197GDO: 3'-DEOXY-GUANOSINE 5'-MONOPHOSPHATE
AGLU211GDO: 3'-DEOXY-GUANOSINE 5'-MONOPHOSPHATE
AASP213GDO: 3'-DEOXY-GUANOSINE 5'-MONOPHOSPHATE
AMET215GDO: 3'-DEOXY-GUANOSINE 5'-MONOPHOSPHATE
ASER291-ALA293GDO: 3'-DEOXY-GUANOSINE 5'-MONOPHOSPHATE
AASP307GDO: 3'-DEOXY-GUANOSINE 5'-MONOPHOSPHATE
AILE309GDO: 3'-DEOXY-GUANOSINE 5'-MONOPHOSPHATE
AVAL348GDO: 3'-DEOXY-GUANOSINE 5'-MONOPHOSPHATE
ALYS350GDO: 3'-DEOXY-GUANOSINE 5'-MONOPHOSPHATE
AARG364-SER368GDO: 3'-DEOXY-GUANOSINE 5'-MONOPHOSPHATE

GH3_4k99_A_604173'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE binding site
ChainResidueligand
AGLY198-TYR200GH3: 3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE
AGLU202GH3: 3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE
ALYS205GH3: 3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE
AGLU211GH3: 3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE
AASP213GH3: 3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE
AASP307GH3: 3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE
AARG364GH3: 3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE
ASER368GH3: 3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE
ALYS402GH3: 3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE
AGLU406GH3: 3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE
ACYS419-TYR421GH3: 3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE
ALYS424GH3: 3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE
AHIS467GH3: 3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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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*

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Catalytic Information from CSA

site_idNumber of ResiduesDetails
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Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

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