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- PDB-4k99: Structure of Ternary Complex of cGAS with dsDNA and Bound 5 -pppd... -

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Basic information

Entry
Database: PDB / ID: 4k99
TitleStructure of Ternary Complex of cGAS with dsDNA and Bound 5 -pppdG(2 ,5 )pdG
Components
  • Cyclic GMP-AMP synthase
  • DNA-F
  • DNA-R
KeywordsTRANSFERASE/DNA / nucleotidyltransferase fold / TRANSFERASE-DNA complex
Function / homology
Function and homology information


regulation of type I interferon production / cyclic GMP-AMP synthase / 2',3'-cyclic GMP-AMP synthase activity / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / cGAS/STING signaling pathway / regulation of immunoglobulin production / regulation of T cell activation / pattern recognition receptor signaling pathway / negative regulation of DNA repair ...regulation of type I interferon production / cyclic GMP-AMP synthase / 2',3'-cyclic GMP-AMP synthase activity / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / cGAS/STING signaling pathway / regulation of immunoglobulin production / regulation of T cell activation / pattern recognition receptor signaling pathway / negative regulation of DNA repair / negative regulation of double-strand break repair via homologous recombination / regulation of innate immune response / cytoplasmic pattern recognition receptor signaling pathway / negative regulation of cGAS/STING signaling pathway / cellular response to exogenous dsRNA / negative regulation of innate immune response / cGMP-mediated signaling / cAMP-mediated signaling / nucleosome binding / positive regulation of type I interferon production / regulation of immune response / positive regulation of defense response to virus by host / molecular condensate scaffold activity / phosphatidylinositol-4,5-bisphosphate binding / activation of innate immune response / determination of adult lifespan / positive regulation of cellular senescence / site of double-strand break / double-stranded DNA binding / defense response to virus / nuclear body / DNA repair / innate immune response / DNA damage response / chromatin binding / GTP binding / protein homodimerization activity / DNA binding / nucleoplasm / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Beta Polymerase; domain 2 - #90 / Poly(a)-polymerase, middle domain - #40 / Poly(a)-polymerase, middle domain / Mab-21-like, nucleotidyltransferase domain / Mab-21-like, HhH/H2TH-like domain / Mab-21 protein HhH/H2TH-like domain / Mab-21 protein nucleotidyltransferase domain / Mab-21-like / Mab-21 / Beta Polymerase; domain 2 ...Beta Polymerase; domain 2 - #90 / Poly(a)-polymerase, middle domain - #40 / Poly(a)-polymerase, middle domain / Mab-21-like, nucleotidyltransferase domain / Mab-21-like, HhH/H2TH-like domain / Mab-21 protein HhH/H2TH-like domain / Mab-21 protein nucleotidyltransferase domain / Mab-21-like / Mab-21 / Beta Polymerase; domain 2 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
3'-deoxy-guanosine 5'-monophosphate / 3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsGao, P. / Wu, Y. / Patel, D.J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2013
Title: Cyclic [G(2',5')pA(3',5')p] is the metazoan second messenger produced by DNA-activated cyclic GMP-AMP synthase.
Authors: 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.
History
DepositionApr 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclic GMP-AMP synthase
D: DNA-F
E: DNA-R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8938
Polymers52,9253
Non-polymers9685
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-41 kcal/mol
Surface area21310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.124, 97.613, 131.372
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-736-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 42512.121 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, UNP residues 147-507
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mb21d1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8C6L5, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases

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DNA chain , 2 types, 2 molecules DE

#2: DNA chain DNA-F


Mass: 5253.451 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence was synthesized by regular protocol
#3: DNA chain DNA-R


Mass: 5159.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence was synthesized by regular protocol

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Non-polymers , 5 types, 319 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GH3 / 3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE


Type: RNA linking / Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#7: Chemical ChemComp-GDO / 3'-deoxy-guanosine 5'-monophosphate


Type: RNA linking / Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details3'-dGTP WAS ADDED TO THE CRYSTALLIZATION CONDITION AND A ppp-3'dG-p-3'dG LIGAND WAS OBSERVED WHICH ...3'-dGTP WAS ADDED TO THE CRYSTALLIZATION CONDITION AND A ppp-3'dG-p-3'dG LIGAND WAS OBSERVED WHICH HAS BEEN REPRESENTED AS GH3 AND GDO WITH A 2' TO 5' LINK

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 0.1 M NaAc, 12% MPD, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 7, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 40199 / Num. obs: 40199 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.95→2.05 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→39.176 Å / SU ML: 0.15 / σ(F): 1.35 / Phase error: 20.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2124 1693 4.21 %RANDOM
Rwork0.176 ---
obs0.1776 40199 99.93 %-
all-40199 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→39.176 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2924 592 56 314 3886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083712
X-RAY DIFFRACTIONf_angle_d1.7185123
X-RAY DIFFRACTIONf_dihedral_angle_d20.6761468
X-RAY DIFFRACTIONf_chiral_restr0.156556
X-RAY DIFFRACTIONf_plane_restr0.004539
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.00740.27061390.22983173X-RAY DIFFRACTION100
2.0074-2.07220.24391400.20663175X-RAY DIFFRACTION100
2.0722-2.14630.25751400.19883170X-RAY DIFFRACTION100
2.1463-2.23220.23111400.18383180X-RAY DIFFRACTION100
2.2322-2.33380.23061390.18283170X-RAY DIFFRACTION100
2.3338-2.45680.20141390.18183165X-RAY DIFFRACTION100
2.4568-2.61070.23561410.18733207X-RAY DIFFRACTION100
2.6107-2.81220.23951420.19053214X-RAY DIFFRACTION100
2.8122-3.09510.23381400.19123210X-RAY DIFFRACTION100
3.0951-3.54270.19411430.16863234X-RAY DIFFRACTION100
3.5427-4.46240.1931430.15213253X-RAY DIFFRACTION100
4.4624-39.18380.19541470.17023355X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.0177-0.23540.26251.8582-0.22764.52280.1038-0.01410.5016-0.09670.03980.1921-0.7865-0.4799-0.12390.2218-0.0920.04010.10570.01610.3714182.6343414.9017172.8272
22.42880.2553-0.63932.7591.31023.3135-0.0460.41480.1113-0.50760.05260.1582-0.0805-0.0083-0.06730.3118-0.04620.00690.22760.05730.2328184.4307405.4958163.9369
33.1463-1.3796-0.37093.1872-0.71271.71930.26860.5516-0.4925-0.9143-0.2755-0.22390.33770.16890.03350.4140.02720.10750.3273-0.0420.3443194.1611390.4467158.093
41.0155-0.0224-0.02953.5201-0.66041.80570.04050.23990.248-0.4384-0.2-0.4111-0.13780.30780.04020.2827-0.0340.1090.27320.07960.2875193.8757410.1476160.0395
51.996-0.2793-0.86191.388-0.40352.23290.11510.0630.0728-0.1885-0.1196-0.41090.01960.2729-0.0230.15590.0070.04530.1428-0.00570.2254188.2509389.6212171.0105
61.90380.05820.23051.64910.46911.0630.1201-0.22780.07590.1479-0.0334-0.259-0.02990.2181-0.09080.1775-0.0386-0.00310.2180.00580.2009190.2979398.134186.5218
74.1604-0.7105-1.3422.86940.99472.9618-0.3148-1.25720.33430.88610.371-0.57460.05540.5501-0.00030.2663-0.1104-0.09420.5699-0.13470.4165201.9576405.9702193.3055
84.52960.35880.01412.7202-0.94991.69820.26150.5370.5276-0.58410.20520.185-0.7945-0.263-0.26070.46040.05710.08610.26720.08720.3276168.6724410.3089170.7274
93.551-0.02830.95424.30881.18312.03720.27680.42490.5443-0.20810.1514-0.00550.5591-1.5638-0.0420.356-0.1477-0.02120.5970.1240.2595166.8405408.7279172.2822
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 149 through 182 )
2X-RAY DIFFRACTION2chain 'A' and (resid 183 through 210 )
3X-RAY DIFFRACTION3chain 'A' and (resid 211 through 258 )
4X-RAY DIFFRACTION4chain 'A' and (resid 259 through 314 )
5X-RAY DIFFRACTION5chain 'A' and (resid 315 through 376 )
6X-RAY DIFFRACTION6chain 'A' and (resid 377 through 482 )
7X-RAY DIFFRACTION7chain 'A' and (resid 483 through 506 )
8X-RAY DIFFRACTION8chain 'D' and (resid 1 through 15 )
9X-RAY DIFFRACTION9chain 'E' and (resid 4 through 17 )

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