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- PDB-6dxg: amidobenzimidazole (ABZI) STING agonists -

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Basic information

Entry
Database: PDB / ID: 6dxg
Titleamidobenzimidazole (ABZI) STING agonists
ComponentsStimulator of interferon protein
Keywordsimmune system/agonist / agonist / STING (stimulator of Interferon genes) / transmembrane protein 173 (TMEM173) / IMMUNE SYSTEM / immune system-inhibitor complex / immune system-agonist complex
Function / homology
Function and homology information


STING complex / STAT6-mediated induction of chemokines / protein localization to endoplasmic reticulum / serine/threonine protein kinase complex / 2',3'-cyclic GMP-AMP binding / proton channel activity / cyclic-di-GMP binding / STING mediated induction of host immune responses / IRF3-mediated induction of type I IFN / positive regulation of type I interferon-mediated signaling pathway ...STING complex / STAT6-mediated induction of chemokines / protein localization to endoplasmic reticulum / serine/threonine protein kinase complex / 2',3'-cyclic GMP-AMP binding / proton channel activity / cyclic-di-GMP binding / STING mediated induction of host immune responses / IRF3-mediated induction of type I IFN / positive regulation of type I interferon-mediated signaling pathway / cGAS/STING signaling pathway / reticulophagy / pattern recognition receptor signaling pathway / cytoplasmic pattern recognition receptor signaling pathway / cellular response to exogenous dsRNA / autophagosome membrane / antiviral innate immune response / positive regulation of macroautophagy / autophagosome assembly / cellular response to organic cyclic compound / autophagosome / positive regulation of type I interferon production / cellular response to interferon-beta / signaling adaptor activity / positive regulation of defense response to virus by host / Regulation of innate immune responses to cytosolic DNA / activation of innate immune response / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of interferon-beta production / secretory granule membrane / cytoplasmic vesicle membrane / positive regulation of DNA-binding transcription factor activity / peroxisome / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of protein binding / protein complex oligomerization / regulation of inflammatory response / cytoplasmic vesicle / defense response to virus / RNA polymerase II-specific DNA-binding transcription factor binding / mitochondrial outer membrane / endosome / Golgi membrane / nucleotide binding / innate immune response / ubiquitin protein ligase binding / Neutrophil degranulation / endoplasmic reticulum membrane / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Stimulator of interferon genes protein / : / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / Transmembrane protein 173 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-HGJ / Stimulator of interferon genes protein / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.905 Å
AuthorsConcha, N.O.
CitationJournal: Nature / Year: 2018
Title: Design of amidobenzimidazole STING receptor agonists with systemic activity.
Authors: Ramanjulu, J.M. / Pesiridis, G.S. / Yang, J. / Concha, N. / Singhaus, R. / Zhang, S.Y. / Tran, J.L. / Moore, P. / Lehmann, S. / Eberl, H.C. / Muelbaier, M. / Schneck, J.L. / Clemens, J. / ...Authors: Ramanjulu, J.M. / Pesiridis, G.S. / Yang, J. / Concha, N. / Singhaus, R. / Zhang, S.Y. / Tran, J.L. / Moore, P. / Lehmann, S. / Eberl, H.C. / Muelbaier, M. / Schneck, J.L. / Clemens, J. / Adam, M. / Mehlmann, J. / Romano, J. / Morales, A. / Kang, J. / Leister, L. / Graybill, T.L. / Charnley, A.K. / Ye, G. / Nevins, N. / Behnia, K. / Wolf, A.I. / Kasparcova, V. / Nurse, K. / Wang, L. / Li, Y. / Klein, M. / Hopson, C.B. / Guss, J. / Bantscheff, M. / Bergamini, G. / Reilly, M.A. / Lian, Y. / Duffy, K.J. / Adams, J. / Foley, K.P. / Gough, P.J. / Marquis, R.W. / Smothers, J. / Hoos, A. / Bertin, J.
History
DepositionJun 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Stimulator of interferon protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3903
Polymers21,9181
Non-polymers4732
Water1,15364
1
A: Stimulator of interferon protein
hetero molecules

A: Stimulator of interferon protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7806
Polymers43,8352
Non-polymers9454
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area2160 Å2
ΔGint-31 kcal/mol
Surface area17440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.607, 92.221, 72.735
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-504-

HOH

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Components

#1: Protein Stimulator of interferon protein


Mass: 21917.639 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STING, LOC340061, hCG_1782396 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21star(DE3) / References: UniProt: A0A2R3XZB7, UniProt: Q86WV6*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-HGJ / 2-[(1-ethyl-3-methyl-1H-pyrazole-5-carbonyl)amino]-1-[(2R)-2-hydroxy-2-phenylethyl]-1H-benzimidazole-5-carboxamide


Mass: 432.475 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H24N6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

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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: 3.12 Å3/Da / Density % sol: 60.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 13-15% PEG8000, 0.07M cacodylate, pH 6.8, 0.8M calcium acetate, and 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 21273 / % possible obs: 97.6 % / Redundancy: 7.8 % / Biso Wilson estimate: 35.59 Å2 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.022 / Rrim(I) all: 0.063 / Χ2: 1.192 / Net I/σ(I): 14.4 / Num. measured all: 166478
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.9360.7678640.8480.3150.8321.01480.7
1.93-1.976.30.6459360.8690.2610.6981.0187.1
1.97-2.016.80.5999780.9020.2370.6461.04492.3
2.01-2.057.10.4810550.9410.1860.5161.02596.2
2.05-2.097.50.40210320.9570.1540.4321.13397.8
2.09-2.147.90.34110840.9660.1280.3651.1199.7
2.14-2.198.20.2810910.9780.1040.2991.072100
2.19-2.258.20.24410630.9860.090.261.274100
2.25-2.328.30.20610770.9880.0760.2191.11100
2.32-2.398.30.15310760.9940.0560.1631.122100
2.39-2.488.30.12810750.9960.0470.1371.169100
2.48-2.588.30.10510810.9970.0390.1121.194100
2.58-2.78.30.08510860.9970.0310.0911.183100
2.7-2.848.30.06810830.9980.0250.0731.324100
2.84-3.028.30.05711010.9990.0210.0610.991100
3.02-3.258.20.05911060.9980.0210.0621.304100
3.25-3.588.20.06510950.9960.0240.0691.321100
3.58-4.098.10.05911180.9970.0220.0631.887100
4.09-5.1680.03511150.9990.0130.0371.213100
5.16-507.30.02411570.9990.010.0261.10597.4

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EMU

4emu


Resolution: 1.905→28.767 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2347 1062 5 %
Rwork0.1925 20180 -
obs0.1946 21242 97.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 291.48 Å2 / Biso mean: 59.7338 Å2 / Biso min: 23.16 Å2
Refinement stepCycle: final / Resolution: 1.905→28.767 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1387 0 57 64 1508
Biso mean--51.54 51.31 -
Num. residues----177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081467
X-RAY DIFFRACTIONf_angle_d0.9091998
X-RAY DIFFRACTIONf_chiral_restr0.051221
X-RAY DIFFRACTIONf_plane_restr0.006260
X-RAY DIFFRACTIONf_dihedral_angle_d13.218874
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9048-1.99150.33551130.28292160227384
1.9915-2.09640.30691270.23362416254396
2.0964-2.22770.28061340.215125562690100
2.2277-2.39970.26821360.204325752711100
2.3997-2.6410.2211360.201825762712100
2.641-3.02280.22571360.20425842720100
3.0228-3.8070.2141380.191326202758100
3.807-28.77030.22791420.17192693283599
Refinement TLS params.Method: refined / Origin x: -13.1703 Å / Origin y: 25.0206 Å / Origin z: -9.3296 Å
111213212223313233
T0.2877 Å2-0.067 Å2-0.0055 Å2-0.2569 Å2-0.005 Å2--0.2852 Å2
L2.8327 °2-1.5468 °2-1.9728 °2-1.2769 °20.8363 °2--2.7683 °2
S0.0546 Å °-0.1552 Å °0.214 Å °0.0433 Å °0.0777 Å °-0.1083 Å °-0.0483 Å °-0.1667 Å °-0.1029 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA153 - 343
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allW1 - 65

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