[English] 日本語
Yorodumi
- PDB-7zku: Crystal structure of human STING in complex with 3',3'-c-(2'F,2'd... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zku
TitleCrystal structure of human STING in complex with 3',3'-c-(2'F,2'dAMP-2'dGMP)
ComponentsStimulator of interferon protein
KeywordsANTIVIRAL PROTEIN / sting / antiviral / activator
Function / homology
Function and homology information


autophagosome membrane / positive regulation of type I interferon production / activation of innate immune response / endoplasmic reticulum-Golgi intermediate compartment membrane / monoatomic ion transmembrane transport / cytoplasmic vesicle / mitochondrial outer membrane / Golgi membrane / nucleotide binding / perinuclear region of cytoplasm
Similarity search - Function
: / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / Transmembrane protein 173
Similarity search - Domain/homology
Chem-JLU / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKlima, M. / Smola, M. / Boura, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of human STING in complex with 3',3'-c-(2'F,2'dAMP-2'dGMP)
Authors: Klima, M. / Smola, M. / Boura, E.
History
DepositionApr 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Stimulator of interferon protein
B: Stimulator of interferon protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0373
Polymers46,3782
Non-polymers6581
Water4,071226
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-18 kcal/mol
Surface area16930 Å2
Unit cell
Length a, b, c (Å)93.158, 93.158, 204.062
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

-
Components

#1: Protein Stimulator of interferon protein


Mass: 23189.064 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STING, LOC340061, hCG_1782396 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2R3XZB7
#2: Chemical ChemComp-JLU / 9-[(1~{S},6~{R},8~{R},9~{R},10~{R},15~{R},17~{R})-8-(6-aminopurin-9-yl)-9-fluoranyl-3,12-bis(oxidanyl)-3,12-bis(oxidanylidene)-2,4,7,11,13-pentaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.3.0.0^{6,10}]octadecan-17-yl]-2-azanyl-3~{H}-purin-6-one


Mass: 658.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H25FN10O10P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Lithium acetate, 20% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.7→15.94 Å / Num. obs: 58210 / % possible obs: 99.8 % / Redundancy: 22.8 % / Biso Wilson estimate: 29.79 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.03036 / Rrim(I) all: 0.1462 / Net I/σ(I): 16.01
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 23.3 % / Rmerge(I) obs: 4.412 / Mean I/σ(I) obs: 0.78 / Num. unique obs: 5703 / CC1/2: 0.307 / CC star: 0.686 / Rpim(I) all: 0.9209 / Rrim(I) all: 4.509 / % possible all: 99.95

-
Processing

Software
NameVersionClassification
XDSxdsapp 2.0data reduction
XDSxdsapp 2.0data scaling
PHASER2.8.3phasing
Coot0.9.6model building
PHENIX1.20_4459refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ksy

4ksy


Resolution: 1.7→15.94 Å / SU ML: 0.2249 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.4078
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2445 2910 5 %random selection
Rwork0.2218 55292 --
obs0.2229 58202 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.37 Å2
Refinement stepCycle: LAST / Resolution: 1.7→15.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3013 0 44 226 3283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00493196
X-RAY DIFFRACTIONf_angle_d0.73554358
X-RAY DIFFRACTIONf_chiral_restr0.0455475
X-RAY DIFFRACTIONf_plane_restr0.0069563
X-RAY DIFFRACTIONf_dihedral_angle_d13.93131226
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.33561360.33552583X-RAY DIFFRACTION99.96
1.73-1.760.33821360.32472594X-RAY DIFFRACTION99.93
1.76-1.790.30811360.31332566X-RAY DIFFRACTION99.96
1.79-1.820.34061360.30542586X-RAY DIFFRACTION99.96
1.82-1.860.31051360.2852581X-RAY DIFFRACTION100
1.86-1.90.32321360.30432596X-RAY DIFFRACTION100
1.9-1.950.30471360.26562593X-RAY DIFFRACTION100
1.95-1.990.28851360.25232585X-RAY DIFFRACTION100
1.99-2.050.23891370.2382598X-RAY DIFFRACTION100
2.05-2.110.27111360.23982602X-RAY DIFFRACTION99.96
2.11-2.180.28161380.23192618X-RAY DIFFRACTION100
2.18-2.250.26491370.22582606X-RAY DIFFRACTION100
2.25-2.340.29121380.22742625X-RAY DIFFRACTION99.96
2.34-2.450.27651390.22492626X-RAY DIFFRACTION100
2.45-2.580.23461380.22632629X-RAY DIFFRACTION100
2.58-2.740.22211410.21462659X-RAY DIFFRACTION100
2.74-2.950.22561380.2242632X-RAY DIFFRACTION100
2.95-3.240.24661410.21532684X-RAY DIFFRACTION99.96
3.24-3.710.2221410.20572684X-RAY DIFFRACTION100
3.71-4.650.21491440.1872748X-RAY DIFFRACTION99.9
4.65-15.940.22691540.21462897X-RAY DIFFRACTION100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more