[English] 日本語
Yorodumi
- PDB-6ydb: Human wtSTING in complex with 2',2'-difluoro-3',3'-c-di-GMP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ydb
TitleHuman wtSTING in complex with 2',2'-difluoro-3',3'-c-di-GMP
ComponentsStimulator of interferon protein
KeywordsPROTEIN BINDING / innate immune system / cyclic dinucleotide / STING
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 / cytoplasmic vesicle / mitochondrial outer 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-GGF / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.801 Å
AuthorsBoura, E. / Smola, M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Ligand Strain and Its Conformational Complexity Is a Major Factor in the Binding of Cyclic Dinucleotides to STING Protein.
Authors: Smola, M. / Gutten, O. / Dejmek, M. / Kozisek, M. / Evangelidis, T. / Tehrani, Z.A. / Novotna, B. / Nencka, R. / Birkus, G. / Rulisek, L. / Boura, E.
History
DepositionMar 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Stimulator of interferon protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8832
Polymers23,1891
Non-polymers6941
Water32418
1
A: Stimulator of interferon protein
hetero molecules

A: Stimulator of interferon protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7674
Polymers46,3782
Non-polymers1,3892
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area4070 Å2
ΔGint-19 kcal/mol
Surface area14450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.073, 111.073, 35.836
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Stimulator of interferon protein


Mass: 23189.064 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 BL21(DE3) (bacteria) / References: UniProt: A0A2R3XZB7
#2: Chemical ChemComp-GGF / 2-azanyl-9-[(1~{R},6~{R},8~{R},9~{R},10~{R},15~{R},17~{R},18~{R})-17-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-9,18-bis(fluoranyl)-3,12-bis(oxidanyl)-3,12-bis(oxidanylidene)-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.3.0.0^{6,10}]octadecan-8-yl]-1~{H}-purin-6-one


Mass: 694.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22F2N10O12P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.38 Å3/Da / Density % sol: 48.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium chloride, 0.1 M Na/K phosphate pH 6.2, 40% (v/v) PEG 400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: PSI 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: 2.801→39.275 Å / Num. obs: 5861 / % possible obs: 99.07 % / Redundancy: 15.7 % / CC1/2: 0.997 / CC star: 0.999 / Net I/σ(I): 9.71
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 561 / CC1/2: 0.581

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.36 Å39.06 Å
Translation5.36 Å39.06 Å

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KSY

4ksy


Resolution: 2.801→39.2741 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.85
RfactorNum. reflection% reflection
Rfree0.2454 293 5 %
Rwork0.2006 --
obs0.2028 5858 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 129.11 Å2 / Biso mean: 65.9723 Å2 / Biso min: 36.86 Å2
Refinement stepCycle: final / Resolution: 2.801→39.2741 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1326 0 66 18 1410
Biso mean--53.49 54.76 -
Num. residues----171
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.801-3.52810.27191430.2422713
3.5281-39.27410.23471500.18642852

+
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