[English] 日本語
Yorodumi
- PDB-7ebl: Bacterial STING in complex with c-di-GMP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ebl
TitleBacterial STING in complex with c-di-GMP
ComponentsSTING
KeywordsSIGNALING PROTEIN / second messenger / complex / cyclic dinucleotide / antiviral pathway
Function / homologyChem-C2E
Function and homology information
Biological speciesMyroides sp. ZB35 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsKo, T.-P. / Wang, Y.-C. / Yang, C.-S. / Hou, M.-H. / Chen, Y.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: Nat Commun / Year: 2022
Title: Crystal structure and functional implication of bacterial STING.
Authors: Ko, T.-P. / Wang, Y.-C. / Yang, C.-S. / Hou, M.-H. / Chen, C.-J. / Chiu, Y.-F. / Chen, Y.
History
DepositionMar 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2Nov 29, 2023Group: 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: STING
B: STING
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0573
Polymers38,3672
Non-polymers6901
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-19 kcal/mol
Surface area17030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.247, 98.599, 50.655
Angle α, β, γ (deg.)90.000, 108.184, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 150 through 159 or resid 161 through 168 or resid 170 through 313))
d_2ens_1(chain "B" and (resid 150 through 159 or resid 161 through 168 or resid 170 through 313))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LEUTHRA1 - 10
d_12ens_1LEUASNA12 - 19
d_13ens_1VALGLUA21 - 164
d_21ens_1LEUTHRB4 - 13
d_22ens_1LEUASNB15 - 22
d_23ens_1VALGLUB24 - 167

NCS oper: (Code: givenMatrix: (-0.9995781002, -0.0166128385123, -0.0238250959639), (0.0200411056817, -0.988214815931, -0.151755829072), (-0.0210232177408, -0.152169284584, 0.98813082795)Vector: 0. ...NCS oper: (Code: given
Matrix: (-0.9995781002, -0.0166128385123, -0.0238250959639), (0.0200411056817, -0.988214815931, -0.151755829072), (-0.0210232177408, -0.152169284584, 0.98813082795)
Vector: 0.568355454871, -20.5175600366, -1.49706698211)

-
Components

#1: Protein STING


Mass: 19183.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myroides sp. ZB35 (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Chemical ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate


Mass: 690.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N10O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Sequence detailsThe sequence has been deposited to NCBI under accession number WP_071307203.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium cacodylate trihydrate pH 6.5, 0.2M sodium acetate trihydrate, 15% w/v polyethylene glycol 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9998 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.17→30 Å / Num. obs: 17092 / % possible obs: 98.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.052 / Net I/σ(I): 15.7
Reflection shellResolution: 2.17→2.25 Å / Redundancy: 3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1680 / CC1/2: 0.859 / Rpim(I) all: 0.215 / % possible all: 96.9

-
Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EBD

7ebd


Resolution: 2.17→24.18 Å / SU ML: 0.2156 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 23.0571
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2311 896 5.29 %
Rwork0.1767 16050 -
obs0.1794 16946 97.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.75 Å2
Refinement stepCycle: LAST / Resolution: 2.17→24.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2672 0 46 229 2947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00432771
X-RAY DIFFRACTIONf_angle_d0.80973741
X-RAY DIFFRACTIONf_chiral_restr0.052433
X-RAY DIFFRACTIONf_plane_restr0.0052464
X-RAY DIFFRACTIONf_dihedral_angle_d14.21021061
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.15037369713 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.310.2851510.21832538X-RAY DIFFRACTION93.89
2.31-2.490.27031710.2012726X-RAY DIFFRACTION99.9
2.49-2.740.25611390.19832745X-RAY DIFFRACTION99.93
2.74-3.130.25441750.19442696X-RAY DIFFRACTION99.86
3.13-3.940.22161390.16422583X-RAY DIFFRACTION93.32
3.94-24.180.18471210.15612762X-RAY DIFFRACTION98.7

+
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