[English] 日本語
Yorodumi
- PDB-7mwz: Structure of drosophila STING in complex with 3'2'-cGAMP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7mwz
TitleStructure of drosophila STING in complex with 3'2'-cGAMP
ComponentsSTING
KeywordsIMMUNE SYSTEM / STING / cyclic dinucleotide receptor
Function / homology3'2'-cGAMP
Function and homology information
Biological speciesDrosophila eugracilis (fry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsSlavik, K.M. / Ragucci, A.E. / Kranzusch, P.J.
CitationJournal: Nature / Year: 2021
Title: cGAS-like receptors sense RNA and control 3'2'-cGAMP signalling in Drosophila.
Authors: Slavik, K.M. / Morehouse, B.R. / Ragucci, A.E. / Zhou, W. / Ai, X. / Chen, Y. / Li, L. / Wei, Z. / Bahre, H. / Konig, M. / Seifert, R. / Lee, A.S.Y. / Cai, H. / Imler, J.L. / Kranzusch, P.J.
History
DepositionMay 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 15, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 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: STING
B: STING
C: STING
D: STING
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,9536
Polymers163,6044
Non-polymers1,3492
Water9,206511
1
A: STING
B: STING
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4773
Polymers81,8022
Non-polymers6741
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-17 kcal/mol
Surface area32610 Å2
MethodPISA
2
C: STING
D: STING
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4773
Polymers81,8022
Non-polymers6741
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-20 kcal/mol
Surface area31130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.923, 95.046, 140.138
Angle α, β, γ (deg.)90.000, 93.934, 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

-
Components

#1: Protein
STING


Mass: 40901.070 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila eugracilis (fry) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-4UR / 3'2'-cGAMP / 2-amino-9-[(2S,5R,7R,8R,10R,12aR,14R,15R,15aS,16R)-7-(6-amino-9H-purin-9-yl)-2,10,15,16-tetrahydroxy-2,10-dioxidooctahydro-12H-5,8-methanofuro[3,2-l][1,3,6,9,11,2,10]pentaoxadiphosphacyclotetradecin-14-yl]-1,9-dihydro-6H-purin-6-one / Cyclic guanosine monophosphate–adenosine monophosphate


Mass: 674.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O13P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 511 / 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: 2.07 Å3/Da / Density % sol: 40.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1-0.2 M sodium acetate pH 4.8, 0.2 M ammonium formate, 20-22% PEG-3350

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→48.84 Å / Num. obs: 89677 / % possible obs: 99.7 % / Redundancy: 7.1 % / Biso Wilson estimate: 42.5 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.032 / Net I/σ(I): 10.7
Reflection shellResolution: 2→2.04 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4600 / CC1/2: 0.561 / Rpim(I) all: 0.759 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: SAD-phased model of the selenomethionine derivative

Resolution: 2→48.84 Å / SU ML: 0.3635 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.0548
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.283 2004 2.24 %
Rwork0.2472 87540 -
obs0.2479 89544 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.01 Å2
Refinement stepCycle: LAST / Resolution: 2→48.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10943 0 90 511 11544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001811262
X-RAY DIFFRACTIONf_angle_d0.435615194
X-RAY DIFFRACTIONf_chiral_restr0.03741666
X-RAY DIFFRACTIONf_plane_restr0.00311905
X-RAY DIFFRACTIONf_dihedral_angle_d12.71814178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.40931460.38416162X-RAY DIFFRACTION98.44
2.05-2.110.42081430.35626211X-RAY DIFFRACTION99.58
2.11-2.170.35921480.34216219X-RAY DIFFRACTION99.78
2.17-2.240.33211280.31646287X-RAY DIFFRACTION99.74
2.24-2.320.35481540.31386243X-RAY DIFFRACTION99.46
2.32-2.410.35131340.31016199X-RAY DIFFRACTION99.29
2.41-2.520.31681500.30716176X-RAY DIFFRACTION98.92
2.52-2.650.36581410.30666250X-RAY DIFFRACTION99.81
2.65-2.820.33441390.29136276X-RAY DIFFRACTION99.69
2.82-3.040.3191400.27366277X-RAY DIFFRACTION99.92
3.04-3.340.30381520.26186248X-RAY DIFFRACTION99.74
3.34-3.830.2531450.2246271X-RAY DIFFRACTION99.44
3.83-4.820.22981390.19966315X-RAY DIFFRACTION99.97
4.82-48.840.24151450.20446406X-RAY DIFFRACTION99.53
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.0351926246888-0.30832303588-0.009694879826252.227238388670.8273724697834.56216884983-0.06706991088270.0128181378556-0.267097846010.188827726532-0.2392312033920.540483343027-0.359857783561-0.860213689040.1738494114770.4079754543440.0005423739290550.01010098151190.584186275672-0.0449932383120.683377439251-34.65949271942.2215318186718.8005057265
22.391172983470.2546277102051.080196252753.09251423764-0.7293351811462.061889008730.141063824478-0.28493358468-0.121317047310.070097375864-0.0111894500420.2841076950040.102912229862-0.256735724905-0.1501415416470.2210185496440.03395137153480.04352771601720.306469160146-0.02142072414010.311304940665-37.6614436927-17.4709007236-15.1446761618
35.11591915809-0.914888876728-0.6226460680135.705124558450.7888433970317.552735830380.07704209462720.5793138912420.4686378805390.567666177797-0.01402583251550.9530772652310.0561933029877-0.690634026052-0.01647648909430.376568517204-0.0655131617680.03924349113970.4557169703880.006038129224390.673146801444-29.6491495082-25.289883917222.8774483713
44.54472589161.70559307665-2.912060264312.717885586750.7458054686625.86214519976-0.1986835712680.09460021540730.1484497989290.387472607996-0.0725286574587-0.468027891621.085020553561.297609769020.1703335128850.7540080241810.1745579445640.07359374483210.8839260885250.2407867903530.825390543446-8.77962488775-22.704547977217.7815033125
52.302520511890.204535798963-1.005204504012.033228244120.05264555789482.008002664560.0672265176893-0.2049247193690.04374586552950.155058304498-0.0881724898096-0.317551215764-0.1472112311290.05826301545080.03586920945110.2565944393930.0255601622872-0.02765033868530.304342424187-0.01637850044850.390018619179-14.3861731884-2.70423851265-13.0721006585
66.95387713178-0.303611197223-3.284030238176.92779888749-0.1077027665797.2978526164-0.077529246322-0.3205155336690.632939869582-0.4776686328870.451253576992-0.971696537060.3844477199160.784784270926-0.212752495850.40207125417-0.00690743244025-0.002412629759790.375028699440.03719370147520.5219309540140.645716730816-14.948402876145.4655156512
73.11403684582-2.3895342326-1.533369990284.792919800421.970329987855.905282364330.2896594298510.9671938361520.589814441903-1.20590197037-0.6044493330520.659436609193-0.346475500212-1.171621922160.3186650833160.9576800787140.124628840507-0.1510287115320.7157813899-0.007194254988261.00591659495-18.1013068895-7.5941150968244.6881042279
8-0.04341054443650.0552983779658-0.7583091483191.146005582270.7526088197148.91719100779-0.02033375085430.120331703799-0.288120972923-0.00361317367075-0.09238593361650.4702834731550.529047996984-0.9704091002850.1244414989840.702080446385-0.07523494390850.02908376436890.65603551376-0.08098193336540.890861502109-19.278209561-7.4078403113766.3040041765
92.04028947228-1.160245772170.03243978393433.35674952441-0.1955664111711.83389307023-0.02805974880530.291879268528-0.0482285972349-0.3291487650830.09251347916640.1580960456420.141216004031-0.124807957725-0.03346483087720.539376032203-0.149931354903-0.03788007281060.396878185241-0.06655500673740.286191191348-16.819117176611.05065002483.6715165117
100.293935040649-0.1711744990361.026861617943.22316952303-2.943042661754.224873849250.1598581553220.1121463834550.243351344929-0.678599079044-0.2199541261340.1138089513440.4779985534060.3749153996910.007232730676460.863348460359-0.0165665692705-0.1139001088650.6196759579470.01639476290170.6869935757421.5489919338513.210872345655.6844400735
111.68425758190.1476803528360.3335817941123.010628445731.256920764032.93607049470.1304622088290.152341723889-0.208041413878-0.1676926059250.1861190986-0.716749464377-0.02895365364930.528542037824-0.3159446381770.572330334745-0.100159294434-0.01026289203180.521337529874-0.1979183301650.6437193454456.50732615975-7.1857688275683.9122737243
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -14 through 162 )AA-14 - 1621 - 177
22chain 'A' and (resid 163 through 337 )AA163 - 337178 - 351
33chain 'B' and (resid -14 through 45 )BC-14 - 451 - 60
44chain 'B' and (resid 46 through 141 )BC46 - 14161 - 156
55chain 'B' and (resid 142 through 337 )BC142 - 337157 - 352
66chain 'C' and (resid -13 through 45 )CD-13 - 451 - 59
77chain 'C' and (resid 46 through 108 )CD46 - 10860 - 122
88chain 'C' and (resid 109 through 176 )CD109 - 176123 - 188
99chain 'C' and (resid 177 through 337 )CD177 - 337189 - 349
1010chain 'D' and (resid -13 through 176 )DF-13 - 1761 - 144
1111chain 'D' and (resid 177 through 333 )DF177 - 333145 - 301

+
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