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- PDB-9q1f: Choanoflagellate Salpingoeca macrocollata STING -

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Basic information

Entry
Database: PDB / ID: 9q1f
TitleChoanoflagellate Salpingoeca macrocollata STING
ComponentsEndolysin,Stimulator of interferon genes
KeywordsIMMUNE SYSTEM / Innate immunity / Cyclic dinucleotide signaling / Stimulator of Interferon Genes / cGAS-STING
Function / homology
Function and homology information


viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium
Similarity search - Function
Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Biological speciesSalpingoeca macrocollata (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsToyoda, H.C. / Li, Y. / Kranzusch, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM146250-01 United States
CitationJournal: Biorxiv / Year: 2025
Title: A choanoflagellate cGLR-STING pathway reveals evolutionary links between bacterial and animal immunity.
Authors: Li, Y. / Toyoda, H.C. / Fernandez, S.G. / Tiwari, B. / McNairy, C. / Woznica, A. / Kranzusch, P.J.
History
DepositionAug 13, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endolysin,Stimulator of interferon genes
B: Endolysin,Stimulator of interferon genes
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9963
Polymers84,3222
Non-polymers6741
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-19 kcal/mol
Surface area32940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.946, 88.743, 76.023
Angle α, β, γ (deg.)90.000, 94.143, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid -16 through 35 or resid 37...
d_2ens_1(chain "B" and resid -16 through 359)

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11METMETARGARGAA-16 - 351 - 52
d_12THRTHRGLNGLNAA37 - 18354 - 200
d_13GLNGLNLYSLYSAA185 - 200202 - 217
d_14VALVALTYRTYRAA202 - 203219 - 220
d_15SERSERARGARGAA207 - 276224 - 293
d_16ASPASPLEULEUAA282 - 359299 - 376
d_21METMETLEULEUBB-16 - 3591 - 376

NCS oper: (Code: givenMatrix: (-0.907451771338, -0.420100325434, 0.006855601072), (-0.319564679501, 0.679509124028, -0.660413329649), (0.272781411227, -0.601484053765, -0.750870984095)Vector: 62. ...NCS oper: (Code: given
Matrix: (-0.907451771338, -0.420100325434, 0.006855601072), (-0.319564679501, 0.679509124028, -0.660413329649), (0.272781411227, -0.601484053765, -0.750870984095)
Vector: 62.3370403233, 52.4124740079, 100.787148375)

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Components

#1: Protein Endolysin,Stimulator of interferon genes / Lysis protein / Lysozyme / Muramidase


Mass: 42160.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal T4 lysosome fused to STING cyclic dinucleotide binding domain
Source: (gene. exp.) Salpingoeca macrocollata (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-1SY / cGAMP / 2',3' cGAMP / c-GMP-AMP / c[G(2',5')pA(3',5')p]


Mass: 674.411 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C20H24N10O13P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.67 Å3/Da / Density % sol: 53.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.65
Details: 5% ethylene glycol, 100 mM MOPS pH 6.65, and 10% (w/v) PEG8000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.65→34.04 Å / Num. obs: 25932 / % possible obs: 99.7 % / Redundancy: 7.1 % / CC1/2: 0.984 / Net I/σ(I): 4.51
Reflection shellResolution: 2.65→2.71 Å / Num. unique obs: 1855 / CC1/2: 0.378

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.65→34.04 Å / SU ML: 0.4261 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.2147
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2748 2024 7.83 %
Rwork0.2433 23836 -
obs0.2457 25860 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.59 Å2
Refinement stepCycle: LAST / Resolution: 2.65→34.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5759 0 45 79 5883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00255962
X-RAY DIFFRACTIONf_angle_d0.62228073
X-RAY DIFFRACTIONf_chiral_restr0.0431900
X-RAY DIFFRACTIONf_plane_restr0.00521032
X-RAY DIFFRACTIONf_dihedral_angle_d12.55772197
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.28031159305 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.710.36631450.331651X-RAY DIFFRACTION96.82
2.72-2.790.33391340.32711703X-RAY DIFFRACTION99.73
2.79-2.870.34961470.32081677X-RAY DIFFRACTION99.84
2.87-2.960.33981410.31841677X-RAY DIFFRACTION100
2.96-3.070.31361380.31831730X-RAY DIFFRACTION100
3.07-3.190.35811490.30451695X-RAY DIFFRACTION100
3.19-3.340.34111550.27741683X-RAY DIFFRACTION100
3.34-3.510.30911450.27811694X-RAY DIFFRACTION100
3.51-3.730.29441320.2651715X-RAY DIFFRACTION99.95
3.73-4.020.27151480.23041718X-RAY DIFFRACTION100
4.02-4.420.23121460.20721704X-RAY DIFFRACTION100
4.42-5.060.21871470.19831723X-RAY DIFFRACTION99.95
5.06-6.370.27551480.23691702X-RAY DIFFRACTION100
6.37-34.040.21991490.18911764X-RAY DIFFRACTION99.79
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)
13.96009881528-0.1653850539870.707870004491.978082548220.08863817379731.127001104590.025408230042-0.827393604191-0.1495804684970.255076058369-0.0855515669322-0.154985984813-0.003511843718550.0310685410132-0.03868536307060.373575231773-0.04406119267950.01973012143980.5354521433510.08645654630640.52475676791855.360747782932.922555711167.8306432263
23.197546704420.8593464401490.303484505512.170385798911.485256264542.60348104772-0.04641618327760.06303915863351.05409426697-0.708908018965-0.0348201822289-0.661045143549-0.7665090188590.135843966295-0.3017197791230.4856398087080.02164128386620.07803161481630.3918729663890.0708248219830.46579759918238.927165319146.683438528956.8305662271
3-0.2861236491780.154895548568-0.1181220641571.6630157842-0.7209989374311.65203762245-0.0916124158451-0.281679807716-0.122086638331-0.3680908466630.229998533809-0.1400624811480.295490816635-0.299432045860.04832026996810.219210672676-0.0690883477947-0.01563111962370.513141581520.1137214731040.46028559923733.091545393411.970081765470.3892144527
40.5285903117530.03269156606710.4923082656481.36879072235-0.2630453430221.07283570498-0.1237566903450.2488928485440.407689602205-0.18647654217-0.128148810521-0.3585959089280.07196138578340.518417736209-0.1019909126130.282964153827-0.0391713665150.0185500664440.5571464214430.1540918568180.54808378861347.52856838194.401495381377.0288277106
5-0.314879977517-0.0891722944097-0.09869672841231.8584532915-0.4014104838290.6438268135040.06976569592710.08425985520050.263295700081-0.2505122467470.0324573935862-0.04114471276010.157910950583-0.0282009117130.8429861896720.32841473526-0.05532302189370.06333538330060.551508835990.1185041245810.44372431111438.72495319997.1546574428271.4201089055
60.17340088279-0.2331461522370.4451192443620.939204144198-0.5265539222931.1113470332-0.1705647764930.2105163545921.073084795970.8078979570380.320713539242-0.0402019052777-0.887253358898-0.492682776370.1100141278360.523257878503-0.107794742824-0.005791802824630.6194859954680.1625470970170.81677771317939.592174479113.514438364779.9369410856
70.106204262411-0.01759351041430.2134722645270.763226858562-0.2786389803680.3247412930180.04333560981410.1758921872250.0303845558183-1.302770153920.2179654742771.36068437666-0.240442672715-0.05095373137210.02299024420570.982989386952-0.102087479901-0.1741324323250.5431701030280.05270407682260.7008539822086.6421395473514.393900471748.0052080626
81.25627497237-1.528128524230.4022762458015.30209808221-1.26268566891.10466049582-0.445978135099-0.222080626852-0.552056449087-1.059057730710.7268851196863.038512153520.504997721885-0.3678965319360.2230566565731.14825975261-0.320513566326-0.6353931368660.7034748623280.05049947714391.35876962677-4.1626083189811.378077647245.2299005929
90.5094467510471.29214603171-0.1514314729673.31287761468-0.2362033060152.02982390138-0.02629881931220.1091724303010.366337325621-2.539574534090.7044805952992.133305885090.361708216464-0.8356269808140.77361161261.43000761027-0.0673119196955-0.6672271610470.5887298958410.09945804688380.7365160130984.7935363252629.285842721136.4921035058
101.629285935180.2167062621931.496502517875.10895419682-1.936121653031.69349156531-0.2356934354360.2975162360510.221047603704-1.45353972219-0.0926906112093-0.7189100654760.339996061845-0.0427267219545-0.6214407652640.556670870285-0.003445742630680.1436525069060.361883608936-0.07049822966160.35071099011219.859901970221.126464948346.5309711171
111.680848419021.0796538971-0.2068588663510.7443722053770.5672735319061.41313095564-0.373501498364-0.371579704379-0.701150536286-0.1417137229960.3818737115030.4806034514790.936754484831-0.3386367778820.008564272613111.15689525405-0.147126700457-0.08146961471780.5781291826690.06416463429540.67382919508220.2217672094-12.500259017253.5396004885
121.69605188767-0.1285680498470.3490484027151.90589877412-0.8054300968941.794566101170.188478844848-0.128315161236-0.242943480864-0.874096262019-0.140822558004-0.3543975661910.464731875468-0.2903393683770.2053997867280.663745464878-0.05287072194240.06338405351220.385901940539-0.03600411228910.38978051512625.5196373502-0.019186863102454.1955957384
130.802656522942-0.8271986201220.3473280234751.99871118997-0.2017312923971.194089346370.4080634406920.140600204806-0.667026044883-1.5723556931-0.0946967269711-0.1694008011870.2187296770610.567868788541-0.09657650286531.0103968744-0.00985645595812-0.1306075382240.822342762532-0.05623800870630.57625402533122.1350336954-4.0330477949342.5071250347
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -16 through 63 )AA-16 - 631 - 80
22chain 'A' and (resid 64 through 125 )AA64 - 12581 - 142
33chain 'A' and (resid 126 through 196 )AA126 - 196143 - 209
44chain 'A' and (resid 197 through 243 )AA197 - 243210 - 256
55chain 'A' and (resid 244 through 325 )AA244 - 325257 - 338
66chain 'A' and (resid 326 through 359 )AA326 - 359339 - 372
77chain 'B' and (resid -16 through 4 )BC-16 - 41 - 21
88chain 'B' and (resid 5 through 62 )BC5 - 6222 - 78
99chain 'B' and (resid 63 through 89 )BC63 - 8979 - 105
1010chain 'B' and (resid 90 through 182 )BC90 - 182106 - 194
1111chain 'B' and (resid 183 through 248 )BC183 - 248195 - 255
1212chain 'B' and (resid 249 through 324 )BC249 - 324256 - 326
1313chain 'B' and (resid 325 through 360 )BC325 - 360327 - 362

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