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- PDB-9p8l: Structure of Lockin in complex with 3'cADPR -

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Basic information

Entry
Database: PDB / ID: 9p8l
TitleStructure of Lockin in complex with 3'cADPR
ComponentsLockin
KeywordsVIRAL PROTEIN / immune evasion / viral sponge
Function / homologyChem-OJC
Function and homology information
Biological speciesphage metagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsChang, R.B. / Kranzusch, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2 GM146250-01 United States
CitationJournal: Biorxiv / Year: 2025
Title: Structural modeling reveals viral proteins that manipulate host immune signaling.
Authors: Tal, N. / Hadari, R. / Chang, R.B. / Osterman, I. / Jacobson, R. / Yirmiya, E. / Bechon, N. / Hochhauser, D. / Rivera, M.L. / Madhala, B. / Garb, J. / Wein, T. / Kranzusch, P. / Amitai, G. / Sorek, R.
History
DepositionJun 23, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 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: Lockin
B: Lockin
C: Lockin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4186
Polymers31,7943
Non-polymers1,6243
Water6,666370
1
A: Lockin
B: Lockin
C: Lockin
hetero molecules

A: Lockin
B: Lockin
C: Lockin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,83612
Polymers63,5886
Non-polymers3,2486
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565x,-y+1,-z1
Buried area17390 Å2
ΔGint-115 kcal/mol
Surface area20800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.584, 74.424, 80.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-303-

HOH

21A-307-

HOH

31B-321-

HOH

41C-326-

HOH

51C-327-

HOH

61C-329-

HOH

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Components

#1: Protein Lockin


Mass: 10597.966 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) phage metagenome (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-OJC / (2R,3R,3aS,5S,6R,7S,8R,11R,13S,15aR)-2-(6-amino-9H-purin-9-yl)-3,6,7,11,13-pentahydroxyoctahydro-2H,5H,11H,13H-5,8-epoxy-11lambda~5~,13lambda~5~-furo[2,3-g][1,3,5,9,2,4]tetraoxadiphosphacyclotetradecine-11,13-dione


Mass: 541.300 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H21N5O13P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.19 Å3/Da / Density % sol: 43.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 11.5% PEG6000, 0.1 M HEPES, pH 7.5, 5% v/v MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 28, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.62→80.33 Å / Num. obs: 36306 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 18.05 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.5
Reflection shellResolution: 1.62→1.65 Å / Redundancy: 13.3 % / Num. unique obs: 1774 / CC1/2: 0.823 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
RAPDdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→46.58 Å / SU ML: 0.1892 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.2736
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2093 1818 5.02 %
Rwork0.1766 34424 -
obs0.1782 36242 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.98 Å2
Refinement stepCycle: LAST / Resolution: 1.62→46.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 105 370 2517
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00542189
X-RAY DIFFRACTIONf_angle_d0.84192992
X-RAY DIFFRACTIONf_chiral_restr0.0565349
X-RAY DIFFRACTIONf_plane_restr0.0048370
X-RAY DIFFRACTIONf_dihedral_angle_d14.385789
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.660.30361560.26282608X-RAY DIFFRACTION99.96
1.66-1.710.27931560.25262575X-RAY DIFFRACTION99.78
1.71-1.770.31651450.24752583X-RAY DIFFRACTION99.85
1.77-1.830.26681530.22872613X-RAY DIFFRACTION99.86
1.83-1.90.23751280.19972610X-RAY DIFFRACTION99.93
1.9-1.990.24931210.18192651X-RAY DIFFRACTION99.96
1.99-2.10.20411240.17312620X-RAY DIFFRACTION99.85
2.1-2.230.22111470.17772632X-RAY DIFFRACTION100
2.23-2.40.21021420.17512640X-RAY DIFFRACTION100
2.4-2.640.18691160.17392678X-RAY DIFFRACTION99.93
2.64-3.020.18791390.16992672X-RAY DIFFRACTION100
3.02-3.810.20061410.15162706X-RAY DIFFRACTION99.93
3.81-46.580.17811500.16232836X-RAY DIFFRACTION99.9
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)
18.12368878181-0.3938747015457.814490191633.337197212470.07510088063027.60526223666-1.03574398448-0.6565816368920.0209896526691.119623887090.5489938689550.0775472243248-0.6183458552590.357116390120.3956613665080.6550954056020.07432716767950.04916712734210.775769697516-0.02345059766320.64502267740613.280378378131.944816807423.038191358
20.4181726230510.0805123591727-0.6259999906362.020585419290.3985875711370.951008832862-0.0668433292382-0.5682317105090.01867592123690.2422442850530.0891986473561-0.2079704702080.05772576351350.288813194768-0.02506875027040.1940459476910.0177198705748-0.03362355267750.3520162118770.01443485847070.20564315468912.069845250132.880483570419.5817236365
33.33807218573-0.559040337669-0.3408872345430.5981756261320.07278206209390.613481246946-0.105127657933-0.258615169446-0.05459862517320.09145711908160.04631291665560.02317635288180.03085196014350.03369257512620.06442185388950.1558964274820.008299909334250.01019370656550.1438130122280.007207340321340.1146474176023.7800121558430.600396164612.2671223122
40.4728311991410.580163995837-0.4916083378871.093257762580.03372825014354.38609251542-0.0964209029803-0.162950892006-0.3472825119690.0378956324796-0.0397690268184-0.273043627280.1977439438720.6099381305310.195681801040.1869960428050.04680432243810.01194197232430.2284192754290.04214115551720.27147930746212.868877813816.94549753196.24743213329
53.23727158325-0.07955088142-0.1915933135630.447114311704-0.08030740226210.336600693222-0.0646373587908-0.0252912822042-0.342263176738-0.02330992835010.01188136841450.0001032879817430.05984535573630.01703673940820.03718410460340.1413030967470.003861766767210.01059018704020.1104633650320.002106755257880.1480619205973.6826463703323.2051997730.406738563491
63.26427156011-4.674477804310.184996180937.118582473950.2842915322193.375681473090.1957708926070.74263244109-0.0419598439734-0.6034464978890.112401582404-0.213889144549-0.06181325096510.0741761458044-0.2287200035690.27102587744-0.04002937756750.03787613354130.278669305453-0.04462896248020.34652818712310.507081376115.8941913975-9.122428914
76.12342563473.09828456204-0.1043709999394.23257585432-0.1599142852780.01638949108350.02290105073190.31308574703-0.530494451871-0.02358173551150.029919730312-0.595798964068-0.1625051196670.7511563529610.06732607898010.142179441855-0.06035696662810.0005017727341260.438804590131-0.03861638383160.17729131428413.89744876431.0376365175-18.4547791354
88.708166853334.56684720499-2.444029616593.6291202783-1.336654712432.52348049352-0.06118272796580.186369896505-0.1447801188450.07825349552880.0645855938769-0.029924215671-0.056035972470.1137517754280.006685484804150.1522365473840.00219738836745-0.002891203146090.1559755419480.001297024918080.1328946028942.606067455128.4870021808-11.5887111794
92.525217153541.234737125310.9109462915390.5801510054610.3482746474940.410599470277-0.07042514077890.084946476262-0.1786834127610.0003361639447390.0828467657355-0.07607287857360.03972453341490.06844527833640.008039945843730.1610837895870.00719819267201-0.002270602833070.166826709383-0.007073569827420.15312854230210.576369703532.3481360851-7.84264143656
103.64750936567-0.1073814299150.01481053861452.65272143190.7209885512163.616818348220.07229388333550.269056719945-0.252314574251-0.180440251618-0.118901154222-0.01126562099690.265158956601-0.1534804936970.05135560182520.182131139673-0.00125193269241-0.0047195077280.138229906637-0.04309016499230.144234456784-6.5649592480527.1071020302-18.5268853442
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 15 )AA4 - 151 - 12
22chain 'A' and (resid 16 through 42 )AA16 - 4213 - 39
33chain 'A' and (resid 43 through 97 )AA43 - 9740 - 94
44chain 'B' and (resid 3 through 42 )BC3 - 421 - 40
55chain 'B' and (resid 43 through 97 )BC43 - 9741 - 95
66chain 'C' and (resid 17 through 30 )CE17 - 301 - 14
77chain 'C' and (resid 31 through 42 )CE31 - 4215 - 26
88chain 'C' and (resid 43 through 54 )CE43 - 5427 - 38
99chain 'C' and (resid 55 through 81 )CE55 - 8139 - 65
1010chain 'C' and (resid 82 through 97 )CE82 - 9766 - 81

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