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

ID or keywords:

Entry

Database: PDB / ID: 9p8l

Title

Structure of Lockin in complex with 3'cADPR

Components

Lockin

Keywords

VIRAL PROTEIN / immune evasion / viral sponge

Function / homology

Chem-OJC

Function and homology information

Biological species

phage metagenome (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.62 Å

Authors

Chang, R.B. / Kranzusch, P.J.

Funding support

United States, 1items

Citation

Journal: 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

Deposition	Jun 23, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 30, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9p8l.cif.gz	151.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9p8l.ent.gz	98.6 KB	Display	PDB format
PDBx/mmJSON format	9p8l.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9p8l_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	9p8l_full_validation.pdf.gz	1.7 MB	Display
Data in XML	9p8l_validation.xml.gz	21.9 KB	Display
Data in CIF	9p8l_validation.cif.gz	28.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p8/9p8l ftp://data.pdbj.org/pub/pdb/validation_reports/p8/9p8l	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Lockin

B: Lockin

C: Lockin

hetero molecules

33.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Lockin

B: Lockin

C: Lockin

hetero molecules

A: Lockin

B: Lockin

C: Lockin

hetero molecules

defined by author&software
66.8 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	18
Space group name H-M	P22₁2₁
Space group name Hall	P22ab(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

ID	Model	Components
1	1	A-303- HOH
2	1	A-307- HOH
3	1	B-321- HOH
4	1	C-326- HOH
5	1	C-327- HOH
6	1	C-329- HOH

#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 interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.19 Å³/Da / Density % sol: 43.83 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 28, 2025
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 1.62→80.33 Å / Num. obs: 36306 / % possible obs: 100 % / Redundancy: 13 % / B_iso Wilson estimate: 18.05 Å² / CC_1/2: 0.998 / Net I/σ(I): 13.5
Reflection shell	Resolution: 1.62→1.65 Å / Redundancy: 13.3 % / Num. unique obs: 1774 / CC_1/2: 0.823 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.21_5207	refinement
RAPD		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Method 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

	R_factor	Num. reflection	% reflection
R_free	0.2093	1818	5.02 %
R_work	0.1766	34424	-
obs	0.1782	36242	99.92 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 27.98 Å²

Refinement step

Cycle: LAST / Resolution: 1.62→46.58 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2042	0	105	370	2517

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0054	2189
X-RAY DIFFRACTION	f_angle_d	0.8419	2992
X-RAY DIFFRACTION	f_chiral_restr	0.0565	349
X-RAY DIFFRACTION	f_plane_restr	0.0048	370
X-RAY DIFFRACTION	f_dihedral_angle_d	14.385	789

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.62-1.66	0.3036	156	0.2628	2608	X-RAY DIFFRACTION	99.96
1.66-1.71	0.2793	156	0.2526	2575	X-RAY DIFFRACTION	99.78
1.71-1.77	0.3165	145	0.2475	2583	X-RAY DIFFRACTION	99.85
1.77-1.83	0.2668	153	0.2287	2613	X-RAY DIFFRACTION	99.86
1.83-1.9	0.2375	128	0.1997	2610	X-RAY DIFFRACTION	99.93
1.9-1.99	0.2493	121	0.1819	2651	X-RAY DIFFRACTION	99.96
1.99-2.1	0.2041	124	0.1731	2620	X-RAY DIFFRACTION	99.85
2.1-2.23	0.2211	147	0.1777	2632	X-RAY DIFFRACTION	100
2.23-2.4	0.2102	142	0.1751	2640	X-RAY DIFFRACTION	100
2.4-2.64	0.1869	116	0.1739	2678	X-RAY DIFFRACTION	99.93
2.64-3.02	0.1879	139	0.1699	2672	X-RAY DIFFRACTION	100
3.02-3.81	0.2006	141	0.1516	2706	X-RAY DIFFRACTION	99.93
3.81-46.58	0.1781	150	0.1623	2836	X-RAY DIFFRACTION	99.9

Refinement TLS params.

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

ID	L11 (°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	8.12368878181	-0.393874701545	7.81449019163	3.33719721247	0.0751008806302	7.60526223666	-1.03574398448	-0.656581636892	0.020989652669	1.11962388709	0.548993868955	0.0775472243248	-0.618345855259	0.35711639012	0.395661366508	0.655095405602	0.0743271676795	0.0491671273421	0.775769697516	-0.0234505976632	0.645022677406	13.2803783781	31.9448168074	23.038191358
2	0.418172623051	0.0805123591727	-0.625999990636	2.02058541929	0.398587571137	0.951008832862	-0.0668433292382	-0.568231710509	0.0186759212369	0.242244285053	0.0891986473561	-0.207970470208	0.0577257635135	0.288813194768	-0.0250687502704	0.194045947691	0.0177198705748	-0.0336235526775	0.352016211877	0.0144348584707	0.205643154689	12.0698452501	32.8804835704	19.5817236365
3	3.33807218573	-0.559040337669	-0.340887234543	0.598175626132	0.0727820620939	0.613481246946	-0.105127657933	-0.258615169446	-0.0545986251732	0.0914571190816	0.0463129166556	0.0231763528818	0.0308519601435	0.0336925751262	0.0644218538895	0.155896427482	0.00829990933425	0.0101937065655	0.143813012228	0.00720734032134	0.114647417602	3.78001215584	30.6003961646	12.2671223122
4	0.472831199141	0.580163995837	-0.491608337887	1.09325776258	0.0337282501435	4.38609251542	-0.0964209029803	-0.162950892006	-0.347282511969	0.0378956324796	-0.0397690268184	-0.27304362728	0.197743943872	0.609938130531	0.19568180104	0.186996042805	0.0468043224381	0.0119419723243	0.228419275429	0.0421411555172	0.271479307462	12.8688778138	16.9454975319	6.24743213329
5	3.23727158325	-0.07955088142	-0.191593313563	0.447114311704	-0.0803074022621	0.336600693222	-0.0646373587908	-0.0252912822042	-0.342263176738	-0.0233099283501	0.0118813684145	0.000103287981743	0.0598453557363	0.0170367394082	0.0371841046034	0.141303096747	0.00386176676721	0.0105901870402	0.110463365032	0.00210675525788	0.148061920597	3.68264637033	23.205199773	0.406738563491
6	3.26427156011	-4.67447780431	0.18499618093	7.11858247395	0.284291532219	3.37568147309	0.195770892607	0.74263244109	-0.0419598439734	-0.603446497889	0.112401582404	-0.213889144549	-0.0618132509651	0.0741761458044	-0.228720003569	0.27102587744	-0.0400293775675	0.0378761335413	0.278669305453	-0.0446289624802	0.346528187123	10.5070813761	15.8941913975	-9.122428914
7	6.1234256347	3.09828456204	-0.104370999939	4.23257585432	-0.159914285278	0.0163894910835	0.0229010507319	0.31308574703	-0.530494451871	-0.0235817355115	0.029919730312	-0.595798964068	-0.162505119667	0.751156352961	0.0673260789801	0.142179441855	-0.0603569666281	0.000501772734126	0.438804590131	-0.0386163838316	0.177291314284	13.897448764	31.0376365175	-18.4547791354
8	8.70816685333	4.56684720499	-2.44402961659	3.6291202783	-1.33665471243	2.52348049352	-0.0611827279658	0.186369896505	-0.144780118845	0.0782534955288	0.0645855938769	-0.029924215671	-0.05603597247	0.113751775428	0.00668548480415	0.152236547384	0.00219738836745	-0.00289120314609	0.155975541948	0.00129702491808	0.132894602894	2.6060674551	28.4870021808	-11.5887111794
9	2.52521715354	1.23473712531	0.910946291539	0.580151005461	0.348274647494	0.410599470277	-0.0704251407789	0.084946476262	-0.178683412761	0.000336163944739	0.0828467657355	-0.0760728785736	0.0397245334149	0.0684452783364	0.00803994584373	0.161083789587	0.00719819267201	-0.00227060283307	0.166826709383	-0.00707356982742	0.153128542302	10.5763697035	32.3481360851	-7.84264143656
10	3.64750936567	-0.107381429915	0.0148105386145	2.6527214319	0.720988551216	3.61681834822	0.0722938833355	0.269056719945	-0.252314574251	-0.180440251618	-0.118901154222	-0.0112656209969	0.265158956601	-0.153480493697	0.0513556018252	0.182131139673	-0.00125193269241	-0.004719507728	0.138229906637	-0.0430901649923	0.144234456784	-6.56495924805	27.1071020302	-18.5268853442

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 4 through 15 )	A	A	4 - 15	1 - 12
2	2	chain 'A' and (resid 16 through 42 )	A	A	16 - 42	13 - 39
3	3	chain 'A' and (resid 43 through 97 )	A	A	43 - 97	40 - 94
4	4	chain 'B' and (resid 3 through 42 )	B	C	3 - 42	1 - 40
5	5	chain 'B' and (resid 43 through 97 )	B	C	43 - 97	41 - 95
6	6	chain 'C' and (resid 17 through 30 )	C	E	17 - 30	1 - 14
7	7	chain 'C' and (resid 31 through 42 )	C	E	31 - 42	15 - 26
8	8	chain 'C' and (resid 43 through 54 )	C	E	43 - 54	27 - 38
9	9	chain 'C' and (resid 55 through 81 )	C	E	55 - 81	39 - 65
10	10	chain 'C' and (resid 82 through 97 )	C	E	82 - 97	66 - 81

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