PDB-9ptq: Structure of Acb2 homolog 43 in complex with 3'cADPR

ID or keywords:

Entry

Database: PDB / ID: 9ptq

Title

Structure of Acb2 homolog 43 in complex with 3'cADPR

Components

Acb2 homolog 43

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: 1.56 Å

Authors

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

Funding support

United States, 1items

Citation

Journal: Biorxiv / Year: 2025
Title: Functional diversity of phage sponge proteins that sequester host immune signals.
Authors: Hadary, R. / Chang, R.B. / Bechon, N. / Tal, N. / Osterman, I. / Yirmiya, E. / Garb, J. / Amitai, G. / Kranzusch, P.J. / Sorek, R.

History

Deposition	Jul 29, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 17, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9ptq.cif.gz	228.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9ptq.ent.gz	151.4 KB	Display	PDB format
PDBx/mmJSON format	9ptq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9ptq_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	9ptq_full_validation.pdf.gz	1.2 MB	Display
Data in XML	9ptq_validation.xml.gz	29.1 KB	Display
Data in CIF	9ptq_validation.cif.gz	39.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pt/9ptq ftp://data.pdbj.org/pub/pdb/validation_reports/pt/9ptq	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: Acb2 homolog 43

B: Acb2 homolog 43

C: Acb2 homolog 43

D: Acb2 homolog 43

E: Acb2 homolog 43

F: Acb2 homolog 43

hetero molecules

51.9 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	60.123, 53.668, 73.479
Angle α, β, γ (deg.)	90.000, 110.489, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Acb2 homolog 43 Mass: 8467.680 Da / Num. of mol.: 6 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.: 2 / Source method: obtained synthetically / Formula: C₁₅H₂₁N₅O₁₃P₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 556 / 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: 43.73 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 20% w/v PEG1500, 0.1 M HEPES, pH 7.5

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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: 1.56→68.83 Å / Num. obs: 62049 / % possible obs: 99.1 % / Redundancy: 6.8 % / B_iso Wilson estimate: 19.66 Å² / CC_1/2: 0.999 / Net I/σ(I): 15.4
Reflection shell	Resolution: 1.56→1.59 Å / Num. unique obs: 3073 / CC_1/2: 0.821 / % possible all: 98.6

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.56→68.83 Å / SU ML: 0.187 / Cross valid method: FREE R-VALUE / Phase error: 20.2775
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1954	2942	4.74 %
R_work	0.1705	59080	-
obs	0.1717	62022	99.1 %

Solvent computation

Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 24.81 Å²

Refinement step

Cycle: LAST / Resolution: 1.56→68.83 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3312	0	70	556	3938

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0094	3431
X-RAY DIFFRACTION	f_angle_d	1.0907	4590
X-RAY DIFFRACTION	f_chiral_restr	0.0579	517
X-RAY DIFFRACTION	f_plane_restr	0.0075	564
X-RAY DIFFRACTION	f_dihedral_angle_d	14.5676	1326

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 (%)
1.56-1.59	0.3383	140	0.2905	2813	X-RAY DIFFRACTION	98.47
1.59-1.61	0.2317	121	0.2464	2787	X-RAY DIFFRACTION	98.91
1.61-1.64	0.3052	144	0.2223	2809	X-RAY DIFFRACTION	99.03
1.64-1.67	0.2498	121	0.2056	2809	X-RAY DIFFRACTION	98.55
1.67-1.71	0.2511	131	0.2038	2775	X-RAY DIFFRACTION	98.34
1.71-1.75	0.2475	138	0.1905	2752	X-RAY DIFFRACTION	97.47
1.75-1.79	0.2242	124	0.1975	2776	X-RAY DIFFRACTION	97.28
1.79-1.83	0.2223	157	0.1973	2799	X-RAY DIFFRACTION	99.56
1.83-1.88	0.2404	150	0.1965	2798	X-RAY DIFFRACTION	99.86
1.88-1.94	0.2357	130	0.19	2828	X-RAY DIFFRACTION	99.9
1.94-2	0.2002	154	0.1735	2813	X-RAY DIFFRACTION	99.87
2-2.07	0.1963	157	0.1599	2810	X-RAY DIFFRACTION	99.53
2.07-2.15	0.1758	144	0.1561	2812	X-RAY DIFFRACTION	99.36
2.15-2.25	0.2065	131	0.1531	2795	X-RAY DIFFRACTION	99.02
2.25-2.37	0.1817	139	0.1601	2819	X-RAY DIFFRACTION	98.96
2.37-2.52	0.1806	133	0.1584	2779	X-RAY DIFFRACTION	97.78
2.52-2.71	0.1955	129	0.1701	2838	X-RAY DIFFRACTION	99.7
2.71-2.98	0.1798	153	0.171	2861	X-RAY DIFFRACTION	99.7
2.98-3.42	0.1878	155	0.1689	2819	X-RAY DIFFRACTION	99.73
3.42-4.3	0.1632	149	0.1451	2868	X-RAY DIFFRACTION	99.51
4.31-68.83	0.1932	142	0.1722	2920	X-RAY DIFFRACTION	99.13

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	3.84508402764	-0.750782065478	-0.469751837013	0.440453209118	-0.333246345916	0.774244120526	0.0851038488634	0.299065347898	0.501626032197	0.0440821457373	-0.123026045907	-0.135414463515	-0.0900692872201	0.101017947396	0.0131345851684	0.177633873587	-0.0458864892728	-0.00583834743554	0.182428623324	0.0351775461974	0.196648669593	33.7771172802	14.9968498068	7.96072376333
2	5.74388049945	-1.42611476804	-0.682900344422	0.873062115306	-0.011985028127	0.276360699781	-0.0528843933853	0.192108525622	0.216900467464	0.0498104296125	-0.0229557829165	-0.122810615746	0.0511340648779	0.0244771339835	0.0551661302387	0.165722751701	-0.0284608199603	-0.00841131205046	0.137823728805	0.0268583606908	0.127320933014	31.8396040286	8.99151098285	11.85037839
3	1.75681662298	-0.605348606944	1.53734274069	1.00696887073	-1.74586828452	3.19140087956	0.110774459249	-0.00469057391289	-0.15870255494	-0.100825161805	0.0588366377849	0.125028876012	0.158527627895	-0.099465285936	-0.224956723409	0.184404036687	0.0136850055019	0.0165966439643	0.0992519203507	-0.0257169773458	0.143547634222	12.2821527867	-15.4814830409	25.7031704801
4	2.76099431138	-0.2791666391	3.30050896108	0.648689037359	-1.39524844022	8.32052444114	0.0113501679365	0.275410206989	-0.0793605175422	-0.0204438503821	-0.0271091105117	-0.0923566597422	0.00454749396223	0.303067957451	0.0280165302206	0.151495347712	0.00862518046417	0.0162120514079	0.109729869938	-0.0151183907532	0.16016300421	16.0038933341	-8.17260719194	16.8315220441
5	7.93804055272	0.0476263158009	-4.60106699757	3.8211640018	-0.945141327556	6.69955668922	0.17381541617	-0.334550276272	0.0334881638841	-0.0521742893503	-0.102767543966	-0.368675682277	-0.423871595986	0.576322799678	-0.0366920705234	0.177941283709	-0.042326871538	0.00954426665648	0.118458591028	0.00391138465919	0.119189358921	23.3726779505	-14.1225581641	39.1075740761
6	5.94684784367	4.80973732666	0.96183555115	3.94313862256	1.06715817636	1.68771667222	-0.106809673303	0.498764434131	-0.792852254869	0.133201121778	0.288759973093	-0.802966593332	-0.0720539554009	0.259958688983	-0.252563659916	0.207867178797	-0.0364204389565	-0.0637205455464	0.242058591623	0.0187728435611	0.281501219031	6.18452298983	6.56309929774	1.75521755862
7	6.28574494865	-2.86898985459	5.88107095728	2.23819776693	-3.3003452995	5.89069841815	0.0581071458309	-0.0620735202261	-0.172080706846	-0.0092880096343	0.133090665892	0.124287293752	0.00885955543116	-0.23791236218	-0.254591567649	0.132962969818	-0.028020388853	0.0186671078625	0.10936446908	0.000482087476737	0.147898421436	0.971290458606	-4.96049449563	17.8615929636
8	1.55640900348	-0.334857595287	2.18039229471	0.36929079502	-0.91185511124	7.19185562758	-0.02390069348	0.0985635783812	0.00699042989534	0.016110738743	0.0136452991374	-0.0172335069227	-0.0920748073423	0.113309561275	0.00372036044855	0.15058807103	-0.00836976075236	0.0105365607474	0.0981513097296	-0.00652884600868	0.14199104326	11.4050168717	-1.47788796343	18.0937289066
9	8.85595776452	6.63511257694	-0.456070681894	5.48669435037	0.822552889941	2.65653757019	-0.425887147151	0.889877241424	0.303899256019	-0.655732413866	0.651632016008	0.0361337354778	-0.251738920037	0.280740642204	-0.177807400078	0.239502341861	-0.0515764051247	0.0147792851531	0.430458487895	0.0522213196133	0.198739430019	5.64333590297	8.34959078604	-2.45224691319
10	4.7060150359	-0.415208123968	-0.639265268244	0.847124450797	-0.188378403122	0.644505998975	0.0582233372501	0.476683629506	0.41213933794	-0.0939053300182	0.0574229244019	0.00546213845729	-0.00294899258451	-0.0302760559255	-0.128994423331	0.180771255007	-0.00520191947193	-0.0265606205206	0.179517441483	0.0200379825001	0.125330145119	12.5191328527	13.7314578055	6.12686594417
11	6.76361240041	-0.62528558096	-1.80461905239	0.536996992789	-0.0743525773007	1.3381890823	-0.0747794232392	0.234957845196	0.0288105672784	0.00349727458406	0.0424472261337	0.0110404064926	0.074974097819	-0.0632811560758	0.0296306674234	0.156610720386	-0.0138538513198	-0.0266992100944	0.128967198083	0.0179917376202	0.102605861163	14.3871605464	7.98799811863	10.3407366731
12	3.25370382851	1.97420907644	0.0791706367436	1.2096241904	0.134727126788	0.72550728687	-0.0196600633022	-0.0503296980254	-0.00119273878897	0.0105523863026	-0.0785929737225	-0.211956463196	0.00537944223616	0.0422184132747	0.098189255423	0.122738475704	0.0215337758665	0.00256674522497	0.180072009208	0.020873392616	0.128654618664	43.9545056195	1.99341802643	20.2006395035
13	1.88718891607	2.24256924224	0.290093118431	6.35500316835	0.854019295952	1.21811200031	-0.0757315678687	-0.00195040348151	0.0877135538323	-0.218573554613	0.0454717051283	-0.0537448595162	-0.0186399916148	0.0502275918984	0.0437478537068	0.14623445766	0.0167786756057	0.00157116160823	0.180591732545	0.0272057199919	0.130715113862	34.7852463944	-1.49222038292	18.2393564532
14	7.43580770439	-4.89446320546	7.07837537311	4.62960806746	-4.13770434453	9.10536576969	-0.409762196188	0.327276612707	0.972884038459	-0.23079626013	-0.324565316345	-0.0149328173724	-1.07121085202	-0.12677077484	0.565392265105	0.34025979489	0.0642844326062	-0.101490579877	0.281430096993	0.0105124496421	0.563324082031	40.6307151488	21.1552018615	16.0608594949
15	1.69564163303	2.29059798176	-0.347558465573	5.88255419284	-0.278895845778	0.138538294641	0.207810400792	-0.270998328235	-0.216441936825	0.198388641335	-0.362130522557	-0.498705982764	0.0551975125297	0.125648530393	0.179554145822	0.207189462683	0.0190880823079	0.00814436203384	0.209295914655	0.0340403284409	0.129784888432	33.8171209902	-13.4415967928	28.795873237
16	2.73698723511	3.8650809512	1.11984882987	8.50522993052	2.95364895669	1.31443607011	-0.0194636889315	-0.205911684191	0.230667310575	0.18225571895	-0.0715489406407	0.473096471168	0.0408278844838	-0.0535466795836	0.100703895048	0.144072353579	0.017816298027	0.00936391552144	0.197216375089	0.0412779744726	0.137574664357	30.2667867711	-2.0729993031	25.0779266182
17	9.45679290783	0.369390627756	-1.10905073089	6.38000687015	-1.94359281937	7.6864089841	-0.246672820457	0.454475670563	-0.359065553378	-0.737797581579	-0.181806385479	0.222319302753	0.444869882779	-0.290310529239	0.366699133459	0.29071629028	0.0102720433216	-0.0138503527461	0.118529402681	-0.0581589575843	0.176260156295	24.1735130849	-26.082942423	22.9317503715

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 'F' and (resid 0 through 32 )	F	H	0 - 32	1 - 33
2	2	chain 'F' and (resid 33 through 71 )	F	H	33 - 71	34 - 72
3	3	chain 'A' and (resid 2 through 32 )	A	A	2 - 32	1 - 31
4	4	chain 'A' and (resid 33 through 59 )	A	A	33 - 59	32 - 58
5	5	chain 'A' and (resid 60 through 70 )	A	A	60 - 70	59 - 69
6	6	chain 'B' and (resid 2 through 8 )	B	C	2 - 8	1 - 7
7	7	chain 'B' and (resid 9 through 32 )	B	C	9 - 32	8 - 31
8	8	chain 'B' and (resid 33 through 63 )	B	C	33 - 63	32 - 62
9	9	chain 'B' and (resid 64 through 70 )	B	C	64 - 70	63 - 69
10	10	chain 'C' and (resid 0 through 32 )	C	E	0 - 32	1 - 33
11	11	chain 'C' and (resid 33 through 71 )	C	E	33 - 71	34 - 72
12	12	chain 'D' and (resid 2 through 32 )	D	F	2 - 32	1 - 31
13	13	chain 'D' and (resid 33 through 63 )	D	F	33 - 63	32 - 62
14	14	chain 'D' and (resid 64 through 70 )	D	F	64 - 70	63 - 69
15	15	chain 'E' and (resid 2 through 32 )	E	G	2 - 32	1 - 31
16	16	chain 'E' and (resid 33 through 58 )	E	G	33 - 58	32 - 57
17	17	chain 'E' and (resid 59 through 69 )	E	G	59 - 69	58 - 68

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