PDB-9zee: QatB-QatC complex in qatABCD anti-phage defense with ATP

ID or keywords:

Entry

Database: PDB / ID: 9zee

Title

QatB-QatC complex in qatABCD anti-phage defense with ATP

Components

QatB
QatC

Keywords

ANTIVIRAL PROTEIN / QueC / anti-phage defense

Function / homology

ADENOSINE-5'-TRIPHOSPHATE

Function and homology information

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.81 Å

Authors

Gao, A. / Wassarman, D.R. / Kranzusch, P.J.

Funding support

United States, 1items

Citation

Journal: Nat Commun / Year: 2026
Title: Structural basis of QueC-family protein function in qatABCD anti-phage defense.
Authors: Gao, A. / Wassarman, D.R. / Kranzusch, P.J.

History

Deposition	Nov 29, 2025	Deposition site: RCSB / Processing site: RCSB
Supersession	Apr 29, 2026	ID: 9Y02
Revision 1.0	Apr 29, 2026	Provider: repository / Type: Initial release
Revision 1.1	May 6, 2026	Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9zee.cif.gz	328.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9zee.ent.gz	217.3 KB	Display	PDB format
PDBx/mmJSON format	9zee.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ze/9zee ftp://data.pdbj.org/pub/pdb/validation_reports/ze/9zee	HTTPS FTP

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Related structure data

Related structure data	9zefC C: citing same article (ref.)
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: QatB

B: QatC

hetero molecules

82 kDa, 2 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)	70.704, 74.366, 134.304
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

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Protein , 2 types, 2 molecules AB

#1: Protein	QatB Mass: 29729.785 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: K6156 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): RIL
#2: Protein	QatC Mass: 51670.227 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: K6156 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): RIL

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Non-polymers , 4 types, 573 molecules

#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 570 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.17 Å³/Da / Density % sol: 43.35 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 0.1 M MES pH 6.3, 14% PEG-20000, 1 mM MgCl2, 1 mM ATP, 1 mM CDG

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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: Jul 8, 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: 1.81→67.15 Å / Num. obs: 64929 / % possible obs: 99.8 % / Redundancy: 12.3 % / B_iso Wilson estimate: 25.89 Å² / CC_1/2: 0.998 / CC star: 0.999 / R_merge(I) obs: 0.151 / R_pim(I) all: 0.044 / R_rim(I) all: 0.157 / Net I/σ(I): 9
Reflection shell	Resolution: 1.81→1.84 Å / Redundancy: 12.1 % / R_merge(I) obs: 1.275 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3179 / CC_1/2: 0.778 / CC star: 0.932 / R_pim(I) all: 0.379 / R_rim(I) all: 1.331 / % possible all: 99.5

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Processing

Software

Name	Version	Classification
PHENIX	1.21.2_5419	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.81→67.15 Å / SU ML: 0.1874 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.8313
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2035	3300	5.08 %
R_work	0.1813	61625	-
obs	0.1824	64925	99.8 %

Solvent computation

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

Displacement parameters

B_iso mean: 34.07 Å²

Refinement step

Cycle: LAST / Resolution: 1.81→67.15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4885	0	33	570	5488

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	5003
X-RAY DIFFRACTION	f_angle_d	0.7687	6780
X-RAY DIFFRACTION	f_chiral_restr	0.0482	766
X-RAY DIFFRACTION	f_plane_restr	0.0076	892
X-RAY DIFFRACTION	f_dihedral_angle_d	13.5088	1860

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 (%)
1.81-1.84	0.2867	134	0.2412	2517	X-RAY DIFFRACTION	99.44
1.84-1.87	0.2932	117	0.2294	2575	X-RAY DIFFRACTION	99.85
1.87-1.89	0.2644	138	0.2215	2513	X-RAY DIFFRACTION	100
1.89-1.93	0.2562	123	0.2226	2536	X-RAY DIFFRACTION	99.92
1.93-1.96	0.254	123	0.22	2517	X-RAY DIFFRACTION	98.47
1.96-1.99	0.2801	144	0.2301	2528	X-RAY DIFFRACTION	99.96
1.99-2.03	0.2515	129	0.2117	2549	X-RAY DIFFRACTION	100
2.03-2.07	0.2263	163	0.1959	2535	X-RAY DIFFRACTION	100
2.07-2.12	0.2257	139	0.1845	2515	X-RAY DIFFRACTION	100
2.12-2.17	0.2082	138	0.1765	2581	X-RAY DIFFRACTION	100
2.17-2.22	0.2089	136	0.1804	2557	X-RAY DIFFRACTION	100
2.22-2.28	0.1888	140	0.1781	2569	X-RAY DIFFRACTION	100
2.28-2.35	0.2538	139	0.1814	2529	X-RAY DIFFRACTION	100
2.35-2.43	0.2217	132	0.1811	2556	X-RAY DIFFRACTION	100
2.43-2.51	0.235	132	0.1833	2565	X-RAY DIFFRACTION	100
2.51-2.61	0.1906	122	0.1841	2592	X-RAY DIFFRACTION	100
2.61-2.73	0.2374	132	0.1812	2562	X-RAY DIFFRACTION	99.93
2.73-2.88	0.2095	160	0.1794	2556	X-RAY DIFFRACTION	99.74
2.88-3.06	0.1834	135	0.1802	2571	X-RAY DIFFRACTION	99.56
3.06-3.29	0.2067	150	0.1866	2562	X-RAY DIFFRACTION	99.2
3.29-3.62	0.187	163	0.1696	2551	X-RAY DIFFRACTION	99.49
3.62-4.15	0.1735	130	0.1531	2659	X-RAY DIFFRACTION	99.96
4.15-5.23	0.158	139	0.1578	2646	X-RAY DIFFRACTION	100
5.23-67.15	0.1942	142	0.1972	2784	X-RAY DIFFRACTION	99.8

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	3.34197642435	0.862672280375	-0.553964953495	7.4159108912	-1.80447464106	4.77716882667	-0.369633556382	-0.466366536683	0.159590490982	0.279159379909	0.0033196899055	-1.3462874071	-1.06467819178	0.83783081208	0.0948604621442	0.487473232456	-0.103569944341	0.00694669766224	0.365852387578	-0.155296940202	0.211638414312	-33.9601669857	11.046918185	36.6082257162
2	3.64213511828	2.95728071432	0.935339120787	6.11960308708	2.080065715	2.96862806652	-0.0617952603894	0.0384232457923	0.289075411078	-0.130151015177	-0.0447834869823	0.593487833588	-0.403397879087	-0.232028752931	0.108685366805	0.18324718634	0.0830438446703	-0.0144148679414	0.182174783946	-0.00265151355672	0.149943994383	-48.2475610661	0.426420930169	16.839206699
3	5.44421159674	1.03323777488	-1.86238258752	5.74734354273	-1.06800725688	7.17241753143	0.0200405322939	0.554709282885	-0.073571794835	-0.513033091123	-0.0309699824708	0.447916387221	0.0305309111466	-0.420794099346	0.0419183051751	0.202791904127	-0.00944597601445	-0.0763677752271	0.210767994474	-0.0772255845236	0.238312285091	-47.6099462308	-17.4385922604	7.4892606708
4	3.931970877	1.94454117084	-1.36126069144	7.7515923362	-1.09936459901	3.43987866835	0.0299124157882	-0.0632478009744	-0.190458717145	0.134474073972	0.0607402771126	-0.131977629187	-0.0241386202559	0.192920635836	-0.0963815304932	0.0801280673588	0.0323737987151	-0.0248921282036	0.154380005167	-0.0178342837931	0.117959735268	-37.649281687	-7.27370560784	17.3408901552
5	4.55378464276	3.70357495982	0.72511432304	7.72930791877	2.48433606511	3.92655537297	0.0822789626521	-0.526994744867	-0.0166974972077	0.366796262581	-0.208576661403	0.197318728603	0.0328692621671	-0.257418820556	0.0651724019515	0.162411764948	0.0417797625909	-0.0170638824315	0.203887325044	0.0253882423127	0.114316569969	-44.5329135167	-6.67319767299	23.9843132094
6	4.90750501799	0.901092595552	-0.405091424845	5.41188886042	0.591699047166	6.96400526696	0.469613555105	-0.359706303308	-0.907200575731	0.815047948279	0.231325973678	-0.367087417873	0.489254263397	0.363834373485	-0.497019593973	0.380538703732	0.00507511322999	-0.0225726988081	0.21243788978	-0.0561234439665	0.29753752835	-43.8826877642	-2.0202128077	33.3510634236
7	2.52459404938	0.391834477954	2.96039452132	2.0145202062	-1.19668776802	8.57086455758	0.243236683904	-0.0412389250572	-0.407356965091	0.06908757475	0.513888760944	0.277256320087	0.372006250314	-0.640425195853	-0.465900844052	0.440473416692	0.067589390835	-0.14775936343	0.96137576656	-0.547065256599	1.417077482	-60.2949034413	0.0320615583976	19.1363306591
8	4.7479406582	0.268734032261	2.39099778292	3.16324963572	1.13521052637	4.22279719795	-0.148499769148	-0.365060337789	0.197729723396	0.293319031569	-0.260445663463	0.444573378952	-0.664076043841	-0.350792154734	0.32858374854	0.267725341156	0.0433217385759	0.0244103139548	0.185489443085	-0.0426867757194	0.212732388879	-48.0677337828	6.95414545834	29.5674947207
9	1.1387118186	-0.591555431685	0.022929295759	1.56070615074	-0.0968115776162	0.417335878851	0.0335259474557	0.0993337935887	0.269403082857	-0.108361380047	-0.0132561184389	-0.0790217241771	-0.0924358046738	-0.0074956698803	-0.0412018191401	0.158144934655	-0.0103223527848	0.0035874043643	0.16579074485	0.0269096570832	0.214605599843	-17.4008262548	11.0013240235	-2.99824624624
10	1.71500127284	-0.124563751261	0.653925165149	1.26179379153	-0.489355622485	1.06371551363	-0.00760260456825	-0.069034253995	0.0843790489467	0.0677676872532	0.0111201771512	-0.0100770475319	-0.116154238508	-0.00921495984803	-0.0400291145648	0.1384418948	0.00600850688407	0.0105803936788	0.140346074939	-0.0160519528741	0.162304438784	-11.817247789	-4.27056749022	4.47631158406
11	2.30593823871	-0.120580227103	-0.633074979282	1.66422903084	-0.41862359106	1.42320379652	0.213573242881	-0.604550311673	0.0247106249037	0.366017063144	-0.0917836566017	-0.0491710528538	-0.224547145669	0.173066712159	-0.0577775062186	0.270242686367	-0.058690278319	0.023942843813	0.262073675297	-0.0128928564094	0.140690145287	-14.2403064264	-8.63492342771	22.8875383283

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 64 through 99 )	A	A	64 - 99	1 - 36
2	2	chain 'A' and (resid 100 through 127 )	A	A	100 - 127	37 - 64
3	3	chain 'A' and (resid 128 through 145 )	A	A	128 - 145	65 - 82
4	4	chain 'A' and (resid 146 through 183 )	A	A	146 - 183	83 - 120
5	5	chain 'A' and (resid 184 through 216 )	A	A	184 - 216	121 - 153
6	6	chain 'A' and (resid 217 through 254 )	A	A	217 - 254	154 - 178
7	7	chain 'A' and (resid 255 through 263 )	A	A	255 - 263	179 - 187
8	8	chain 'A' and (resid 264 through 287 )	A	A	264 - 287	188 - 211
9	9	chain 'B' and (resid 2 through 187 )	B	B	2 - 187	1 - 181
10	10	chain 'B' and (resid 188 through 330 )	B	B	188 - 330	182 - 313
11	11	chain 'B' and (resid 331 through 457 )	B	B	331 - 457	314 - 427

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