PDB-9zef: QatB-QatC complex in qatABCD anti-phage defense

ID or keywords:

Entry

Database: PDB / ID: 9zef

Title

QatB-QatC complex in qatABCD anti-phage defense

Components

QatB
QatC

Keywords

ANTIVIRAL PROTEIN / QueC / anti-phage defense

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.55 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: 9Y01
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	9zef.cif.gz	328.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9zef.ent.gz	218.5 KB	Display	PDB format
PDBx/mmJSON format	9zef.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/9zef ftp://data.pdbj.org/pub/pdb/validation_reports/ze/9zef	HTTPS FTP

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Related structure data

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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: QatB

B: QatC

hetero molecules

81.5 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)	70.892, 74.610, 133.629
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

#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
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 592 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 43.4 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M NaCl, 18% PEG-3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9199 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 24, 2025
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9199 Å / Relative weight: 1
Reflection	Resolution: 1.55→66.81 Å / Num. obs: 102996 / % possible obs: 100 % / Redundancy: 8.6 % / B_iso Wilson estimate: 21.68 Å² / CC_1/2: 0.999 / CC star: 1 / R_merge(I) obs: 0.073 / R_pim(I) all: 0.026 / R_rim(I) all: 0.077 / Net I/σ(I): 12.3
Reflection shell	Resolution: 1.55→1.58 Å / Redundancy: 8.2 % / R_merge(I) obs: 1.071 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5114 / CC_1/2: 0.767 / CC star: 0.93 / R_pim(I) all: 0.399 / R_rim(I) all: 1.144 / % possible all: 100

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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: 1.55→51.39 Å / SU ML: 0.1763 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.0595
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.193	5280	5.13 %
R_work	0.1767	97709	-
obs	0.1775	102989	99.98 %

Solvent computation

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

Displacement parameters

B_iso mean: 31.61 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→51.39 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4949	0	1	592	5542

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0106	5036
X-RAY DIFFRACTION	f_angle_d	1.0952	6820
X-RAY DIFFRACTION	f_chiral_restr	0.0653	772
X-RAY DIFFRACTION	f_plane_restr	0.0116	903
X-RAY DIFFRACTION	f_dihedral_angle_d	13.3004	1846

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 (%)
1.55-1.57	0.2871	183	0.2764	3188	X-RAY DIFFRACTION	100
1.57-1.59	0.2936	183	0.2581	3269	X-RAY DIFFRACTION	100
1.59-1.61	0.2665	197	0.2519	3192	X-RAY DIFFRACTION	100
1.61-1.63	0.2473	170	0.2277	3188	X-RAY DIFFRACTION	99.94
1.63-1.65	0.2412	188	0.2143	3228	X-RAY DIFFRACTION	100
1.65-1.67	0.2674	166	0.207	3194	X-RAY DIFFRACTION	100
1.67-1.7	0.2325	173	0.202	3256	X-RAY DIFFRACTION	100
1.7-1.72	0.2466	188	0.1951	3209	X-RAY DIFFRACTION	100
1.72-1.75	0.2198	168	0.1916	3198	X-RAY DIFFRACTION	100
1.75-1.78	0.2104	176	0.1874	3283	X-RAY DIFFRACTION	100
1.78-1.81	0.2296	161	0.1855	3225	X-RAY DIFFRACTION	100
1.81-1.84	0.2129	171	0.1863	3209	X-RAY DIFFRACTION	100
1.84-1.88	0.2476	162	0.2019	3266	X-RAY DIFFRACTION	100
1.88-1.91	0.2552	160	0.2084	3272	X-RAY DIFFRACTION	100
1.91-1.96	0.2375	148	0.1905	3209	X-RAY DIFFRACTION	100
1.96-2	0.2307	188	0.1859	3226	X-RAY DIFFRACTION	100
2-2.05	0.1948	163	0.1782	3248	X-RAY DIFFRACTION	100
2.05-2.11	0.2014	204	0.1765	3250	X-RAY DIFFRACTION	100
2.11-2.17	0.1896	172	0.1739	3230	X-RAY DIFFRACTION	99.97
2.17-2.24	0.1928	186	0.178	3262	X-RAY DIFFRACTION	100
2.24-2.32	0.2089	181	0.1768	3230	X-RAY DIFFRACTION	100
2.32-2.41	0.2135	163	0.1698	3283	X-RAY DIFFRACTION	100
2.41-2.52	0.1896	173	0.1789	3260	X-RAY DIFFRACTION	100
2.52-2.65	0.1911	142	0.1763	3304	X-RAY DIFFRACTION	100
2.65-2.82	0.1913	194	0.17	3271	X-RAY DIFFRACTION	100
2.82-3.04	0.1786	191	0.1762	3278	X-RAY DIFFRACTION	100
3.04-3.34	0.2049	198	0.1745	3273	X-RAY DIFFRACTION	100
3.34-3.83	0.1632	178	0.1543	3332	X-RAY DIFFRACTION	100
3.83-4.82	0.1396	167	0.1491	3377	X-RAY DIFFRACTION	100
4.82-51.39	0.1782	186	0.1843	3499	X-RAY DIFFRACTION	99.49

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	2.55983721376	-1.32204162496	-0.12613802931	5.92371116851	-1.02419173968	3.92699778023	-0.381099001833	-0.234189045427	0.21724180239	0.442768967266	0.256498188074	-0.701067871058	-1.12347468637	0.551204139051	0.102822840733	0.520829238249	-0.0587837618247	-0.0557332794858	0.342262268364	-0.076444187594	0.253812260702	-34.1038545231	11.184934186	36.4425322514
2	4.38594373431	3.24305881474	0.93336451288	7.39346713541	2.47443217281	3.12574930992	-0.104653224889	0.0602592565348	0.0415350549429	-0.103422663088	0.0602512807944	0.353854698219	-0.342849233216	-0.190715728705	0.0915067788819	0.17372227826	0.0807554581074	-0.0186849844459	0.176952899272	0.0139898502776	0.129275084636	-48.6079785223	0.424251282703	16.7972215949
3	5.92048379909	1.31458228346	-1.00161175606	7.40595142724	-2.05224186012	2.10929840287	-0.068624874661	0.507063968875	-0.086746976719	-0.502881334385	-0.0827120621101	0.321234993047	0.247355446281	-0.447632420216	0.107383582714	0.252044064015	0.00879996330433	-0.052314166914	0.248009768881	-0.0923478367351	0.264404686866	-48.0226741296	-17.5137035852	7.49145576842
4	4.48510918762	1.87852374855	-0.477403650346	7.25336286389	-0.213830165022	3.54787650352	0.0738756805231	-0.0558144655743	-0.240086370558	0.133536349244	-0.0502686348859	-0.111566865876	0.122548238423	0.131203951293	-0.00493883317341	0.0737541774939	0.0305967388745	-0.00591011484415	0.145828279691	-0.0103013887529	0.13170349718	-38.037751987	-7.28752971544	17.2296380901
5	5.91594691456	-0.412570702158	-4.46963083144	2.3416896418	0.146730031405	4.31290582653	-0.179427641419	-0.333866887409	-0.74125407805	0.964655839356	-0.354596500108	0.191400220041	1.10065617451	-0.279769929152	0.525131714159	0.397434599998	-0.0993489083315	0.0702835011417	0.266988492784	0.0367572105815	0.346667226042	-49.4432236777	-19.3929056945	19.7689570762
6	1.65358395394	-0.173855151481	-0.128886277457	3.66358866245	-0.167715007211	2.64061517909	-0.0667517820179	-0.414507065399	0.119459371988	0.310817059391	0.0274305691773	0.0941140670898	-0.129410648624	-0.0194540214297	0.0503704384007	0.182300989252	0.0281713465974	0.00332033280361	0.209965291992	-0.0222158469118	0.0972271326087	-42.35253579	-2.53601663071	25.749059652
7	2.20931001142	-0.248297101659	4.31564158377	4.85793176429	0.0798306649858	8.52320479839	0.335796337851	-0.329622872613	-0.670859637351	0.45591661166	0.152080373472	-0.152890182035	0.355111535254	0.0531789870771	-0.435615336695	0.343799096462	-0.0108517341465	0.0618914443981	0.173993520367	-0.0105335423713	0.268275536622	-42.4611786379	-2.55873087089	34.0829011796
8	6.24250432888	0.597249540052	-1.73760820816	5.46072911967	-3.02488909429	6.34656807297	0.350994486596	-0.549941901579	-0.234622010298	-0.14997458026	-0.0421788376223	1.20956668866	0.256762650666	-1.57029513621	-0.299591738109	0.399356710171	0.0270702332734	-0.0938047883654	0.831355112971	-0.259424575575	0.961094505676	-60.7196802712	0.0658185215032	19.3992832198
9	2.80286350948	0.405784798834	0.571679233984	3.24028595569	2.31831867482	7.77893121764	-0.131038446616	-0.445323598546	0.0959989803833	0.275707782812	-0.0552908333202	0.244438591282	-0.611257416174	-0.395971307664	0.23728742692	0.25782724591	0.0585399499315	0.0334297710079	0.191665940774	-0.0234357909363	0.167053909233	-48.1747159566	7.04756543791	29.5631630712
10	1.88379380077	-0.526393613637	-0.712018388336	1.80483367419	0.158643724433	1.09788687204	0.0682711360066	0.0300361273942	0.279986675797	-0.0283802786305	0.0200656810859	-0.00385940602143	-0.14899797769	0.00287836486991	-0.0861744929367	0.147245508507	-0.00214371884868	-0.00715933819739	0.14141307127	0.0087751154835	0.184026923039	-21.5206709353	15.6065114141	-2.83669511159
11	1.4160799447	0.360803070313	-0.137815429098	1.16258926081	-0.321879750986	0.641764888903	0.129365430967	-0.227889583043	0.0292544030746	0.186887649468	-0.0887829224462	-0.0354328438853	-0.110815090615	0.0810582469141	-0.0311843076046	0.176450726144	-0.019860683844	0.0143668600563	0.168737104368	-0.0313039929555	0.161617935473	-11.9765355172	-5.69708502003	10.6011460569

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 192 )	A	A	184 - 192	121 - 129
6	6	chain 'A' and (resid 193 through 227 )	A	A	193 - 227	130 - 155
7	7	chain 'A' and (resid 228 through 254 )	A	A	228 - 254	156 - 182
8	8	chain 'A' and (resid 255 through 263 )	A	A	255 - 263	183 - 191
9	9	chain 'A' and (resid 264 through 287 )	A	A	264 - 287	192 - 215
10	10	chain 'B' and (resid 2 through 139 )	B	B	2 - 139	1 - 138
11	11	chain 'B' and (resid 140 through 457 )	B	B	140 - 457	139 - 431

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