PDB-9nto: Structure of Cap9-CdnD complex containing NDG modification

ID or keywords:

Entry

Database: PDB / ID: 9nto

Title

Structure of Cap9-CdnD complex containing NDG modification

Components

Cap9
CdnD

Keywords

ANTIVIRAL PROTEIN / CD-NTase / QueC / CBASS

Function / homology

Chem-2KA / ADENOSINE / ADENOSINE MONOPHOSPHATE

Function and homology information

Biological species

Hyphomicrobiales (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

Wassarman, D.R. / Pfaff, P. / Paulo, J.A. / Gygi, S.P. / Shokat, K.M. / Kranzusch, P.J.

Funding support

United States, 1items

Citation

Journal: Biorxiv / Year: 2025
Title: Deazaguanylation is a nucleobase-protein conjugation required for type IV CBASS immunity.
Authors: Wassarman, D.R. / Pfaff, P. / Paulo, J.A. / Gygi, S.P. / Shokat, K.M. / Kranzusch, P.J.

History

Deposition	Mar 18, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 7, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9nto.cif.gz	236.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9nto.ent.gz	155.9 KB	Display	PDB format
PDBx/mmJSON format	9nto.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/nt/9nto ftp://data.pdbj.org/pub/pdb/validation_reports/nt/9nto	HTTPS FTP

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Related structure data

Related structure data	9ntnC 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
Related items in Molecule of the Month	#265 - Jan 2022 Golgi Casein Kinase similarity (1) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #24 - Dec 2001 Glycogen Phosphorylase similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1)

Deposited unit

A: CdnD

B: Cap9

hetero molecules

55.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: CdnD

B: Cap9

hetero molecules

A: CdnD

B: Cap9

hetero molecules

defined by author&software
111 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	92.664, 58.219, 89.228
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2
Space group name Hall	P22ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x+1/2,y+1/2,-z #4: -x,-y,z

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Protein , 2 types, 2 molecules AB

#1: Protein	CdnD Mass: 34453.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hyphomicrobiales (bacteria) / Production host: Escherichia coli BW25113 (bacteria)
#2: Protein	Cap9 Mass: 20042.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hyphomicrobiales (bacteria) / Production host: Escherichia coli BW25113 (bacteria)

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Non-polymers , 5 types, 215 molecules

#3: Chemical	ChemComp-AMP / ADENOSINE MONOPHOSPHATE Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₇P / Comment: AMP*YM
#4: Chemical	ChemComp-2KA / 2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidine-5-carboxylic acid Mass: 194.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₇H₆N₄O₃ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical	ChemComp-ADN / ADENOSINE Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₅O₄
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	Y

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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: 43.91 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris-HCl pH 8.5, 24% PEG-3350, 5 mM MgCl2, 1 mM AMP

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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-2 / Wavelength: 0.979 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 30, 2025
Radiation	Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.15→43.15 Å / Num. obs: 25975 / % possible obs: 96.43 % / Redundancy: 8.2 % / B_iso Wilson estimate: 26.81 Å² / CC_1/2: 0.993 / CC star: 0.998 / R_merge(I) obs: 0.2997 / R_pim(I) all: 0.1096 / R_rim(I) all: 0.3196 / Net I/σ(I): 6.32
Reflection shell	Resolution: 2.15→2.23 Å / Redundancy: 8.5 % / R_merge(I) obs: 2.042 / Num. unique obs: 2661 / CC_1/2: 0.378 / CC star: 0.74 / R_pim(I) all: 0.7334 / R_rim(I) all: 2.172 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.21.1_5286	refinement
AutoProcess	1.0.5	data processing
Coot	0.9.8.95	model building
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.15→43.15 Å / SU ML: 0.2754 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.7234
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2317	1359	5.25 %
R_work	0.2048	24529	-
obs	0.2063	25888	96.43 %

Solvent computation

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

Displacement parameters

B_iso mean: 42.7 Å²

Refinement step

Cycle: LAST / Resolution: 2.15→43.15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3472	0	60	211	3743

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0029	3597
X-RAY DIFFRACTION	f_angle_d	0.5654	4866
X-RAY DIFFRACTION	f_chiral_restr	0.041	548
X-RAY DIFFRACTION	f_plane_restr	0.0055	623
X-RAY DIFFRACTION	f_dihedral_angle_d	16.3129	1314

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 (%)
2.15-2.23	0.3586	135	0.3128	2526	X-RAY DIFFRACTION	100
2.23-2.32	0.2912	125	0.2909	2147	X-RAY DIFFRACTION	86.26
2.32-2.42	0.3041	118	0.2645	2522	X-RAY DIFFRACTION	99.92
2.42-2.55	0.3073	147	0.2347	2487	X-RAY DIFFRACTION	100
2.55-2.71	0.2503	112	0.2241	2295	X-RAY DIFFRACTION	90.52
2.71-2.92	0.2682	139	0.2139	2527	X-RAY DIFFRACTION	100
2.92-3.22	0.2075	136	0.1941	2543	X-RAY DIFFRACTION	100
3.22-3.68	0.2322	136	0.1867	2301	X-RAY DIFFRACTION	90.53
3.68-4.64	0.184	161	0.1572	2473	X-RAY DIFFRACTION	96.87
4.64-43.15	0.1934	150	0.1825	2708	X-RAY DIFFRACTION	99.93

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	2.62955669678	0.237400983546	0.828094425972	1.5009561947	-0.0631686451149	1.48416157876	0.0031590699513	0.240469972189	0.3732814662	-0.0277642795596	-0.109882269369	0.0718836917623	0.00920070465032	-0.0908005488859	0.142275596755	0.247936013781	0.0114049143118	-0.00790246782766	0.15931619966	-0.023079940089	0.132369908309	-7.21261654131	43.6399576405	-17.5513151603
2	4.06039222524	1.38939579757	0.896979628415	2.68704600041	-0.950915126474	0.927613789461	-0.412350693175	-0.404136431279	0.215956018729	-0.666620477471	-0.193426256267	-0.298320172888	-0.0123515702815	-0.753803793497	-0.0948856764361	0.324904230038	0.022209147734	-0.00343482766812	0.550425980233	-0.193334386495	0.403867916311	-29.7748950022	39.8263245906	-26.4726617646
3	2.0514939177	-1.06078344478	0.136322496465	3.16427912796	-0.637013076871	0.129706565813	-0.221311249637	0.0202875238461	0.467935234389	-0.564326393262	0.0337984835578	0.943557123811	-0.0890883813634	-1.19738470237	-0.116275560226	0.384499504925	0.0210760037131	-0.188172683586	1.13890346543	-0.041165124146	0.660107464843	-39.7299287989	40.2201218641	-32.1584813996
4	0.240155031161	0.321472380917	0.560286997103	2.35779639902	-2.90556093122	8.25867880257	-0.131945965506	-0.742805018574	0.544257530951	0.0203098026107	0.236232867305	0.509267303003	-0.0731471602896	-1.30573003347	-0.0675335603139	0.641579548988	0.357137203338	-0.138871904139	0.921748317801	-0.0787017056613	0.630644799743	-38.6152951818	47.0037488269	-24.8729162342
5	3.14247426913	-0.102040969806	0.256419961972	2.03274792417	0.432901596149	3.87433209529	-0.202939361082	0.553583219096	0.120815364137	-0.292114538623	0.0127503231369	0.490269195366	-0.163249911252	-0.927066286303	0.140822397225	0.376584941098	-0.0521490655966	-0.0393718766303	0.543910295744	0.0109341117509	0.354511474525	-29.7345255537	35.2490970683	-33.1920198436
6	2.98525708261	0.457810803881	1.10463021128	2.47470356042	0.269066000809	3.60818981875	-0.128406058615	0.587409459377	0.126660499263	-0.338123269907	0.0261371304813	-0.126216664889	0.0247539806985	0.240274221186	0.0541208816685	0.246334539998	-0.00447157777553	-0.0162147867154	0.310793417625	-0.0259426559209	0.194012075202	-13.4317963151	39.7777617052	-33.6936013492
7	1.36710920568	0.232513423026	0.497522678868	1.51075552755	0.633129470094	1.8256615787	-0.121138808619	0.849458238687	0.126466533846	-0.610202162443	0.0294865306112	0.121217313745	-0.124627135372	-0.184453140072	0.0331057977742	0.44425747156	-0.0237154227606	-0.00691562149522	0.513055111567	-0.027810265019	0.206292036562	-10.9433827307	43.1237739965	-39.494305545
8	4.21893862983	0.499894136184	2.35421925334	4.99676319377	-2.26511156229	7.85761905207	-0.560257211963	0.16711101706	0.464409462227	0.44641495407	0.24821311143	0.138492741992	-0.240100180027	-0.0900276291926	0.398208763877	0.13293352668	0.0141999840179	0.025880345063	0.121477344773	-0.020446621992	0.274952350972	7.4865668271	43.4554697437	-3.78561649193
9	1.68509063926	-2.54468571093	0.789714431316	6.18615432378	-3.92901474639	5.38238176323	-0.073312933867	-0.311964947081	0.267063884992	-0.409666809771	-0.0633821488856	-0.720094941635	0.48481245356	0.174807929837	0.233782138411	0.201905038007	-0.0474763505882	-0.0853209557071	0.19310955041	-0.0573198624131	0.332822234725	14.5795562041	47.6467879867	-6.71292541044
10	2.62650905038	-0.175908554145	-0.048229453597	5.20686358135	-2.68399162309	4.45175819352	0.0337968710103	-0.427180665179	-0.0579191181283	0.119217252614	-0.000779244784045	0.902360772344	-0.0915543853995	-0.316275516753	0.0725123162783	0.131663302692	-0.0109264583147	-0.0929216836818	0.154195629933	-0.0735327230591	0.267434625839	7.04209667814	40.8775375206	-0.518204935627
11	1.63882287816	0.488450228232	0.330107405427	2.10895176626	-0.832514097867	1.80292748386	0.16317404212	-0.0508288207783	0.241304171786	0.0345259264373	-0.172486496927	-0.125537987051	-0.00850876206619	0.24724653295	0.0872119446292	0.327805553046	-0.0223450082805	-0.0976866533743	0.191967599639	-0.035715485596	0.266624985027	14.2929478582	42.8429524333	6.2385002298
12	2.49122549222	0.243022151716	0.00349197035949	0.162198544749	0.291799228431	2.03740352701	0.0956281269187	-0.485581775566	-0.291767337278	0.281288674583	-0.0181144644022	-0.228280074545	0.411026977867	0.12694808926	0.0112773100814	0.29210822849	-0.0107020185581	-0.0363940099672	0.21584707567	0.0404739820505	0.257410577657	8.09536590898	29.3466044409	2.48301239055
13	1.3228900458	0.169498758838	-0.372486141383	1.61758921566	-0.261264481666	1.486233728	0.106667599931	0.0256690983446	0.108315984199	-0.0169475056088	-0.0764480190932	-0.0589120660428	0.0248696891796	-0.0158695295373	-0.0285971228947	0.151715163234	-0.0122196606556	-0.00984061702069	0.120964128521	-0.0100825258235	0.207533946602	5.63596202016	35.6968358625	-11.7549665095
14	0.810853401823	-0.923319107464	1.39914240659	3.41840686098	0.770043780981	4.8159948354	-0.270786626178	0.286959190438	0.687238979762	-0.311475973509	-0.0148830486869	-0.290060959412	-0.4387417426	0.560482531269	-0.0265179008205	0.190814485318	-0.0558032161796	-0.12993099116	0.184869187959	0.0521032106647	0.531333617949	23.7364662257	46.214965235	-5.0959033134
15	2.01247652066	-1.05999578632	-0.237592289012	3.12934319363	-0.243350379783	0.285201223657	0.41596588763	-0.103817312972	0.1217850527	0.221782667168	0.180706136927	-0.844916502494	0.398982224006	0.151995066038	-0.438572068105	0.369972889593	-0.011939476733	-0.143246159854	0.298177879848	-0.0480719085993	0.486534953014	23.5112666936	31.1740710104	4.29219493727
16	4.28367722264	2.38009124952	-2.51373755181	8.26450186799	1.03543878754	6.55359100365	0.344337681861	0.226630822938	0.469328300654	0.563052545126	-0.357902346225	-0.0876532427879	-0.787125931029	-0.111829415905	0.0113478519746	0.322272690866	-0.0306718956171	-0.146172742678	0.33931797337	0.11815356183	0.679889785564	28.4648095126	34.1963647649	-3.26124624346

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 3 through 63 )	A	B	3 - 63	2 - 54
2	2	chain 'A' and (resid 64 through 88 )	A	B	64 - 88	55 - 74
3	3	chain 'A' and (resid 89 through 125 )	A	B	89 - 125	75 - 106
4	4	chain 'A' and (resid 126 through 143 )	A	B	126 - 143	107 - 122
5	5	chain 'A' and (resid 144 through 191 )	A	B	144 - 191	123 - 165
6	6	chain 'A' and (resid 192 through 253 )	A	B	192 - 253	166 - 227
7	7	chain 'A' and (resid 254 through 309 )	A	B	254 - 309	228 - 283
8	8	chain 'B' and (resid 11 through 20 )	B000	C	11 - 20	1 - 10
9	9	chain 'B' and (resid 21 through 32 )	B000	C	21 - 32	11 - 22
10	10	chain 'B' and (resid 33 through 48 )	B000	C	33 - 48	23 - 38
11	11	chain 'B' and (resid 49 through 63 )	B000	C	49 - 63	39 - 53
12	12	chain 'B' and (resid 64 through 85 )	B000	C	64 - 85	54 - 75
13	13	chain 'B' and (resid 86 through 148 )	B000	C	86 - 148	76 - 138
14	14	chain 'B' and (resid 149 through 165 )	B000	C	149 - 165	139 - 155
15	15	chain 'B' and (resid 166 through 180 )	B000	C	166 - 180	156 - 170
16	16	chain 'B' and (resid 181 through 191 )	B000	C	181 - 191	171 - 181

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