PDB-9erw: Mouse CNPase catalytic domain with nanobody 8C

ID or keywords:

Entry

Database: PDB / ID: 9erw

Title

Mouse CNPase catalytic domain with nanobody 8C

Components

2',3'-cyclic-nucleotide 3'-phosphodiesterase
Chains: E

Keywords

PROTEIN BINDING / CNPase / myelin / nanobody / single-domain antibody / complex

Function / homology

Function and homology information

cyclic nucleotide catabolic process / 2',3'-cyclic-nucleotide 3'-phosphodiesterase / 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity / myelin sheath adaxonal region / myelin sheath abaxonal region / cyclic nucleotide binding / regulation of mitochondrial membrane permeability / oligodendrocyte differentiation / pseudopodium / microvillus ...
Similarity search - Function

Biological species

Vicugna pacos (alpaca)

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.73 Å

Authors

Markusson, S. / Raasakka, A. / Opazo, F. / Kursula, P.

Funding support

1items

Citation

Journal: To Be Published
Title: Mouse CNPase catalytic domain with nanobody 8C
Authors: Markusson, S. / Raasakka, A. / Opazo, F. / Kursula, P.

History

Deposition	Mar 25, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 11, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9erw.cif.gz	247.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9erw.ent.gz	167.8 KB	Display	PDB format
PDBx/mmJSON format	9erw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9erw_validation.pdf.gz	429.3 KB	Display	wwPDB validaton report
Full document	9erw_full_validation.pdf.gz	431.2 KB	Display
Data in XML	9erw_validation.xml.gz	17.5 KB	Display
Data in CIF	9erw_validation.cif.gz	23.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/er/9erw ftp://data.pdbj.org/pub/pdb/validation_reports/er/9erw	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.5281/zenodo.10868769 / Data set type: diffraction image data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#136 - Apr 2011 Nanobodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

E: Chains: E

B: 2',3'-cyclic-nucleotide 3'-phosphodiesterase

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

1

Idetical with deposited unit
defined by author
Evidence: isothermal titration calorimetry

Unit cell

Length a, b, c (Å)	39.860, 54.170, 80.400
Angle α, β, γ (deg.)	90.000, 96.355, 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: Antibody	Chains: E Mass: 14013.450 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Anti-CNPase nanobody 8C / Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#2: Protein	2',3'-cyclic-nucleotide 3'-phosphodiesterase / CNP / CNPase Mass: 24236.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Mouse CNPase catalytic domain / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cnp, Cnp1 / Production host: Escherichia coli (E. coli) References: UniProt: P16330, 2',3'-cyclic-nucleotide 3'-phosphodiesterase
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H₂O
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: 2.26 Å³/Da / Density % sol: 45.46 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M MIB pH 8.0, 25% PEG1500

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 20, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.033 Å / Relative weight: 1
Reflection	Resolution: 1.73→50 Å / Num. obs: 35411 / % possible obs: 99.1 % / Redundancy: 5.6 % / B_iso Wilson estimate: 34.46 Å² / CC_1/2: 0.998 / R_rim(I) all: 0.08 / Net I/σ(I): 11.8
Reflection shell	Resolution: 1.73→1.77 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 2582 / CC_1/2: 0.359 / R_rim(I) all: 2.256 / % possible all: 98.7

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Processing

Software

Name	Version	Classification
PHENIX	1.21rc1_5127	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.73→44.84 Å / SU ML: 0.2871 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.6162
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2152	2000	5.65 %
R_work	0.1906	33389	-
obs	0.192	35389	99.08 %

Solvent computation

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

Displacement parameters

B_iso mean: 50.94 Å²

Refinement step

Cycle: LAST / Resolution: 1.73→44.84 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2590	0	0	156	2746

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0112	2660
X-RAY DIFFRACTION	f_angle_d	1.0499	3592
X-RAY DIFFRACTION	f_chiral_restr	0.0581	380
X-RAY DIFFRACTION	f_plane_restr	0.0087	460
X-RAY DIFFRACTION	f_dihedral_angle_d	16.8671	969

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 (%)
1.73-1.77	0.4395	140	0.3965	2338	X-RAY DIFFRACTION	98.69
1.77-1.82	0.387	144	0.3331	2407	X-RAY DIFFRACTION	99.69
1.82-1.87	0.3156	144	0.2889	2390	X-RAY DIFFRACTION	99.8
1.87-1.94	0.3004	140	0.2429	2357	X-RAY DIFFRACTION	99.76
1.94-2	0.263	145	0.2187	2407	X-RAY DIFFRACTION	99.84
2-2.08	0.2578	142	0.2165	2375	X-RAY DIFFRACTION	99.33
2.08-2.18	0.2747	138	0.2237	2321	X-RAY DIFFRACTION	96.36
2.18-2.29	0.2363	144	0.1893	2385	X-RAY DIFFRACTION	99.61
2.29-2.44	0.2434	143	0.2	2375	X-RAY DIFFRACTION	99.72
2.44-2.63	0.2227	144	0.1971	2410	X-RAY DIFFRACTION	99.65
2.63-2.89	0.2557	142	0.2189	2385	X-RAY DIFFRACTION	99.18
2.89-3.31	0.2444	142	0.2024	2374	X-RAY DIFFRACTION	97.67
3.31-4.17	0.1819	146	0.1686	2412	X-RAY DIFFRACTION	99.49
4.17-44.84	0.1604	146	0.1548	2453	X-RAY DIFFRACTION	98.45

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	8.60136653129	-1.76732495502	-2.23982219406	6.54588727657	1.38614203932	4.42509934349	-0.141080315399	-0.802322988871	-1.37306230034	0.276632335335	0.218271747531	1.10441822066	1.85739177975	-1.1597546559	-0.00495482022147	0.515834753088	-0.0284147081004	0.120453746223	0.440638408825	0.16814751427	0.811325656787	2.64809186223	24.2492924029	45.5795755551
2	5.27111451753	0.32803195343	-2.01639477329	5.57681670765	-2.12369005845	2.00800099333	-0.275185783206	0.644813882078	-0.13124483225	-0.697915997926	-0.228097847957	-0.00515859912066	-0.587205882384	-0.212184555966	0.613201697659	0.438276693383	-0.0929281588632	-0.0883469440277	0.275892939564	-0.000637768774582	0.373793634614	11.8221566234	28.1554032946	25.406079776
3	6.6214578123	1.84705562256	-4.54331253309	4.93063487452	-2.8477914621	3.7062879299	0.140485137969	0.00760741986762	0.257359762219	-0.372051766458	-0.0683028884294	0.303732905145	-0.0118673639582	-0.215800737952	0.051309737933	0.439552637017	-0.0249526438944	-0.0240102741049	0.288628262558	-0.0432783231071	0.376996828165	8.38454360504	32.514583175	29.9785474257
4	3.8328638512	0.268597321877	1.16322330311	9.33403186585	0.0806741402751	4.9217207366	-0.408783300514	-0.0862271443734	0.544499451817	-0.281833610891	0.0720179708909	-0.624143467619	-0.635749965052	0.495318268279	0.283025685026	0.318584415651	-0.00455336730881	-0.0851832055459	0.233577072195	0.00904157346886	0.257243242481	25.8728624649	50.9156160754	58.1059372844
5	0.481822114698	0.503667506684	-1.11725147599	0.672718860387	-1.06766336225	3.13869244205	-0.185414960614	-1.2251696625	-0.174583184208	0.266599515814	0.340446153353	0.238960886871	-0.739594363316	-1.80496062603	-0.126982742778	0.377131273203	0.0762895718443	0.0610553609088	0.96647646285	0.0604982124641	0.361832086292	10.6117957702	36.4743034585	71.828577686
6	0.0206079591456	0.0938019501499	-0.0329305712764	0.853256753379	-0.859153040782	1.42108092916	-0.353042937098	-0.967405501181	-0.314922863767	0.456431849411	-0.0724965461784	0.020462388373	0.649785880844	0.431272959772	-0.12336663944	0.804542063469	0.418503862706	0.164110365403	2.20171301374	0.29931020118	-0.0229389484354	14.8104142333	35.741021421	89.0983129167
7	0.0718049362935	0.115134677324	-0.429971536436	1.88505519134	-3.33538051538	6.90009892207	0.0916878712346	-1.187637112	0.085212522213	0.759792203935	0.0969689655273	0.0398499583783	-1.08060575936	-0.697980946486	-0.290189319779	0.492343786276	0.141054954267	-0.0283450465108	0.596090366617	-0.0285387284534	0.307423220107	20.4905065069	47.1012171731	68.2364303702
8	2.23192556124	0.378810532234	0.15021321377	3.47437523586	-0.584787199918	4.45341777847	-0.199501436906	-0.528513146972	0.0480510292181	0.0745465036594	-0.121276974803	-0.458840478341	-0.302308000889	0.407661850902	0.298199088677	0.183089599921	0.0627147790696	-0.0537912124549	0.387138664112	0.0343510261196	0.336925601666	27.7054171622	43.4685550005	61.7968943802
9	2.4353433169	1.30541974894	-2.28752580443	3.42923357983	-3.58651923316	4.18682271404	-0.233869603174	0.055387955451	-0.89055181399	-0.107444318503	-0.148514362618	-0.857961445153	0.878834099509	0.7702340822	0.27003688029	0.333720346342	0.0747267999198	0.0191065957525	0.385562074424	0.0553423241149	0.42879143928	32.0285900863	36.249275773	59.3151089184
10	1.66770187192	3.07557016976	-0.324344359429	6.71104224448	-1.32262671975	1.10053513468	0.3199667752	-0.561048570633	0.603613785819	0.550547188088	-0.0194295349995	0.033798300751	-0.721191691501	0.812782996624	-0.25510511165	0.675465941043	0.239119267801	0.161584417792	1.32503671366	0.132108800252	0.645464301042	39.6150414943	37.9379692809	73.1404815978
11	2.90950516283	1.77012701241	1.59229505955	2.21028163088	-0.918833482447	3.92046572828	-0.195403660986	-1.28241217119	0.279843697875	0.23109043762	-0.084011484131	-0.422212521765	-0.424008606462	0.450796062439	0.368855567547	0.430100164045	0.113861996228	-0.0643339534135	0.840947127615	0.0360886831588	0.332457303998	27.5305568972	40.2963779827	75.4966584515
12	4.50844959573	-1.77704512013	6.1464302297	3.11696155794	-0.485954641672	2.01490891226	-0.226115614493	0.433984993565	0.376305976239	0.185850359293	-0.179042197388	0.139205974129	0.604663492383	-0.393648424995	0.454850730767	0.660249987121	0.0308847377523	0.0796139568322	1.48925704003	0.37463889213	0.7497756038	21.0541199955	23.1728308092	81.0327892646
13	1.32018352862	-0.145066334182	0.616328357278	1.39525978521	-2.79738080603	5.83982086616	-0.104923101171	-1.05416179807	-0.284376363173	0.207585418552	0.0854948380753	-0.111413048218	0.208840616332	-0.214560605644	0.0676705743776	0.373593791738	0.0662016815911	0.0253798656441	0.720760146612	0.187847827828	0.378678648491	21.2821756644	34.3061220071	70.9053769837
14	5.44043532589	0.463954874134	-0.45258713143	4.52326922685	0.860187196723	5.36075529021	-0.0199115020225	-0.301451648687	-0.0806855995325	0.42930937733	-0.210226946115	0.677358650421	0.0101335544378	-0.729807550883	0.26374385778	0.30283732853	0.0165021885354	0.0173575808197	0.254797162761	-0.047812879325	0.308929719922	7.03173057509	32.2674095369	45.0132361993
15	4.41060771666	-3.29798009338	-2.90963182741	9.09788233188	3.62842956261	4.7717310418	-0.126931550909	-0.270237829676	-0.0451664545215	-0.116179922133	0.265828554848	0.201921433348	-0.0744553847786	0.191543033605	-0.123412939391	0.340635904102	-0.00885031201905	-0.0287612879595	0.222617033407	0.00927114802131	0.358343681858	15.2573294769	35.1242384044	41.8812639982
16	4.36909176195	-1.18735883342	0.416857725881	4.92083360152	0.431421306746	5.76755261646	-0.00588333831726	0.0677909734382	0.654461595146	-0.735468694087	0.0902428965986	-0.245128979928	-0.731030565218	0.112120519714	-0.0407107409179	0.397411496443	-0.0288645118192	0.00298511942277	0.155354404117	0.0253289935743	0.37505793762	14.8178321149	40.5177959113	35.7185193084
17	4.27807914324	-0.439787055096	-5.31953709596	7.11793927428	0.459274623063	6.60346418661	0.147457573288	0.210767764148	0.197852646114	-0.00446983312678	-0.199906349132	0.710792296606	-0.738006144865	-0.773364674938	0.0633404643938	0.32872614676	-0.0118669554154	-0.0812015974305	0.437752023653	-0.0125075052747	0.415395836719	3.28722339953	35.9770087381	37.1941494666
18	3.09563823305	0.058230819053	1.72151330308	4.81038297694	-4.30751353676	5.0018183435	-0.110448427456	0.546242084737	0.990591729466	0.219569178773	-0.462383923903	-1.48309259625	-0.808271177846	0.575824380512	0.528036298032	0.475890517714	-0.0777954689477	0.0477054615811	0.342015445481	0.0543058428131	0.404136025515	19.4590047998	34.5673242202	25.81693709
19	1.28804458819	-0.249076521196	-0.898017414373	1.82300980265	2.94755745974	7.34574310228	-0.0463099119592	-0.020731607274	-0.173674851444	0.0737871696147	0.0372270475044	-0.0101011369061	0.367566477417	0.0748896538033	0.000859332984009	0.32406519778	0.021484128116	-0.00149460365006	0.178558791128	0.0162443748826	0.327292434463	14.7516686824	30.2206620877	43.6817989604

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 'E' and (resid 1 through 5 )	E	A	1 - 5	1 - 5
2	2	chain 'E' and (resid 6 through 15 )	E	A	6 - 15	6 - 15
3	3	chain 'E' and (resid 16 through 22 )	E	A	16 - 22	16 - 22
4	4	chain 'B' and (resid 161 through 174 )	B	C	161 - 174	1 - 14
5	5	chain 'B' and (resid 175 through 193 )	B	C	175 - 193	15 - 33
6	6	chain 'B' and (resid 194 through 220 )	B	C	194 - 220	34 - 52
7	7	chain 'B' and (resid 221 through 236 )	B	C	221 - 236	53 - 68
8	8	chain 'B' and (resid 237 through 279 )	B	C	237 - 279	69 - 111
9	9	chain 'B' and (resid 280 through 291 )	B	C	280 - 291	112 - 123
10	10	chain 'B' and (resid 295 through 303 )	B	C	295 - 303	124 - 132
11	11	chain 'B' and (resid 304 through 336 )	B	C	304 - 336	133 - 165
12	12	chain 'B' and (resid 337 through 348 )	B	C	337 - 348	166 - 177
13	13	chain 'B' and (resid 349 through 378 )	B	C	349 - 378	178 - 207
14	14	chain 'E' and (resid 23 through 39 )	E	A	23 - 39	23 - 39
15	15	chain 'E' and (resid 40 through 57 )	E	A	40 - 57	40 - 57
16	16	chain 'E' and (resid 58 through 73 )	E	A	58 - 73	58 - 73
17	17	chain 'E' and (resid 74 through 83 )	E	A	74 - 83	74 - 83
18	18	chain 'E' and (resid 84 through 91 )	E	A	84 - 91	84 - 91
19	19	chain 'E' and (resid 92 through 127 )	E	A	92 - 127	92 - 127

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