PDB-5f1o: human CD38 in complex with nanobody MU551

ID or keywords:

Entry

Database: PDB / ID: 5f1o

Title

human CD38 in complex with nanobody MU551

Components

ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
nanobody MU551

Keywords

HYDROLASE/IMMUNE SYSTEM / CD38 / ADP-ribosyl cyclase / cyclic ADP-ribose / X-crystallography / Calcium signaling / nanobody / MU551 / HYDROLASE-IMMUNE SYSTEM complex

Function / homology

Function and homology information

2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / artery smooth muscle contraction / Nicotinate metabolism / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD metabolic process / NAD+ nucleotidase, cyclic ADP-ribose generating / negative regulation of bone resorption / response to hydroperoxide ...
Similarity search - Function

Biological species

Homo sapiens (human)

Lama glama (llama)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.2 Å

Authors

Zhang, H. / Hao, Q.

Citation

Journal: Sci Rep / Year: 2016
Title: Immuno-targeting the multifunctional CD38 using nanobody
Authors: Li, T. / Qi, S. / Unger, M. / Hou, Y.N. / Deng, Q.W. / Liu, J. / Lam, C.M. / Wang, X.W. / Xin, D. / Zhang, P. / Koch-Nolte, F. / Hao, Q. / Zhang, H. / Lee, H.C. / Zhao, Y.J.

History

Deposition	Nov 30, 2015	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jun 15, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5f1o.cif.gz	174.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5f1o.ent.gz	137.9 KB	Display	PDB format
PDBx/mmJSON format	5f1o.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5f1o_validation.pdf.gz	431 KB	Display	wwPDB validaton report
Full document	5f1o_full_validation.pdf.gz	431.7 KB	Display
Data in XML	5f1o_validation.xml.gz	16.9 KB	Display
Data in CIF	5f1o_validation.cif.gz	24 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f1/5f1o ftp://data.pdbj.org/pub/pdb/validation_reports/f1/5f1o	HTTPS FTP

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Related structure data

Related structure data	5f1kC 5f21C 1yh3S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4ben-3 5nvz-1 4b4x-4 5nw2-3 4b4x-3 5lli-2 4ajy-d 5nvy-4 5nw0-1 4w9l-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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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) #143 - Nov 2011 Toll-like Receptors similarity (1)

Deposited unit

A: ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1

B: nanobody MU551

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	33.141, 96.190, 143.254
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 / CD38 Mass: 29536.451 Da / Num. of mol.: 1 / Fragment: ectodomain, UNP residues 46-300 / Mutation: Q49T, N100D, N164D, N219D, N209D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD38 / Plasmid: pPICZalpha / Production host: Komagataella pastoris (fungus) / Strain (production host): X33 References: UniProt: P28907, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
#2: Antibody	nanobody MU551 Mass: 18043.748 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Plasmid: pHEN2 / Production host: Escherichia coli (E. coli)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.4 Å³/Da / Density % sol: 48.79 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.2M sodium acetate, 0.1M Tris-HCl, 25% PEG4000

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL17U / Wavelength: 0.97852 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2012

Radiation

Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97852 Å / Relative weight: 1

Reflection

Resolution: 2.2→50 Å / Num. obs: 24162 / % possible obs: 99.2 % / Redundancy: 7.6 % / R_merge(I) obs: 0.074 / Χ²: 0.956 / Net I/av σ(I): 22.596 / Net I/σ(I): 13.4 / Num. measured all: 182459

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	% possible all
2.2-2.28	7.6	0.461	2353	1.006	100
2.28-2.37	7.6	0.317	2422	0.949	100
2.37-2.48	7.7	0.239	2360	0.947	100
2.48-2.61	7.6	0.165	2400	0.888	100
2.61-2.77	7.7	0.118	2417	0.836	100
2.77-2.99	7.8	0.089	2400	0.817	100
2.99-3.29	7.7	0.085	2420	1.121	99.9
3.29-3.76	7.6	0.081	2437	1.424	99.5
3.76-4.74	7.1	0.058	2404	0.945	96.7
4.74-50	7.2	0.045	2549	0.623	96.6

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
REFMAC	5.8.0135	refinement
PDB_EXTRACT	3.15	data extraction
Blu-Ice		data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1YH3

1yh3

Resolution: 2.2→50 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.916 / WR_factor R_free: 0.2598 / WR_factor R_work: 0.1829 / FOM work R set: 0.8428 / SU B: 11.517 / SU ML: 0.131 / SU R_free: 0.2021 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2366	1200	5.1 %	RANDOM
R_work	0.1679	-	-	-
obs	0.1713	22212	96.35 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 91.72 Å² / B_iso mean: 34.51 Å² / B_iso min: 14.55 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.06 Å²	0 Å²	0 Å²
2-	-	0.94 Å²	0 Å²
3-	-	-	-0.99 Å²

Refinement step

Cycle: final / Resolution: 2.2→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2958	0	0	207	3165
B_iso mean	-	-	-	40.09	-
Num. residues	-	-	-	-	369

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	3035
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	2769
X-RAY DIFFRACTION	r_angle_refined_deg	1.305	1.934	4112
X-RAY DIFFRACTION	r_angle_other_deg	0.918	3	6382
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.191	5	365
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.336	23.893	149
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.67	15	513
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.052	15	21
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	436
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	3435
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	730
X-RAY DIFFRACTION	r_mcbond_it	1.071	1.71	1472
X-RAY DIFFRACTION	r_mcbond_other	1.071	1.71	1471
X-RAY DIFFRACTION	r_mcangle_it	1.374	2.555	1833
X-RAY DIFFRACTION	r_rigid_bond_restr	0.951	3	5804
X-RAY DIFFRACTION	r_sphericity_free	28.62	5	71
X-RAY DIFFRACTION	r_sphericity_bonded	4.49	5	5863

LS refinement shell

Resolution: 2.196→2.253 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.247	77	-
R_work	0.166	1257	-
all	-	1334	-
obs	-	-	77.02 %

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	4.547	-3.4546	-2.5425	4.8249	2.3747	3.7586	-0.2082	0.0536	-0.3839	0.1035	-0.0807	0.4398	0.3755	-0.217	0.2889	0.1411	-0.0724	0.0283	0.0456	-0.0428	0.1952	16.571	0.709	140.26
2	15.6626	-7.2312	-15.0367	9.889	13.0357	20.1111	-0.7651	-0.1041	-0.4645	0.5954	0.7248	-0.2278	1.002	0.744	0.0403	0.3655	0.1355	0.0231	0.1166	-0.0158	0.0877	28.382	-3.685	143.128
3	4.2895	-2.6294	-1.0833	4.5966	1.858	2.2978	-0.1661	-0.056	0.1297	0.1547	0.1851	-0.3294	0.1144	0.1964	-0.019	0.0661	0.0011	-0.0118	0.0616	-0.0147	0.1594	24.59	10.212	146.734
4	4.1972	-1.08	-0.0545	5.0072	0.882	3.3279	0.0304	0.0644	-0.0137	-0.2091	-0.0255	0.2206	0.1714	-0.1319	-0.0048	0.1311	-0.0337	0.0339	0.0833	-0.0078	0.1049	24.086	7.598	122.546
5	1.3887	-1.0756	-1.3204	1.9012	1.7068	5.3178	-0.0207	0.1339	-0.0532	-0.1573	-0.0291	-0.0324	0.1592	-0.0269	0.0499	0.1148	-0.035	0.0179	0.0407	-0.0198	0.1663	22.486	4.484	132.56
6	2.2559	-1.0899	-0.6498	9.6423	-0.1619	3.6771	-0.147	0.0021	-0.1662	0.1301	-0.2632	0.4209	0.213	-0.5461	0.4102	0.0193	-0.0297	0.0233	0.0984	-0.0742	0.1958	9.6	14.457	147.858
7	5.5843	-1.1807	-3.7331	1.4141	1.0634	5.6199	0.02	-0.1794	0.3285	-0.0532	0.1005	-0.1711	-0.0236	0.1807	-0.1206	0.0677	-0.0145	0.0011	0.0733	-0.0182	0.2042	23.307	15.152	138.822
8	6.3301	-0.3952	2.4746	1.7194	-0.5138	3.6684	0.1417	-0.4272	0.3473	-0.015	-0.0061	0.0854	-0.2883	-0.3078	-0.1357	0.0941	-0.0396	0.0769	0.1096	-0.026	0.1161	24.34	18.775	123.153
9	18.7131	-8.447	-7.8237	5.2064	3.9223	9.0795	-0.3957	-0.3354	0.0749	0.1578	0.3958	-0.5444	0.2462	0.3315	-0.0001	0.0646	-0.0561	-0.0054	0.1207	-0.0711	0.1964	36.012	19.418	127.828
10	3.7382	0.3968	1.7848	1.7965	0.5111	4.3977	0.0026	0.1489	0.0997	-0.2782	0.0426	0.0296	-0.4504	0.032	-0.0452	0.1488	-0.0429	0.0749	0.0711	-0.0186	0.1032	27.83	22.083	115.49
11	1.4272	-5.6867	1.6467	23.192	-6.9865	6.8898	0.1285	0.1583	-0.1013	-0.6687	-0.2372	0.3012	1.0833	-0.0086	0.1088	0.3429	-0.0549	0.0045	0.3167	-0.0909	0.0436	22.801	4.342	108.549
12	19.1939	-16.9435	3.7176	22.6558	-2.8369	3.7733	0.2212	0.4675	0.163	-0.387	-0.3139	0.1805	-0.118	0.1229	0.0926	0.2289	-0.0557	0.0772	0.1701	-0.0815	0.0815	36.226	-21.955	111.791
13	1.8012	-1.6231	-0.6498	4.1999	1.0396	2.1665	-0.1098	-0.0021	-0.1433	0.3315	0.0108	0.1078	0.3933	0.0919	0.099	0.2242	-0.0243	0.0635	0.0356	-0.0448	0.0866	34.613	-21.723	122.054
14	1.5766	-2.9439	-1.3204	6.6178	2.5935	1.6043	-0.1781	0.0985	-0.2593	0.6459	-0.103	0.409	0.3816	-0.0788	0.2811	0.267	-0.0344	0.095	0.0373	-0.064	0.1839	29.107	-20.753	121.701
15	48.1826	19.3731	-7.042	14.7575	6.6874	14.0395	-1.8661	0.7367	-0.0871	-0.9272	-0.1348	1.4085	-0.0086	-0.6738	2.0009	0.3887	-0.1405	-0.0243	0.1109	-0.0333	0.4501	20.825	-18.091	127.845
16	9.3495	-4.3596	-1.317	6.3936	3.3439	3.9291	0.0732	0.0994	-0.4979	0.1732	-0.16	0.5885	0.2609	-0.1294	0.0867	0.3043	-0.0732	0.0842	0.0918	-0.0499	0.1717	32.283	-27.213	114.787

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	49 - 75
2	X-RAY DIFFRACTION	2	A	76 - 86
3	X-RAY DIFFRACTION	3	A	87 - 117
4	X-RAY DIFFRACTION	4	A	118 - 138
5	X-RAY DIFFRACTION	5	A	139 - 161
6	X-RAY DIFFRACTION	6	A	162 - 179
7	X-RAY DIFFRACTION	7	A	180 - 197
8	X-RAY DIFFRACTION	8	A	198 - 225
9	X-RAY DIFFRACTION	9	A	226 - 236
10	X-RAY DIFFRACTION	10	A	237 - 276
11	X-RAY DIFFRACTION	11	A	277 - 296
12	X-RAY DIFFRACTION	12	B	1 - 12
13	X-RAY DIFFRACTION	13	B	13 - 86
14	X-RAY DIFFRACTION	14	B	87 - 106
15	X-RAY DIFFRACTION	15	B	107 - 113
16	X-RAY DIFFRACTION	16	B	114 - 128

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