PDB-5f21: human CD38 in complex with nanobody MU375

ID or keywords:

Entry

Database: PDB / ID: 5f21

Title

human CD38 in complex with nanobody MU375

Components

ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
nanobody MU375

Keywords

HYDROLASE/IMMUNE SYSTEM / CD38 / ADP-ribosyl cyclase / cyclic ADP-ribose / X-crystallography / Calcium signaling / nanobody / MU375 / 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 / Nicotinate metabolism / artery smooth muscle contraction / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ metabolic process / NAD+ nucleosidase activity, cyclic ADP-ribose generating / long-term synaptic depression / 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 / Resolution: 1.9 Å

Authors

Hao, Q. / Zhang, H.

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	Dec 1, 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
Revision 1.2	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	5f21_validation.pdf.gz	450.7 KB	Display	wwPDB validaton report
Full document	5f21_full_validation.pdf.gz	451.2 KB	Display
Data in XML	5f21_validation.xml.gz	17.6 KB	Display
Data in CIF	5f21_validation.cif.gz	25.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f2/5f21 ftp://data.pdbj.org/pub/pdb/validation_reports/f2/5f21	HTTPS FTP

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Related structure data

Related structure data	5f1kC 5f1oC 1yh3S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3p2d-1 3gd1-1 2fau-d 4k1p-2 1zot-d 11978 3hbu-d 3lh8-2 1wwh-d 4wat-d 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) #143 - Nov 2011 Toll-like Receptors similarity (1)

Deposited unit

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

B: nanobody MU375

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	45.149, 69.666, 123.476
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: Protein	nanobody MU375 Mass: 16597.363 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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.1 Å³/Da / Density % sol: 41.56 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS, 25%(w/v) PEG3350

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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: 1.9→50 Å / Num. obs: 31133 / % possible obs: 99.3 % / Redundancy: 6.1 % / R_merge(I) obs: 0.069 / Χ²: 0.912 / Net I/av σ(I): 22.198 / Net I/σ(I): 10.6 / Num. measured all: 191446

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	% possible all
1.9-1.97	6.1	0.614	3022	0.956	98.1
1.97-2.05	6.1	0.422	3050	0.94	99.1
2.05-2.14	6.1	0.298	3044	0.961	99.2
2.14-2.25	6.1	0.205	3097	0.97	99.5
2.25-2.39	6.1	0.159	3086	0.922	99.6
2.39-2.58	6.1	0.123	3104	0.964	99.9
2.58-2.84	6.2	0.103	3111	1.158	99.8
2.84-3.25	6.2	0.078	3136	1.175	99.9
3.25-4.09	6.3	0.043	3191	0.623	99.6
4.09-50	6.3	0.037	3292	0.504	98.3

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1YH3

1yh3

Resolution: 1.9→50 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.934 / WR_factor R_free: 0.2207 / WR_factor R_work: 0.1694 / FOM work R set: 0.8717 / SU B: 7.148 / SU ML: 0.093 / SU R Cruickshank DPI: 0.1196 / SU R_free: 0.1394 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.139 / 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	0.2107	1499	5.1 %	RANDOM
R_work	0.1625	-	-	-
obs	0.165	28138	94.53 %	-

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: 68.81 Å² / B_iso mean: 27.244 Å² / B_iso min: 12.06 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.26 Å²	0 Å²	0 Å²
2-	-	0.96 Å²	0 Å²
3-	-	-	-1.22 Å²

Refinement step

Cycle: final / Resolution: 1.9→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2855	0	16	273	3144
B_iso mean	-	-	27.98	37.59	-
Num. residues	-	-	-	-	362

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	2957
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	2750
X-RAY DIFFRACTION	r_angle_refined_deg	1.303	1.945	4012
X-RAY DIFFRACTION	r_angle_other_deg	0.906	3	6345
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.047	5	362
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.986	24.03	134
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.588	15	511
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.977	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	445
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	3309
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	681
X-RAY DIFFRACTION	r_mcbond_it	0.728	1.2	1448
X-RAY DIFFRACTION	r_mcbond_other	0.722	1.2	1447
X-RAY DIFFRACTION	r_mcangle_it	0.883	1.792	1804
X-RAY DIFFRACTION	r_rigid_bond_restr	0.944	3	5707
X-RAY DIFFRACTION	r_sphericity_free	24.384	5	90
X-RAY DIFFRACTION	r_sphericity_bonded	4.15	5	5823

LS refinement shell

Resolution: 1.903→1.952 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.193	66	-
R_work	0.155	1290	-
all	-	1356	-
obs	-	-	59.76 %

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	4.0635	-0.2366	1.3711	1.5948	-1.4554	3.7141	-0.0908	-0.2509	0.0911	0.154	0.1435	0.17	-0.1456	-0.132	-0.0527	0.0228	0.0143	0.0125	0.0703	0.0934	0.1895	41.925	-7.696	60.816
2	3.3714	-1.0688	2.4715	1.5642	-1.9019	4.8711	-0.0541	0.3177	-0.1125	-0.1013	0.0565	-0.0073	0.0166	-0.0502	-0.0024	0.0211	-0.0229	-0.0045	0.1015	0.0608	0.1584	47.609	-11.457	50.381
3	6.1446	-1.4728	0.206	4.1233	0.2768	5.7371	-0.0443	-0.0303	0.013	0.0626	0.2902	0.3646	0.0098	-0.3511	-0.246	0.0498	-0.0194	0.0038	0.0906	0.113	0.1821	48.792	9.975	48.155
4	2.8055	-0.2102	-0.1269	2.6123	-1.9921	2.0131	0.0062	-0.2744	0.0417	0.1467	0.0224	-0.0307	-0.1286	0.0699	-0.0286	0.0411	-0.0101	-0.0091	0.0722	0.0693	0.1744	51.705	-7.615	61.426
5	1.8077	-0.1429	-0.7679	3.4505	-0.4719	3.1743	0.0147	-0.2165	-0.0136	0.1684	0.0126	-0.2867	-0.0901	0.1907	-0.0273	0.0184	-0.0116	-0.003	0.071	0.04	0.106	62.87	11.718	50.104
6	1.8466	1.3756	0.2417	4.868	-3.6009	5.7013	-0.0006	-0.0399	0.2556	0.7466	0.5653	0.7919	-0.6444	-0.8202	-0.5647	0.1598	0.1101	0.1384	0.1316	0.0917	0.1771	45.166	27.279	48.288
7	2.1073	2.4979	-1.967	22.0359	-14.2467	14.4552	0.0357	-0.1199	-0.2918	-0.1172	-0.075	-0.3047	0.2453	0.35	0.0392	0.0184	0.0207	0.017	0.0729	0.0337	0.1383	62.158	33.13	30.889
8	2.6633	-1.9792	1.0642	24.1801	-2.7011	1.6208	-0.0603	0.0931	0.2806	-0.5961	0.0044	-0.5174	-0.233	0.0351	0.0559	0.106	0.0123	0.0325	0.0193	0.0202	0.0895	57.166	43.48	25.144
9	1.7803	1.2378	-1.5664	7.9645	-2.5819	3.3324	0.0202	-0.1992	0.0236	0.5105	0.0734	-0.123	-0.3434	0.1023	-0.0936	0.0878	0.0291	-0.0028	0.0832	0.0162	0.1098	56.037	33.159	39.299
10	3.0941	1.3523	-0.0035	4.5707	-2.3914	4.2491	0.0114	-0.0025	0.004	0.2203	0.2853	0.2003	-0.2479	-0.4517	-0.2967	0.0544	0.0645	0.0507	0.0854	0.0596	0.1456	49.112	37.057	34.278
11	1.5329	1.4901	-1.6707	5.6926	-4.5512	6.2483	-0.0096	-0.1752	0.2471	0.3793	0.2105	0.2369	-0.4967	-0.1799	-0.2009	0.0991	0.0375	-0.0018	0.0636	-0.022	0.0937	56.418	42.359	35.663
12	5.4407	1.1999	-4.8662	9.1302	-5.0424	6.6857	0.0027	-0.6859	-0.2672	0.3268	-0.8162	-0.9783	-0.2196	0.9653	0.8135	0.0503	-0.0577	-0.0523	0.1845	0.0993	0.1707	62.133	36.955	37.158

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	49 - 70
2	X-RAY DIFFRACTION	2	A	71 - 117
3	X-RAY DIFFRACTION	3	A	118 - 144
4	X-RAY DIFFRACTION	4	A	145 - 193
5	X-RAY DIFFRACTION	5	A	194 - 276
6	X-RAY DIFFRACTION	6	A	277 - 300
7	X-RAY DIFFRACTION	7	B	3 - 11
8	X-RAY DIFFRACTION	8	B	12 - 22
9	X-RAY DIFFRACTION	9	B	23 - 44
10	X-RAY DIFFRACTION	10	B	45 - 87
11	X-RAY DIFFRACTION	11	B	88 - 104
12	X-RAY DIFFRACTION	12	B	105 - 120

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