PDB-9goy: Crystal structure of Fab E2-RecA in complex with CD38

ID or keywords:

Entry

Database: PDB / ID: 9goy

Title

Crystal structure of Fab E2-RecA in complex with CD38

Components

ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Fab E2-RecA heavy chain
Fab E2-RecA light chain

Keywords

IMMUNE SYSTEM / Fab / Biparatopic bispecific antibody / antibody / Innate cell modulator / CD38

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)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Dreyfus, C. / Fritz, G.

Funding support

Switzerland, 1items

Citation

Journal: Mabs / Year: 2025
Title: Biparatopic binding of ISB 1442 to CD38 in trans enables increased cell antibody density and increased avidity.
Authors: Loyau, J. / Monney, T. / Montefiori, M. / Bokhovchuk, F. / Streuli, J. / Blackburn, M. / Goepfert, A. / Caro, L.N. / Chakraborti, S. / De Angelis, S. / Grandclement, C. / Blein, S. / Mbow, M. ...

History

Deposition	Sep 6, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 12, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9goy.cif.gz	285 KB	Display	PDBx/mmCIF format
PDB format	pdb9goy.ent.gz	230.4 KB	Display	PDB format
PDBx/mmJSON format	9goy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9goy_validation.pdf.gz	442 KB	Display	wwPDB validaton report
Full document	9goy_full_validation.pdf.gz	444.4 KB	Display
Data in XML	9goy_validation.xml.gz	28.5 KB	Display
Data in CIF	9goy_validation.cif.gz	37.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/go/9goy ftp://data.pdbj.org/pub/pdb/validation_reports/go/9goy	HTTPS FTP

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Related structure data

Related structure data	9goxC C: citing same article (ref.)
Similar structure data	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	#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

H: Fab E2-RecA heavy chain

L: Fab E2-RecA light chain

hetero molecules

78.4 kDa, 3 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)	131.290, 61.070, 124.120
Angle α, β, γ (deg.)	90.00, 108.60, 90.00
Int Tables number	5
Space group name H-M	C121

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Protein , 1 types, 1 molecules A

#1: Protein	ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 / 2'-phospho-ADP-ribosyl cyclase / 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose ...2'-phospho-ADP-ribosyl cyclase / 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / 2'-phospho-cyclic-ADP-ribose transferase / ADP-ribosyl cyclase 1 / ADPRC 1 / Cyclic ADP-ribose hydrolase 1 / cADPR hydrolase 1 / T10 Mass: 30781.818 Da / Num. of mol.: 1 / Mutation: N100D, N164A, N209D and N219D Source method: isolated from a genetically manipulated source Details: Extracellular domain of Uniprot entry P28907, containing the following mutations on the four N-linked glycosylation sites (N100D, N164A, N209D and N219D) and fused to a C-terminal 8-histidine peptide tag Source: (gene. exp.) Homo sapiens (human) / Gene: CD38 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) References: UniProt: P28907, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase, 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase

#1: Protein

ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 / 2'-phospho-ADP-ribosyl cyclase / 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose ...

Mass: 30781.818 Da / Num. of mol.: 1 / Mutation: N100D, N164A, N209D and N219D
Source method: isolated from a genetically manipulated source
Details: Extracellular domain of Uniprot entry P28907, containing the following mutations on the four N-linked glycosylation sites (N100D, N164A, N209D and N219D) and fused to a C-terminal 8-histidine peptide tag
Source: (gene. exp.)

Homo sapiens (human) / Gene: CD38 / Cell line (production host): Expi293F / Production host:

Homo sapiens (human)
References: UniProt: P28907, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase, 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase

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Antibody , 2 types, 2 molecules HL

#2: Antibody	Fab E2-RecA heavy chain Mass: 24100.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: Expi293F / Production host: Homo sapiens (human)
#3: Antibody	Fab E2-RecA light chain Mass: 23414.951 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 85 molecules

#4: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
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: 3.01 Å³/Da / Density % sol: 59.16 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 70% v/v MPD, 0.1M HEPES, pH 7.5

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Data collection

Diffraction	Mean temperature: 80 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9998 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 18, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9998 Å / Relative weight: 1
Reflection	Resolution: 2.7→47.22 Å / Num. obs: 24595 / % possible obs: 99.85 % / Redundancy: 7 % / CC_1/2: 0.99 / R_rim(I) all: 0.307 / Net I/σ(I): 6.62
Reflection shell	Resolution: 2.7→2.8 Å / Mean I/σ(I) obs: 0.72 / Num. unique obs: 1821 / CC_1/2: 0.44 / R_rim(I) all: 3.32 / R_sym value: 2.88 / % possible all: 99.64

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
XSCALE		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.7→47.22 Å / Cor.coef. F_o:F_c: 0.938 / Cor.coef. F_o:F_c free: 0.919 / SU B: 47.062 / SU ML: 0.41 / Cross valid method: THROUGHOUT / ESU R: 0.909 / ESU R Free: 0.36 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27926	1295	5 %	RANDOM
R_work	0.24304	-	-	-
obs	0.24481	24595	99.85 %	-

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 mean: 82.112 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.71 Å²	0 Å²	4.22 Å²
2-	-	-3.97 Å²	-0 Å²
3-	-	-	-0.48 Å²

Refinement step

Cycle: 1 / Resolution: 2.7→47.22 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5309	0	4	81	5394

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.002	0.012	5465
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	4932
X-RAY DIFFRACTION	r_angle_refined_deg	0.61	1.647	7432
X-RAY DIFFRACTION	r_angle_other_deg	0.247	1.563	11495
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.326	5	687
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	1.761	5	29
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.545	10	909
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.03	0.2	823
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	6279
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1165
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.821	6.217	2734
X-RAY DIFFRACTION	r_mcbond_other	0.821	6.217	2733
X-RAY DIFFRACTION	r_mcangle_it	1.439	9.324	3416
X-RAY DIFFRACTION	r_mcangle_other	1.438	9.324	3417
X-RAY DIFFRACTION	r_scbond_it	0.669	6.279	2731
X-RAY DIFFRACTION	r_scbond_other	0.669	6.279	2732
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.194	9.383	4013
X-RAY DIFFRACTION	r_long_range_B_refined	2.729	75.583	5939
X-RAY DIFFRACTION	r_long_range_B_other	2.682	75.18	5936
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.7→2.77 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.495	96	-
R_work	0.526	1821	-
obs	-	-	99.64 %

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	7.8596	1.1299	-2.8553	0.4934	-0.1861	1.6357	-0.0612	0.1552	-0.36	-0.2053	-0.0345	0.1007	-0.1135	-0.1437	0.0957	0.1717	0.0048	-0.0411	0.1874	0.0044	0.182	-7.0984	-19.4714	42.6023
2	4.475	0.2399	-2.1966	0.4927	-0.0433	2.5526	-0.1807	-0.1867	-0.0507	0.0654	-0.0745	0.1086	0.1671	0.1787	0.2551	0.2327	0.0675	0.1186	0.2243	0.0479	0.2254	-0.0614	-23.4726	52.1341
3	5.0231	-0.2412	-1.4431	2.8385	-0.8292	7.1004	-0.1044	0.4386	0.055	-0.2527	-0.0682	0.1554	-0.7574	0.5054	0.1726	0.277	-0.0826	-0.0166	0.2174	0.0075	0.3099	6.5181	-1.9326	47.4105
4	6.4213	0.775	-0.7902	2.6352	0.3807	3.8167	-0.0128	-0.1037	-0.0841	-0.0285	-0.0551	0.1887	0.1959	-0.0774	0.068	0.092	0.0197	0.0544	0.1331	0.0223	0.0551	-8.9402	-16.6137	50.5437
5	3.2467	0.7924	-0.0866	2.2837	0.543	4.3114	0.0054	0.064	0.5812	-0.2664	-0.0028	0.1936	-0.5873	-0.0627	-0.0027	0.3531	0.0035	0.0488	0.3691	-0.0331	0.4148	2.1803	5.7506	55.5829
6	2.776	1.1399	-1.5873	4.2353	-0.027	3.0928	0.0316	-0.0052	-0.1633	0.1398	0.2814	0.2871	0.1319	-0.3343	-0.313	0.1244	-0.0457	0.073	0.1531	0.037	0.2702	9.8774	-26.4165	18.3245
7	4.8118	-2.3852	-1.1754	1.2016	0.7929	7.0482	0.2139	0.0925	0.1976	-0.1197	-0.0418	-0.0576	-0.0526	-0.2445	-0.1721	0.1357	-0.0142	0.0204	0.0383	0.0459	0.191	11.4113	-19.8018	26.3385
8	3.279	1.0637	-0.2426	6.5661	-0.8276	3.2303	0.119	-0.2741	0.2516	0.1915	-0.0793	-0.3105	-0.242	-0.1912	-0.0398	0.1289	0.0921	0.0824	0.229	-0.0369	0.2419	7.2026	-17.2948	19.7876
9	0.8303	-0.3312	-1.0319	1.0732	0.5719	2.4642	-0.0646	0.0058	0.0567	-0.1965	0.0709	-0.0411	0.1117	-0.1794	-0.0063	0.1818	-0.0128	0.1518	0.1013	0.0144	0.1901	22.9866	-27.67	6.8156
10	1.6446	-3.2861	-0.6948	6.6255	1.5306	0.7051	0.2782	0.0744	-0.1765	-0.5703	-0.1842	0.2658	-0.0741	-0.1944	-0.094	0.2789	-0.0183	0.0884	0.1252	0.0197	0.1868	25.5573	-34.3004	-5.3518
11	1.3824	1.8372	0.1965	3.1386	1.6571	2.9085	0.0476	-0.1114	-0.2079	-0.0223	0.2778	-0.4756	-0.0756	0.731	-0.3254	0.143	-0.0164	0.1582	0.3912	-0.07	0.3172	36.7324	-18.9034	28.2415
12	4.0449	-0.8805	-0.7592	1.8891	-0.0686	3.5807	-0.0846	-0.2636	-0.1119	0.1567	0.1429	-0.4248	0.1766	0.2528	-0.0583	0.159	0.0266	0.0714	0.0361	-0.0217	0.2216	29.9339	-25.0829	29.1245
13	3.6242	-0.8624	4.5237	1.6766	-0.3255	8.6307	0.2785	0.1617	0.0222	-0.1879	-0.0747	0.0056	0.426	0.1261	-0.2038	0.091	-0.0034	0.0484	0.0287	0.0081	0.1207	39.0417	-29.1662	-4.8082
14	3.4991	1.5884	4.4983	1.7377	0.4795	8.2781	-0.1813	-0.0526	0.0058	-0.1162	-0.0267	-0.1865	-0.2282	-0.0082	0.2079	0.1066	0.0402	0.0728	0.0919	-0.0332	0.1281	40.6526	-23.8992	-3.2478
15	1.9389	0.2997	0.5319	2.2171	-1.1877	5.8743	-0.1184	0.2152	0.1303	-0.2402	0.0712	-0.1112	-0.2493	0.3332	0.0471	0.2353	-0.014	0.1559	0.0922	-0.021	0.1846	41.215	-23.0788	-9.2735

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	2	A	46 - 72
2	X-RAY DIFFRACTION	3	A	73 - 100
3	X-RAY DIFFRACTION	4	A	101 - 150
4	X-RAY DIFFRACTION	5	A	151 - 246
5	X-RAY DIFFRACTION	6	H	1 - 38
6	X-RAY DIFFRACTION	7	H	39 - 61
7	X-RAY DIFFRACTION	8	H	62 - 89
8	X-RAY DIFFRACTION	9	H	90 - 181
9	X-RAY DIFFRACTION	10	H	182 - 214
10	X-RAY DIFFRACTION	11	L	1 - 26
11	X-RAY DIFFRACTION	12	L	27 - 105
12	X-RAY DIFFRACTION	13	L	106 - 126
13	X-RAY DIFFRACTION	14	L	127 - 147
14	X-RAY DIFFRACTION	15	L	148 - 212

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