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- PDB-9gox: Crystal structure of Fab B6-D9 in complex with CD38 -

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Basic information

Entry
Database: PDB / ID: 9gox
TitleCrystal structure of Fab B6-D9 in complex with CD38
Components
  • ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
  • Fab B6-D9 heavy chain
  • Fab B6-D9 light chain
KeywordsIMMUNE 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 ...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 / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / B cell proliferation / response to retinoic acid / positive regulation of vasoconstriction / positive regulation of B cell proliferation / response to interleukin-1 / response to progesterone / female pregnancy / B cell receptor signaling pathway / apoptotic signaling pathway / positive regulation of insulin secretion / response to estradiol / transferase activity / negative regulation of neuron projection development / positive regulation of cytosolic calcium ion concentration / positive regulation of cell growth / basolateral plasma membrane / nuclear membrane / response to hypoxia / response to xenobiotic stimulus / negative regulation of DNA-templated transcription / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular exosome / identical protein binding / membrane / plasma membrane
Similarity search - Function
ADP-ribosyl cyclase (CD38/157) / ADP-ribosyl cyclase
Similarity search - Domain/homology
ACETATE ION / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsDreyfus, C. / Freier, R.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Other private Switzerland
CitationJournal: 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. ...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.L. / Srivastava, A. / Perro, M. / Sammicheli, S. / Zhukovsky, E.A. / Dyson, M. / Dreyfus, C.
History
DepositionSep 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab B6-D9 heavy chain
L: Fab B6-D9 light chain
A: ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,01020
Polymers78,2063
Non-polymers1,80417
Water12,538696
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9300 Å2
ΔGint-17 kcal/mol
Surface area30580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.045, 166.045, 78.769
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11L-591-

HOH

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody Fab B6-D9 heavy chain


Mass: 23968.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK cells / Production host: Homo sapiens (human)
#2: Antibody Fab B6-D9 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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Protein / Sugars , 2 types, 4 molecules A

#3: 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: 30821.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Extracellular domain of Uniprot entry P28907 fused to a C-terminal 8-histidine peptide tag
Source: (gene. exp.) Homo sapiens (human) / Gene: CD38 / 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
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 710 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#9: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 696 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.52 Å3/Da / Density % sol: 65.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 7 % v/v T-mate pH 7.0, 0.1 M HEPES pH 7.2, 20 % v/v PEG Smear Medium (BCS screen, Molecular Dimensions)

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.84→71.27 Å / Num. obs: 73151 / % possible obs: 77 % / Redundancy: 11.4 % / Biso Wilson estimate: 34.964 Å2 / Rmerge(I) obs: 0.136 / Rrim(I) all: 0.143 / Rsym value: 0.136 / Net I/σ(I): 12.2
Reflection shellResolution: 1.843→2.02 Å / Redundancy: 12.8 % / Num. unique obs: 1843 / Rsym value: 1.64 / % possible all: 68.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
XDS(VERSION Jan 31data reduction
autoPROCdata reduction
autoPROC(Version 1.1.7)data scaling
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→71.27 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.306 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20831 3668 5 %RANDOM
Rwork0.17443 ---
obs0.17616 69483 76.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.964 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.84→71.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5341 0 113 696 6150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0135756
X-RAY DIFFRACTIONr_bond_other_d0.0020.0175250
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.6587869
X-RAY DIFFRACTIONr_angle_other_deg1.2161.58112182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5995746
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.11222.962260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88915924
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4471525
X-RAY DIFFRACTIONr_chiral_restr0.0620.2773
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027264
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021307
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8563.5662849
X-RAY DIFFRACTIONr_mcbond_other1.8513.5642847
X-RAY DIFFRACTIONr_mcangle_it2.8745.3383586
X-RAY DIFFRACTIONr_mcangle_other2.8745.343587
X-RAY DIFFRACTIONr_scbond_it2.4373.7852907
X-RAY DIFFRACTIONr_scbond_other2.4373.7842905
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7825.5544265
X-RAY DIFFRACTIONr_long_range_B_refined6.25842.216378
X-RAY DIFFRACTIONr_long_range_B_other6.0941.476219
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.843→1.891 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.537 9 -
Rwork0.303 169 -
obs--2.57 %

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