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- PDB-7vke: Crystal structure of human CD38 ECD in complex with UniDab(TM) F11A -

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Basic information

Entry
Database: PDB / ID: 7vke
TitleCrystal structure of human CD38 ECD in complex with UniDab(TM) F11A
Components
  • ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
  • Unidab F11A
KeywordsHYDROLASE / Complex / Transferase / antibody / receptor
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 ...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 / long-term synaptic depression / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / B cell proliferation / response to retinoic acid / positive regulation of B cell proliferation / positive regulation of vasoconstriction / response to interleukin-1 / response to progesterone / female pregnancy / apoptotic signaling pathway / B cell receptor signaling pathway / positive regulation of insulin secretion / negative regulation of neuron projection development / response to estradiol / positive regulation of cytosolic calcium ion concentration / transferase activity / 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
ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSchooten, W.V. / Schellenberger, U. / Ugamraj, H.S. / Manicka, S. / Bijpuria, S. / Gondu, R.K.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Mabs / Year: 2022
Title: TNB-738, a biparatopic antibody, boosts intracellular NAD+ by inhibiting CD38 ecto-enzyme activity.
Authors: Ugamraj, H.S. / Dang, K. / Ouisse, L.H. / Buelow, B. / Chini, E.N. / Castello, G. / Allison, J. / Clarke, S.C. / Davison, L.M. / Buelow, R. / Deng, R. / Iyer, S. / Schellenberger, U. / ...Authors: Ugamraj, H.S. / Dang, K. / Ouisse, L.H. / Buelow, B. / Chini, E.N. / Castello, G. / Allison, J. / Clarke, S.C. / Davison, L.M. / Buelow, R. / Deng, R. / Iyer, S. / Schellenberger, U. / Manika, S.N. / Bijpuria, S. / Musnier, A. / Poupon, A. / Cuturi, M.C. / van Schooten, W. / Dalvi, P.
History
DepositionSep 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
B: Unidab F11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6108
Polymers45,3412
Non-polymers2696
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-33 kcal/mol
Surface area17530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.820, 64.820, 201.316
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein / Antibody , 2 types, 2 molecules AB

#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: 30754.795 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD38 / Production host: Komagataella pastoris (fungus)
References: UniProt: P28907, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase, 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase
#2: Antibody Unidab F11A


Mass: 14586.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Non-polymers , 5 types, 322 molecules

#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.91 Å3/Da / Density % sol: 57.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Sodium Citrate, PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.79→49.08 Å / Num. obs: 47342 / % possible obs: 100 % / Redundancy: 10.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Net I/σ(I): 12.1
Reflection shellResolution: 1.79→1.83 Å / Rmerge(I) obs: 1.379 / Num. unique obs: 2686 / CC1/2: 0.653

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YH3, 6PZW

1yh3

6pzw


Resolution: 1.9→49.075 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / Cross valid method: FREE R-VALUE / ESU R: 0.139 / ESU R Free: 0.134
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2308 1962 4.94 %
Rwork0.1927 37754 -
all0.195 --
obs-39716 99.987 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 37.307 Å2
Baniso -1Baniso -2Baniso -3
1-0.102 Å20.051 Å20 Å2
2--0.102 Å2-0 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.9→49.075 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3003 0 15 316 3334
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133156
X-RAY DIFFRACTIONr_bond_other_d0.0350.0172891
X-RAY DIFFRACTIONr_angle_refined_deg1.61.6434295
X-RAY DIFFRACTIONr_angle_other_deg2.3811.5856677
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8985398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47522.317164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04115534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9771520
X-RAY DIFFRACTIONr_chiral_restr0.0890.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023603
X-RAY DIFFRACTIONr_gen_planes_other0.010.02741
X-RAY DIFFRACTIONr_nbd_refined0.220.2686
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2310.22803
X-RAY DIFFRACTIONr_nbtor_refined0.1640.21508
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.21380
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0570.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2120.213
X-RAY DIFFRACTIONr_nbd_other0.2230.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2140.210
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0240.21
X-RAY DIFFRACTIONr_mcbond_it3.2073.7741556
X-RAY DIFFRACTIONr_mcbond_other3.2083.7721555
X-RAY DIFFRACTIONr_mcangle_it4.7645.6541954
X-RAY DIFFRACTIONr_mcangle_other4.7635.6571955
X-RAY DIFFRACTIONr_scbond_it4.0294.0971598
X-RAY DIFFRACTIONr_scbond_other4.0274.0981599
X-RAY DIFFRACTIONr_scangle_it6.0526.0042337
X-RAY DIFFRACTIONr_scangle_other6.056.0042338
X-RAY DIFFRACTIONr_lrange_it8.51245.8923715
X-RAY DIFFRACTIONr_lrange_other8.40945.5333634
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.3571670.3152700X-RAY DIFFRACTION100
1.949-2.0030.3081450.292667X-RAY DIFFRACTION100
2.003-2.0610.3141200.2752591X-RAY DIFFRACTION100
2.061-2.1240.2811240.2552533X-RAY DIFFRACTION100
2.124-2.1940.2711150.2452461X-RAY DIFFRACTION100
2.194-2.2710.262870.2182439X-RAY DIFFRACTION99.9604
2.271-2.3560.2221130.2042300X-RAY DIFFRACTION100
2.356-2.4520.2441040.1992239X-RAY DIFFRACTION100
2.452-2.5610.2351230.2032120X-RAY DIFFRACTION100
2.561-2.6860.2671080.22051X-RAY DIFFRACTION100
2.686-2.8310.2471070.2011924X-RAY DIFFRACTION100
2.831-3.0020.2211200.1841816X-RAY DIFFRACTION100
3.002-3.2090.224700.1891773X-RAY DIFFRACTION100
3.209-3.4660.219980.1921607X-RAY DIFFRACTION100
3.466-3.7950.2361050.1611493X-RAY DIFFRACTION100
3.795-4.2420.181700.1511370X-RAY DIFFRACTION100
4.242-4.8950.179790.1331223X-RAY DIFFRACTION100
4.895-5.9870.215420.161062X-RAY DIFFRACTION100
5.987-8.4330.194370.188844X-RAY DIFFRACTION100

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