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- PDB-8zye: Crystal structure of CD38 in complex with RP02 antibody -

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Basic information

Entry
Database: PDB / ID: 8zye
TitleCrystal structure of CD38 in complex with RP02 antibody
Components
  • ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
  • RP02 scFv
KeywordsMEMBRANE PROTEIN / NADase / complex / antibody
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 / positive regulation of vasoconstriction / B cell proliferation / response to retinoic acid / positive regulation of B cell proliferation / response to progesterone / response to interleukin-1 / B cell receptor signaling pathway / apoptotic signaling pathway / female pregnancy / positive regulation of insulin secretion / response to estradiol / negative regulation of neuron projection development / transferase activity / positive regulation of cytosolic calcium ion concentration / positive regulation of cell growth / nuclear membrane / basolateral plasma 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
DI(HYDROXYETHYL)ETHER / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsLei, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: CD38 CAR antigen engagement mechanisms and affinity tuning
Authors: Lei, Y.
History
DepositionJun 17, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release

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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: RP02 scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,96913
Polymers52,1412
Non-polymers82911
Water84747
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.793, 96.220, 242.459
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-303-

SO4

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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 / CD38 / 2'-phospho-ADP-ribosyl cyclase / 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose ...CD38 / 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: 28182.041 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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
#2: Antibody RP02 scFv


Mass: 23958.572 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 , 4 types, 58 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.67 Å3/Da / Density % sol: 53.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris, pH 6.5, 0.2 M lithium sulfate, and 25% PEG3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jun 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.72→48.11 Å / Num. obs: 54357 / % possible obs: 90 % / Redundancy: 1 % / CC1/2: 0.996 / Net I/σ(I): 10.3
Reflection shellResolution: 2.72→2.87 Å / Num. unique obs: 8096 / CC1/2: 0.739

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.72→48.11 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2707 1554 10 %
Rwork0.214 --
obs0.2196 15545 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.72→48.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3657 0 50 47 3754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043783
X-RAY DIFFRACTIONf_angle_d0.6985122
X-RAY DIFFRACTIONf_dihedral_angle_d18.5441365
X-RAY DIFFRACTIONf_chiral_restr0.047556
X-RAY DIFFRACTIONf_plane_restr0.004647
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.72-2.810.33121400.26421265X-RAY DIFFRACTION100
2.81-2.910.3661370.26151229X-RAY DIFFRACTION100
2.91-3.020.3091400.26571251X-RAY DIFFRACTION100
3.02-3.160.31571400.24841268X-RAY DIFFRACTION100
3.16-3.330.33051370.24611240X-RAY DIFFRACTION100
3.33-3.540.29911400.23271254X-RAY DIFFRACTION100
3.54-3.810.27081410.21241272X-RAY DIFFRACTION100
3.81-4.190.26081410.18221265X-RAY DIFFRACTION100
4.19-4.80.2171430.17351289X-RAY DIFFRACTION100
4.8-6.040.24391440.19381293X-RAY DIFFRACTION100
6.05-48.110.25711510.22451365X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 9.3198 Å / Origin y: 27.9332 Å / Origin z: 32.2737 Å
111213212223313233
T0.3709 Å2-0.1168 Å20.0591 Å2-0.4808 Å20.0278 Å2--0.4659 Å2
L0.5492 °2-0.2476 °2-0.024 °2-1.1457 °20.351 °2--2.2831 °2
S-0.0529 Å °0.3676 Å °0.0062 Å °-0.3136 Å °0.2187 Å °-0.1402 Å °0.1306 Å °0.1123 Å °-0.1537 Å °
Refinement TLS groupSelection details: all

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