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- PDB-7duo: Crystal structure of daratumumab fab and CD38 complex -

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Basic information

Entry
Database: PDB / ID: 7duo
TitleCrystal structure of daratumumab fab and CD38 complex
Components
  • ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
  • Fab heavy chainFragment antigen-binding
  • Fab light chainFragment antigen-binding
KeywordsANTITUMOR PROTEIN/HYDROLASE / daratumumab / CD38 / multiple myeloma / ANTIMICROBIAL PROTEIN / ANTITUMOR PROTEIN-HYDROLASE complex
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 / NAD+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD metabolic process / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / negative regulation of bone resorption ...2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / artery smooth muscle contraction / Nicotinate metabolism / NAD+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD metabolic process / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / 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 / response to estradiol / negative regulation of neuron projection development / positive regulation of cytosolic calcium ion concentration / transferase activity / positive regulation of cell growth / 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 / membrane / identical protein binding / 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: 2.81 Å
AuthorsYu, X.J. / Wang, L. / Yu, C.F.
CitationJournal: To Be Published
Title: Crystal structure of daratumumab fab and CD38 complex
Authors: Yu, X.J. / Wang, L. / Yu, C.F.
History
DepositionJan 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Fab heavy chain
B: ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
L: Fab light chain


Theoretical massNumber of molelcules
Total (without water)73,5493
Polymers73,5493
Non-polymers00
Water0
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)81.611, 54.658, 93.052
Angle α, β, γ (deg.)90.000, 98.160, 90.000
Int Tables number3
Space group name H-MP121

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Components

#1: Antibody Fab heavy chain / Fragment antigen-binding


Mass: 23595.488 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)
#2: 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: 26650.408 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD38
Production host: Mammalian expression vector BsrGI-MCS-pcDNA3.1 (others)
References: UniProt: P28907, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase, 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase
#3: Antibody Fab light chain / Fragment antigen-binding


Mass: 23302.799 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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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.96 %
Crystal growTemperature: 291 K / Method: evaporation, recrystallization
Details: 0.2M Sodium phosphate monobasic monohydrate, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9798 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.81→50 Å / Num. obs: 19416 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.969 / Rmerge(I) obs: 0.183 / Net I/σ(I): 12.18
Reflection shellResolution: 2.81→2.9 Å / Rmerge(I) obs: 0.183 / Num. unique obs: 19416 / CC1/2: 0.969

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1yh3

1yh3


Resolution: 2.81→46.055 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 26.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2376 956 10.01 %
Rwork0.2305 17473 -
obs-19416 96.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.93 Å2 / Biso mean: 36.1454 Å2 / Biso min: 7.85 Å2
Refinement stepCycle: final / Resolution: 2.81→46.055 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5085 0 0 0 5085
Num. residues----652
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8103-2.88050.3002720.258765451
2.8805-2.95840.32691410.25771255100
2.9584-3.04540.32341430.24611298100
3.0454-3.14370.30071400.24831262100
3.1437-3.25610.26971440.24161296100
3.2561-3.38640.28211450.23351302100
3.3864-3.54040.33551390.22491253100
3.5404-3.7270.2811450.22081303100
3.727-3.96040.26111430.21651286100
3.9604-4.2660.23591450.19881305100
4.266-4.69490.24251430.18141293100
4.6949-5.37340.22231460.18921304100
5.3734-6.76650.27421460.23571317100
6.7665-46.0550.2471510.2245134599
Refinement TLS params.Method: refined / Origin x: 39.1934 Å / Origin y: 30.0133 Å / Origin z: 21.1732 Å
111213212223313233
T0.1308 Å20.0161 Å2-0.0003 Å2-0.0747 Å2-0.0162 Å2--0.0992 Å2
L0.2847 °2-0.2435 °2-0.0894 °2-0.2363 °20.3236 °2--0.3756 °2
S-0.0515 Å °-0.0089 Å °0.0011 Å °0.0736 Å °0.1029 Å °0.0075 Å °0.1631 Å °0.031 Å °0.0322 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allH1 - 222
2X-RAY DIFFRACTION1allB13 - 241
3X-RAY DIFFRACTION1allL1 - 213

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