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- PDB-4cmh: Crystal structure of CD38 with a novel CD38-targeting antibody SA... -

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Basic information

Entry
Database: PDB / ID: 4cmh
TitleCrystal structure of CD38 with a novel CD38-targeting antibody SAR650984
Components
  • ADP-RIBOSYL CYCLASE 1
  • HEAVY CHAIN OF SAR650984-FAB FRAGMENT
  • LIGHT CHAIN OF SAR650984-FAB FRAGMENT
KeywordsHYDROLASE/IMMUNE SYSTEM / HYDROLASE-IMMUNE SYSTEM COMPLEX / MULTIPLE MYELOMA
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; Chain A, domain 1 / ADP Ribosyl Cyclase; Chain A, domain 1 / ADP-ribosyl cyclase (CD38/157) / ADP-ribosyl cyclase / NAD(P)-binding Rossmann-like Domain / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Rossmann fold ...ADP Ribosyl Cyclase; Chain A, domain 1 / ADP Ribosyl Cyclase; Chain A, domain 1 / ADP-ribosyl cyclase (CD38/157) / ADP-ribosyl cyclase / NAD(P)-binding Rossmann-like Domain / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsDeckert, J. / Wetzel, M.C. / Park, P.U. / Bartle, L.M. / Skaletskaya, A. / Goldmacher, V. / Vallee, F. / ZhouLiu, Q. / Ferrari, P. / Pouzieux, S. ...Deckert, J. / Wetzel, M.C. / Park, P.U. / Bartle, L.M. / Skaletskaya, A. / Goldmacher, V. / Vallee, F. / ZhouLiu, Q. / Ferrari, P. / Pouzieux, S. / Lahoute, C. / Dumontet, C. / Plesa, A. / Chiron, M. / Lejeune, P. / Chittenden, T. / Blanc, V.
CitationJournal: Clin. Cancer Res. / Year: 2014
Title: SAR650984, a novel humanized CD38-targeting antibody, demonstrates potent antitumor activity in models of multiple myeloma and other CD38+ hematologic malignancies.
Authors: Deckert, J. / Wetzel, M.C. / Bartle, L.M. / Skaletskaya, A. / Goldmacher, V.S. / Vallee, F. / Zhou-Liu, Q. / Ferrari, P. / Pouzieux, S. / Lahoute, C. / Dumontet, C. / Plesa, A. / Chiron, M. ...Authors: Deckert, J. / Wetzel, M.C. / Bartle, L.M. / Skaletskaya, A. / Goldmacher, V.S. / Vallee, F. / Zhou-Liu, Q. / Ferrari, P. / Pouzieux, S. / Lahoute, C. / Dumontet, C. / Plesa, A. / Chiron, M. / Lejeune, P. / Chittenden, T. / Park, P.U. / Blanc, V.
History
DepositionJan 15, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Oct 24, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_src_gen / entity_src_nat
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.title / _citation_author.name / _entity.src_method

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADP-RIBOSYL CYCLASE 1
B: HEAVY CHAIN OF SAR650984-FAB FRAGMENT
C: LIGHT CHAIN OF SAR650984-FAB FRAGMENT


Theoretical massNumber of molelcules
Total (without water)78,2333
Polymers78,2333
Non-polymers00
Water10,629590
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-27.4 kcal/mol
Surface area29910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.619, 111.492, 147.877
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ADP-RIBOSYL CYCLASE 1 / CYCLIC ADP-RIBOSE HYDROLASE 1 / CADPR HYDROLASE 1 / T10 / CD38 / ACYL-RIBOSE CYCLASE 1


Mass: 29676.660 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 45-300 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK-293T / Production host: Homo sapiens (human) / References: UniProt: P28907, NAD+ glycohydrolase
#2: Antibody HEAVY CHAIN OF SAR650984-FAB FRAGMENT


Mass: 25042.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse)
#3: Antibody LIGHT CHAIN OF SAR650984-FAB FRAGMENT


Mass: 23513.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 590 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 46.98 % / Description: NONE
Crystal growpH: 6.5 / Details: PEG 400 44%, MES 50MM PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9395
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 1.53→26.21 Å / Num. obs: 109141 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 25.83 Å2 / Rmerge(I) obs: 0.09

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Processing

SoftwareName: BUSTER / Version: 2.11.4 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→26.21 Å / Cor.coef. Fo:Fc: 0.9624 / Cor.coef. Fo:Fc free: 0.9577 / SU R Cruickshank DPI: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.079 / SU Rfree Blow DPI: 0.076 / SU Rfree Cruickshank DPI: 0.074
RfactorNum. reflection% reflectionSelection details
Rfree0.2082 5462 5 %RANDOM
Rwork0.1878 ---
obs0.1889 109141 99.46 %-
Displacement parametersBiso mean: 32.38 Å2
Baniso -1Baniso -2Baniso -3
1--1.0827 Å20 Å20 Å2
2--0.1203 Å20 Å2
3---0.9624 Å2
Refine analyzeLuzzati coordinate error obs: 0.188 Å
Refinement stepCycle: LAST / Resolution: 1.53→26.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5206 0 0 590 5796
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015464HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.077455HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1862SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes124HARMONIC2
X-RAY DIFFRACTIONt_gen_planes806HARMONIC5
X-RAY DIFFRACTIONt_it5464HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.96
X-RAY DIFFRACTIONt_other_torsion16.47
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion718SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6742SEMIHARMONIC4
LS refinement shellResolution: 1.53→1.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2383 414 5.16 %
Rwork0.228 7607 -
all0.2286 8021 -
obs--99.46 %

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