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- PDB-8d0m: Human CD38 ectodomain bound to a 78c-ADPR adduct -

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Basic information

Entry
Database: PDB / ID: 8d0m
TitleHuman CD38 ectodomain bound to a 78c-ADPR adduct
ComponentsADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
KeywordsHYDROLASE/INHIBITOR / NAD / hydrolase / axon degeneration / neuroscience / HYDROLASE-INHIBITOR 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 / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD metabolic process / NAD+ nucleotidase, cyclic ADP-ribose generating / long-term synaptic depression / 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 / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD metabolic process / NAD+ nucleotidase, cyclic ADP-ribose generating / long-term synaptic depression / negative regulation of bone resorption / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / response to hydroperoxide / B cell proliferation / response to retinoic acid / positive regulation of B cell proliferation / positive regulation of vasoconstriction / response to interleukin-1 / apoptotic signaling pathway / response to progesterone / female pregnancy / 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
Chem-Q2C / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsBratkowski, M.A. / Gu, W.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Neuron / Year: 2022
Title: Uncompetitive, adduct-forming SARM1 inhibitors are neuroprotective in preclinical models of nerve injury and disease.
Authors: Bratkowski, M. / Burdett, T.C. / Danao, J. / Wang, X. / Mathur, P. / Gu, W. / Beckstead, J.A. / Talreja, S. / Yang, Y.S. / Danko, G. / Park, J.H. / Walton, M. / Brown, S.P. / Tegley, C.M. / ...Authors: Bratkowski, M. / Burdett, T.C. / Danao, J. / Wang, X. / Mathur, P. / Gu, W. / Beckstead, J.A. / Talreja, S. / Yang, Y.S. / Danko, G. / Park, J.H. / Walton, M. / Brown, S.P. / Tegley, C.M. / Joseph, P.R.B. / Reynolds, C.H. / Sambashivan, S.
History
DepositionMay 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6292
Polymers30,6731
Non-polymers9561
Water2,108117
1
A: ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
hetero molecules

A: ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2574
Polymers61,3452
Non-polymers1,9122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area1590 Å2
ΔGint1 kcal/mol
Surface area21810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.612, 129.018, 81.712
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-521-

HOH

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Components

#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: 30672.686 Da / Num. of mol.: 1 / Fragment: ectodomain / Mutation: N100D, N164A, N209D, N219D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD38 / Production host: Escherichia coli (E. coli)
References: UniProt: P28907, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase, 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase
#2: Chemical ChemComp-Q2C / [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-[5-[4-[[4-(2-methoxyethoxy)cyclohexyl]amino]-1-methyl-2-oxidanylidene-quinolin-6-yl]-1,3-thiazol-3-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate


Mass: 955.841 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H49N8O16P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
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: 2.73 Å3/Da / Density % sol: 54.99 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 100 mM Bis-Tris pH 5.5, 100 mM Ammonium sulfate, and 15% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.04→46.78 Å / Num. obs: 21620 / % possible obs: 99.3 % / Redundancy: 13.2 % / Biso Wilson estimate: 35.99 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.038 / Rrim(I) all: 0.101 / Net I/σ(I): 19.1
Reflection shellResolution: 2.04→2.1 Å / Rmerge(I) obs: 1.255 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2112 / CC1/2: 0.667 / Rpim(I) all: 0.509 / Rrim(I) all: 1.355

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8D0J

8d0j


Resolution: 2.04→35.63 Å / SU ML: 0.2059 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.8636
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2242 2000 9.25 %
Rwork0.1936 19620 -
obs0.1965 21620 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.16 Å2
Refinement stepCycle: LAST / Resolution: 2.04→35.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1920 0 64 117 2101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00672039
X-RAY DIFFRACTIONf_angle_d0.85052773
X-RAY DIFFRACTIONf_chiral_restr0.0535298
X-RAY DIFFRACTIONf_plane_restr0.0055345
X-RAY DIFFRACTIONf_dihedral_angle_d21.582735
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.090.30051390.26311368X-RAY DIFFRACTION98.56
2.09-2.150.25811400.24761360X-RAY DIFFRACTION98.62
2.15-2.210.26871400.2231382X-RAY DIFFRACTION98.77
2.21-2.280.31431400.23451377X-RAY DIFFRACTION98.96
2.28-2.360.27161410.22521384X-RAY DIFFRACTION99.09
2.36-2.460.29511410.21631383X-RAY DIFFRACTION99.22
2.46-2.570.22161420.19951385X-RAY DIFFRACTION98.77
2.57-2.710.26231410.20361391X-RAY DIFFRACTION99.55
2.71-2.870.23011450.20761417X-RAY DIFFRACTION99.3
2.88-3.10.26381400.21731374X-RAY DIFFRACTION99.47
3.1-3.410.25951450.20091427X-RAY DIFFRACTION99.49
3.41-3.90.22691450.17091422X-RAY DIFFRACTION99.75
3.9-4.910.17621470.15941446X-RAY DIFFRACTION99.81
4.91-35.630.16971540.18531504X-RAY DIFFRACTION99.4

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