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Basic information

Entry
Database: PDB / ID: 2o3u
TitleStructural Basis for Formation and Hydrolysis of Calcium Messenger Cyclic ADP-ribose by Human CD38
ComponentsADP-ribosyl cyclase 1
KeywordsHYDROLASE / Human CD38 E226Q mutant / the catalytic pocket / NGD binding and hydrolysis
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 interleukin-1 / response to progesterone / 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; 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 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-NGD / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsLiu, Q. / Kriksunov, I.A. / Graeff, R. / Lee, H.C. / Hao, Q.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural basis for formation and hydrolysis of the calcium messenger cyclic ADP-ribose by human CD38
Authors: Liu, Q. / Kriksunov, I.A. / Graeff, R. / Lee, H.C. / Hao, Q.
History
DepositionDec 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1204
Polymers60,7592
Non-polymers1,3612
Water3,315184
1
A: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0602
Polymers30,3791
Non-polymers6801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0602
Polymers30,3791
Non-polymers6801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.975, 53.091, 65.678
Angle α, β, γ (deg.)106.08, 91.92, 95.18
Int Tables number1
Space group name H-MP1
DetailsThere are two biological units in the crystallographic asymmetric unit.

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Components

#1: Protein ADP-ribosyl cyclase 1 / Cyclic ADP-ribose hydrolase 1 / cADPr hydrolase 1 / Lymphocyte differentiation antigen CD38 / T10 / ...Cyclic ADP-ribose hydrolase 1 / cADPr hydrolase 1 / Lymphocyte differentiation antigen CD38 / T10 / Acute lymphoblastic leukemia cells antigen CD38


Mass: 30379.408 Da / Num. of mol.: 2 / Fragment: Extracellular domain, residues 45-300 / Mutation: Q49T, N100D, N164D, N209D, N219D, E226Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD38 / Plasmid: pPICZaA / Production host: Pichia pastoris (fungus) / Strain (production host): X-33 / References: UniProt: P28907, NAD+ glycohydrolase
#2: Chemical ChemComp-NGD / 3-(AMINOCARBONYL)-1-[(2R,3R,4S,5R)-5-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)-3,4-DIHYD ROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-3,4-DIHYDROXYTETRAHYDROFURAN-2- YL]PYRIDINIUM / NICOTINAMIDE GUANINE DINUCLEOTIDE


Mass: 680.432 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O15P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
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: 2.3 Å3/Da / Density % sol: 46.52 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM MES, 12% PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 29, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 30854 / Num. obs: 29497 / % possible obs: 95.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.1→2.18 Å / % possible all: 78.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQUANTUMdata collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YH3

1yh3


Resolution: 2.11→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.931 / SU B: 10.08 / SU ML: 0.14 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.251 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22268 1474 5 %RANDOM
Rwork0.17791 ---
all0.18019 29500 --
obs0.18019 27999 94.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.619 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å21.79 Å21.51 Å2
2--1 Å22.14 Å2
3---1.58 Å2
Refinement stepCycle: LAST / Resolution: 2.11→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4100 0 90 184 4374
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224312
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.965866
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8575502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.57324.038208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.01715742
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3161530
X-RAY DIFFRACTIONr_chiral_restr0.0990.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023250
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.21854
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22888
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2222
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0970.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5951.52591
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.9524114
X-RAY DIFFRACTIONr_scbond_it1.60432002
X-RAY DIFFRACTIONr_scangle_it2.5264.51752
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.11→2.166 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 71 -
Rwork0.221 1452 -
obs--67.84 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
100.007-0.013431.0478-59.3331113.38691.2640.25642.1398-0.4662-3.1112-2.4172.90161.02311.84710.30360.0439-0.14850.4702-0.03520.428323.5563-17.360312.0229
29.8877-2.97831.16273.9198-1.32932.26840.24920.2689-1.2286-0.18150.0550.53650.2583-0.1816-0.3042-0.09710.0069-0.0107-0.2203-0.02230.18060.7946-14.972-2.3705
33.818-3.1428-0.25085.7444-0.03260.03460.24470.4062-0.529-0.4733-0.18210.15710.09650.1551-0.0626-0.1252-0.00480.0085-0.0922-0.0059-0.1414-2.7425-1.71-5.3805
417.82151.82341.29998.34911.810514.7610.2492-0.0496-0.24910.0606-0.16670.95170.4672-0.7287-0.08250.0196-0.02830.0553-0.1530.0468-0.1389-12.64072.32115.8651
56.8931-3.85810.89535.7361-1.40252.0646-0.0338-0.3073-0.37420.19990.0399-0.3805-0.02210.2634-0.0062-0.1644-0.00820.004-0.16670.0157-0.04688.2211-9.0910.6023
64.8518-0.55180.5694.1947-0.40736.1688-0.03510.1888-0.04080.21820.0349-0.17950.02890.50210.0002-0.2055-0.01550.0032-0.21030.016-0.230.80699.6696-2.4159
74.80180.715-0.19875.17970.05085.15690.132-0.59350.39730.8126-0.0963-0.142-0.6623-0.0959-0.0357-0.0357-0.0172-0.0418-0.1185-0.0339-0.1563-1.297918.99064.4376
819.459112.5232-4.200821.0896-5.94626.98840.465-0.80561.2760.89160.19141.5649-0.5757-1.3203-0.65640.16070.08460.08950.167-0.0424-0.1665-15.962512.37414.3546
919.7759-2.51319.321414.9222.4118113.4597-0.0859-1.40590.3760.92980.3866-0.0024-0.909-2.6684-0.30070.07410.17290.01470.10080.0451-0.182824.636512.17084.2107
1021.39144.1491-7.31216.5528-4.780111.3259-0.0661-0.18350.17120.17070.0433-0.01240.03030.31080.0227-0.2230.0072-0.0551-0.2344-0.0511-0.311825.030213.9158-10.7221
112.93630.5783-1.58361.8786-1.60036.5150.10020.39760.2894-0.19160.02270.0282-0.6526-0.1779-0.1228-0.04940.01-0.0088-0.18140.0146-0.147519.27722.9084-25.4297
1211.306-2.27042.14274.21031.129510.4484-0.05370.70760.067-0.4694-0.0122-0.5714-0.02580.89220.0659-0.0399-0.04390.0294-0.0761-0.1365-0.12524.74266.1903-37.2461
133.9661-0.3873-1.48634.68352.65428.6942-0.1890.0691-0.0901-0.1170.04050.1716-0.08770.47120.1485-0.2018-0.0419-0.0026-0.25420.0038-0.21421.386616.2412-23.5595
143.79930.10650.8612.55330.75488.77440.13920.0953-0.56750.01440.0910.18440.2177-0.3037-0.2302-0.25260.0006-0.0022-0.1956-0.0271-0.148816.201610.7942-17.1519
154.2736-0.1551-0.56256.15830.30767.1842-0.19580.1894-0.93640.1701-0.04880.35130.9616-0.44660.24460.0738-0.13390.0080.0186-0.15930.019415.0332-4.0593-35.813
1616.00545.2031-3.11718.812-1.26534.5443-0.31791.4127-1.1609-1.81230.0465-1.98560.82910.94520.27150.27240.1550.16640.4859-0.22690.1933.2541-3.8587-44.734
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA45 - 497 - 11
2X-RAY DIFFRACTION2AA50 - 10312 - 65
3X-RAY DIFFRACTION3AA104 - 12966 - 91
4X-RAY DIFFRACTION4AA130 - 14392 - 105
5X-RAY DIFFRACTION5AA144 - 193106 - 155
6X-RAY DIFFRACTION6AA194 - 235156 - 197
7X-RAY DIFFRACTION7AA236 - 275198 - 237
8X-RAY DIFFRACTION8AA276 - 296238 - 258
9X-RAY DIFFRACTION9BB45 - 487 - 10
10X-RAY DIFFRACTION10BB49 - 5811 - 20
11X-RAY DIFFRACTION11BB59 - 11621 - 78
12X-RAY DIFFRACTION12BB117 - 14079 - 102
13X-RAY DIFFRACTION13BB141 - 167103 - 129
14X-RAY DIFFRACTION14BB168 - 195130 - 157
15X-RAY DIFFRACTION15BB196 - 275158 - 237
16X-RAY DIFFRACTION16BB276 - 296238 - 258

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