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- PDB-6edr: Crystal Structure of Human CD38 in Complex with 4'-Thioribose NAD+ -

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Basic information

Entry
Database: PDB / ID: 6edr
TitleCrystal Structure of Human CD38 in Complex with 4'-Thioribose NAD+
ComponentsADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Inhibitor / CD38 / HYDROLASE / HYDROLASE-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 / 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 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-ZNA / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsDai, Z. / Zhang, X.N. / Nasertorabi, F. / Cheng, Q. / Pei, H. / Louie, S.G. / Stevens, C.R. / Zhang, Y.
Funding support United States, 2items
OrganizationGrant numberCountry
Other privateV2016-021 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)P30DK048522 United States
CitationJournal: Chem Sci / Year: 2018
Title: Facile chemoenzymatic synthesis of a novel stable mimic of NAD.
Authors: Dai, Z. / Zhang, X.N. / Nasertorabi, F. / Cheng, Q. / Pei, H. / Louie, S.G. / Stevens, R.C. / Zhang, Y.
History
DepositionAug 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.0May 15, 2024Group: Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.formula / _chem_comp.name ..._chem_comp.formula / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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


Theoretical massNumber of molelcules
Total (without water)60,8884
Polymers59,5272
Non-polymers1,3612
Water1,56787
1
A: ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4442
Polymers29,7641
Non-polymers6801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4442
Polymers29,7641
Non-polymers6801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.742, 51.106, 100.674
Angle α, β, γ (deg.)90.000, 96.890, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 44 - 292 / Label seq-ID: 1 - 249

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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: 29763.738 Da / Num. of mol.: 2 / Fragment: Extracellular domain residues 45-300 / Mutation: N100D, N164A, N209D, N219D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD38 / Plasmid: pFuse mammalian / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
References: UniProt: P28907, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase, 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase
#2: Chemical ChemComp-ZNA / [[(2~{R},3~{S},4~{R},5~{R})-5-(3-aminocarbonylpyridin-1-ium-1-yl)-3,4-bis(oxidanyl)thiolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate


Mass: 680.499 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O13P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.55 Å3/Da / Density % sol: 51.72 % / Description: Thin platelets
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100mM HEPES pH 7.0, 14-18% PEG 4000 / PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2018
Details: Mirror: Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.395→99.948 Å / Num. obs: 23158 / % possible obs: 99.9 % / Redundancy: 8.7 % / CC1/2: 0.961 / Rmerge(I) obs: 0.368 / Rpim(I) all: 0.133 / Rrim(I) all: 0.392 / Rsym value: 0.368 / Net I/av σ(I): 1 / Net I/σ(I): 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible allRmerge(I) obs
2.4-2.538.71.333360.7360.5251.5611.46899.9
2.53-2.6890.731770.3741.1331.0681001.068
2.68-2.878.70.829960.3170.9370.8899.90.88
2.87-3.18.9127850.2170.6510.6131000.613
3.1-3.398.91.125840.1680.4990.4691000.469
3.39-3.798.71.223210.1360.3980.37499.80.374
3.79-4.388.51.420600.1080.3140.29499.90.294
4.38-5.378.61.517480.0970.2820.26499.90.264
5.37-7.598.41.613800.0940.2720.25599.80.255
7.59-29.21982.17710.0640.1850.17398.20.173

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0158refinement
XDSdata reduction
SCALA3.3.22data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZVM

1zvm


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.92 / SU B: 29.077 / SU ML: 0.299 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.453 / ESU R Free: 0.276
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2618 1176 5.1 %RANDOM
Rwork0.2157 ---
obs0.2181 21875 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 172.31 Å2 / Biso mean: 48.4 Å2 / Biso min: 21.53 Å2
Baniso -1Baniso -2Baniso -3
1-4.09 Å20 Å2-2.72 Å2
2---3.04 Å20 Å2
3----0.38 Å2
Refinement stepCycle: final / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3893 0 88 87 4068
Biso mean--118.74 42.33 -
Num. residues----495
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.024118
X-RAY DIFFRACTIONr_bond_other_d0.0020.023605
X-RAY DIFFRACTIONr_angle_refined_deg1.421.9595623
X-RAY DIFFRACTIONr_angle_other_deg0.9873.0078369
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1155498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.15223.829175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.75715662
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5031522
X-RAY DIFFRACTIONr_chiral_restr0.0820.2624
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214500
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02860
Refine LS restraints NCS

Ens-ID: 1 / Number: 15346 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 85 -
Rwork0.337 1574 -
all-1659 -
obs--99.64 %
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)
10.2891-0.24140.14760.4695-0.16150.17010.0638-0.011-0.0327-0.0038-0.02830.0541-0.00260.0349-0.03550.3781-0.0017-0.1380.0445-0.01310.0658-13.3845-4.9891-6.795
20.35220.0709-0.02180.5493-0.1010.17930.06860.01480.0304-0.0091-0.0871-0.04430.02930.00290.01850.44430.0172-0.11360.02680.00510.0435-9.9096-25.4132-39.4767
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 292
2X-RAY DIFFRACTION2B44 - 292

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