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- PDB-5f1k: human CD38 in complex with nanobody MU1053 -

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Basic information

Entry
Database: PDB / ID: 5f1k
Titlehuman CD38 in complex with nanobody MU1053
Components
  • ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
  • nanobody MU1053
KeywordsHYDROLASE/IMMUNE SYSTEM / CD38 / ADP-ribosyl cyclase / cyclic ADP-ribose / X-crystallography / Calcium signaling / nanobody / MU1053 / HYDROLASE-IMMUNE SYSTEM 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 / long-term synaptic depression ...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 / long-term synaptic depression / response to hydroperoxide / 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)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsZhang, H. / Hao, Q.
CitationJournal: Sci Rep / Year: 2016
Title: Immuno-targeting the multifunctional CD38 using nanobody
Authors: Li, T. / Qi, S. / Unger, M. / Hou, Y.N. / Deng, Q.W. / Liu, J. / Lam, C.M. / Wang, X.W. / Xin, D. / Zhang, P. / Koch-Nolte, F. / Hao, Q. / Zhang, H. / Lee, H.C. / Zhao, Y.J.
History
DepositionNov 30, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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

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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
C: nanobody MU1053
D: nanobody MU1053


Theoretical massNumber of molelcules
Total (without water)93,5134
Polymers93,5134
Non-polymers00
Water5,819323
1
A: ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
C: nanobody MU1053


Theoretical massNumber of molelcules
Total (without water)46,7572
Polymers46,7572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-5 kcal/mol
Surface area17180 Å2
MethodPISA
2
B: ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
D: nanobody MU1053


Theoretical massNumber of molelcules
Total (without water)46,7572
Polymers46,7572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-8 kcal/mol
Surface area16910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.552, 96.242, 133.777
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRASNASNAA49 - 2905 - 246
21THRTHRASNASNBB49 - 2905 - 246
12VALVALSERSERCC2 - 1242 - 124
22VALVALSERSERDD2 - 1242 - 124

NCS ensembles :
ID
1
2

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Components

#1: Protein ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 / CD38


Mass: 29693.645 Da / Num. of mol.: 2 / Fragment: ectodomain, UNP residues 45-300 / Mutation: Q49T, N100D, N164D, N219D, N209D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD38 / Plasmid: pPICZalpha / Production host: Komagataella pastoris (fungus) / Strain (production host): X33
References: UniProt: P28907, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
#2: Antibody nanobody MU1053


Mass: 17062.939 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Plasmid: pHEN2 / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 3.05 Å3/Da / Density % sol: 59.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Tris, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 51358 / % possible obs: 99.7 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.092 / Χ2: 0.936 / Net I/av σ(I): 21.812 / Net I/σ(I): 9.7 / Num. measured all: 501783
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.389.10.57650750.776100
2.38-2.489.30.43450690.78699.9
2.48-2.599.60.32150760.794100
2.59-2.739.80.2450980.848100
2.73-2.9100.19451000.888100
2.9-3.12100.14651191.02100
3.12-3.44100.10351521.09100
3.44-3.939.60.08151411.13999.9
3.93-4.9510.30.0751851.17799.3
4.95-50100.05653430.898.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SCALEPACKdata scaling
PHASERphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.15data extraction
DENZOdata reduction
HKL-2000data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YH3

1yh3


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.91 / WRfactor Rfree: 0.2326 / WRfactor Rwork: 0.2031 / FOM work R set: 0.8483 / SU B: 14.552 / SU ML: 0.153 / SU Rfree: 0.2129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2313 2259 5 %RANDOM
Rwork0.198 ---
obs0.1996 42953 87.75 %-
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 max: 113.51 Å2 / Biso mean: 42.654 Å2 / Biso min: 11.32 Å2
Baniso -1Baniso -2Baniso -3
1--2.59 Å20 Å20 Å2
2--0.37 Å20 Å2
3---2.22 Å2
Refinement stepCycle: final / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5755 0 0 323 6078
Biso mean---33.8 -
Num. residues----727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195922
X-RAY DIFFRACTIONr_bond_other_d0.0040.025496
X-RAY DIFFRACTIONr_angle_refined_deg1.3831.9358031
X-RAY DIFFRACTIONr_angle_other_deg1.181312657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7655725
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.19123.741278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51415998
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4241542
X-RAY DIFFRACTIONr_chiral_restr0.0820.2865
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216707
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021419
X-RAY DIFFRACTIONr_mcbond_it0.5070.912906
X-RAY DIFFRACTIONr_mcbond_other0.5070.912905
X-RAY DIFFRACTIONr_mcangle_it0.6581.3633623
X-RAY DIFFRACTIONr_rigid_bond_restr1.459311418
X-RAY DIFFRACTIONr_sphericity_free30.5495128
X-RAY DIFFRACTIONr_sphericity_bonded3.163511462
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A28040
12B28040
21C13206
22D13206
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 98 -
Rwork0.223 1796 -
all-1894 -
obs--50.41 %
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)
12.3901-1.4038-1.08614.64243.02674.5939-0.1011-0.03080.5366-0.30990.2572-0.177-0.507-0.0971-0.15620.28240.04330.0550.162-0.06230.305161.38435.00694.596
25.6919-2.4999-0.23781.22870.45021.049-0.0299-0.18230.45460.07450.0962-0.234-0.0036-0.0315-0.06640.35450.02720.02590.1521-0.09340.329775.15426.52798.222
39.64434.3134-6.82358.2096-6.006811.8289-0.2662-0.6842.28020.190.4675-0.0266-0.44520.1195-0.20140.54090.2195-0.0230.2657-0.27110.948658.85445.637106.319
42.2039-1.7644-0.29373.4125-0.93591.3799-0.3034-0.67190.26680.64340.36440.0359-0.13490.0511-0.06110.41370.11180.01820.3198-0.2120.265374.33423.554110.377
55.22271.4427-0.83793.6528-1.71363.4066-0.2401-0.687-0.140.6221-0.1045-0.6289-0.06320.33610.34470.46110.1121-0.11980.24-0.1560.345686.56718.311109.258
63.53671.21021.57233.86911.33942.74520.164-0.343-0.10190.21190.17010.04070.2799-0.1587-0.33420.2733-0.01680.04790.18230.11780.201355.5991.49788.525
74.05482.6885-1.27882.524-2.08242.50870.09170.097-0.1222-0.0573-0.0346-0.02370.07070.1974-0.05710.31670.00230.0440.20470.0490.21969.3164.85379.204
83.6795-3.8486-1.0144.41582.1619.01960.13340.0192-0.66730.10010.00270.59480.2482-0.662-0.13610.3775-0.0933-0.09150.2910.16250.479245.668-8.14781.504
911.20568.10682.54359.46190.56141.87860.04970.29460.3594-0.36360.11320.63530.05270.038-0.16290.29940.0265-0.00450.18010.12930.356252.583.13475.294
104.162-0.6304-0.09266.4119-1.05592.04310.09340.452-0.1341-1.1039-0.05120.1480.38970.1196-0.04210.4399-0.02430.01580.22860.04320.060170.63410.77265.532
114.1269-4.0163.10115.3826-0.59996.4380.14580.03550.4240.17640.1004-0.91060.48390.2941-0.24620.3634-0.0058-0.24160.1550.09660.759689.363-11.213103.497
1212.91076.9859-2.3817.7841-5.47471.8218-0.1239-0.4856-0.27930.2339-0.0724-1.4419-0.03740.24440.19630.36660.0141-0.20850.5287-0.2510.718293.591-1.747103.482
137.39052.64950.44276.5331-0.31831.1274-0.0447-0.29690.241-0.26650.1483-0.1940.0773-0.1328-0.10370.28040.0387-0.02920.1684-0.01230.229385.6760.21799.018
147.782219.212613.527465.61831.273129.82920.04050.0234-0.2426-2.4142-0.48620.553-0.0832-1.77230.44570.45020.1994-0.18170.7239-0.20990.456676.914-7.94594.674
153.41991.63520.35047.4105-0.10262.1008-0.0254-0.54140.30470.76170.17850.11780.0387-0.0984-0.15320.34430.0665-0.05060.2343-0.01070.138881.5112.436107.091
164.34231.2446-0.37967.2461-1.27422.2938-0.0364-0.53140.09730.79080.1592-0.2690.0988-0.0112-0.12290.36490.0706-0.0740.26840.04460.237186.897-4.973108.579
173.54250.7804-0.46510.2796-1.53830.27360.0908-0.1638-0.1054-0.0941-0.0847-0.16950.02650.0483-0.00610.30950.0245-0.05790.1354-0.04180.238382.696-0.03297.646
182.60251.5230.71515.4218-2.744.93650.1347-0.0525-0.3359-0.63180.1104-0.03950.42670.1597-0.2450.20620.0438-0.0680.19670.04150.295185.005-8.03397.9
193.1066-2.9941-2.767417.117517.486817.8987-0.4805-1.19380.39340.64361.2313-0.78810.60751.1647-0.75070.25380.0676-0.1030.76650.37471.180496.11228.09473.33
207.4798-8.94341.324119.3433-1.38030.3897-0.3028-0.71970.00610.15970.3628-1.2451-0.0208-0.0256-0.060.34140.07460.21080.44680.32010.576189.88734.25266.633
212.72780.76861.092118.9624-0.13122.7180.1913-0.05650.15670.4741-0.7601-1.4475-0.19680.25530.56880.2479-0.09750.0080.3740.22650.334585.47129.33875.464
222.8103-0.2812-0.608312.5468-0.10242.90710.11050.04960.12120.0614-0.3701-0.14850.00520.19610.25950.2398-0.04580.10390.30730.16030.185578.86928.19970.4
235.2033-0.4297-0.466710.8471-1.24532.08510.17820.40950.1937-0.363-0.6922-0.9433-0.03050.18420.5140.2716-0.01540.12680.38930.25370.318484.92434.42467.168
245.1323-3.4631-3.97823.7806-0.710612.1466-0.06510.26240.78530.4825-0.6115-1.1389-0.06290.45580.67660.9128-0.4616-0.32870.50690.3920.45682.78422.5678.171
250.5705-0.52181.8519.6704-3.72428.33020.1410.07770.29561.4468-0.9569-1.4067-0.46850.69520.81590.4903-0.15850.04230.35840.27890.5587.88635.22375.659
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A49 - 112
2X-RAY DIFFRACTION2A113 - 160
3X-RAY DIFFRACTION3A161 - 179
4X-RAY DIFFRACTION4A180 - 256
5X-RAY DIFFRACTION5A257 - 296
6X-RAY DIFFRACTION6B49 - 116
7X-RAY DIFFRACTION7B117 - 159
8X-RAY DIFFRACTION8B160 - 176
9X-RAY DIFFRACTION9B177 - 195
10X-RAY DIFFRACTION10B196 - 291
11X-RAY DIFFRACTION11C2 - 15
12X-RAY DIFFRACTION12C16 - 30
13X-RAY DIFFRACTION13C31 - 39
14X-RAY DIFFRACTION14C40 - 47
15X-RAY DIFFRACTION15C48 - 72
16X-RAY DIFFRACTION16C73 - 89
17X-RAY DIFFRACTION17C90 - 109
18X-RAY DIFFRACTION18C110 - 124
19X-RAY DIFFRACTION19D2 - 6
20X-RAY DIFFRACTION20D7 - 29
21X-RAY DIFFRACTION21D30 - 43
22X-RAY DIFFRACTION22D44 - 72
23X-RAY DIFFRACTION23D73 - 95
24X-RAY DIFFRACTION24D96 - 109
25X-RAY DIFFRACTION25D110 - 124

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