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- PDB-7bbj: CD73 in complex with the humanized antagonistic antibody mAb19 -

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Basic information

Entry
Database: PDB / ID: 7bbj
TitleCD73 in complex with the humanized antagonistic antibody mAb19
Components
  • 5'-nucleotidase
  • heavy chain mAb19
  • light chain mAB19
KeywordsIMMUNE SYSTEM / antibody complex
Function / homology
Function and homology information


thymidylate 5'-phosphatase / thymidylate 5'-phosphatase activity / ADP catabolic process / 5'-deoxynucleotidase / 5'-deoxynucleotidase activity / 7-methylguanosine nucleotidase / inhibition of non-skeletal tissue mineralization / adenosine biosynthetic process / Pyrimidine catabolism / AMP catabolic process ...thymidylate 5'-phosphatase / thymidylate 5'-phosphatase activity / ADP catabolic process / 5'-deoxynucleotidase / 5'-deoxynucleotidase activity / 7-methylguanosine nucleotidase / inhibition of non-skeletal tissue mineralization / adenosine biosynthetic process / Pyrimidine catabolism / AMP catabolic process / GMP 5'-nucleotidase activity / IMP-specific 5'-nucleotidase / IMP 5'-nucleotidase activity / Nicotinate metabolism / Purine catabolism / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / DNA metabolic process / leukocyte cell-cell adhesion / response to ATP / response to inorganic substance / calcium ion homeostasis / Purinergic signaling in leishmaniasis infection / ATP metabolic process / negative regulation of inflammatory response / external side of plasma membrane / nucleotide binding / cell surface / extracellular exosome / zinc ion binding / nucleoplasm / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
5'-nucleotidase signature 1. / 5'-Nucleotidase, conserved site / 5'-nucleotidase signature 2. / 5'-Nucleotidase, C-terminal / 5'-nucleotidase, C-terminal domain / 5'-Nucleotidase/apyrase / 5'-Nucleotidase, C-terminal domain superfamily / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsBoettcher, J. / Han, F.
Funding support Australia, 1items
OrganizationGrant numberCountry
Austrian Research Promotion AgencyFFG; 852068 Australia
CitationJournal: Mol.Cancer Ther. / Year: 2021
Title: A Novel Antagonistic CD73 Antibody for Inhibition of the Immunosuppressive Adenosine Pathway.
Authors: Wurm, M. / Schaaf, O. / Reutner, K. / Ganesan, R. / Mostbock, S. / Pelster, C. / Bottcher, J. / de Andrade Pereira, B. / Taubert, C. / Alt, I. / Serna, G. / Auguste, A. / Stadermann, K.B. / ...Authors: Wurm, M. / Schaaf, O. / Reutner, K. / Ganesan, R. / Mostbock, S. / Pelster, C. / Bottcher, J. / de Andrade Pereira, B. / Taubert, C. / Alt, I. / Serna, G. / Auguste, A. / Stadermann, K.B. / Delic, D. / Han, F. / Capdevila, J. / Nuciforo, P.G. / Kroe-Barrett, R. / Adam, P.J. / Vogt, A.B. / Hofmann, I.
History
DepositionDec 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 26, 2022Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-nucleotidase
B: 5'-nucleotidase
H: heavy chain mAb19
L: light chain mAB19
M: heavy chain mAb19
N: light chain mAB19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,42412
Polymers216,1136
Non-polymers3106
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13800 Å2
ΔGint-248 kcal/mol
Surface area76500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.350, 67.740, 150.050
Angle α, β, γ (deg.)90.00, 100.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 5'-nucleotidase / / 5'-NT / Ecto-5'-nucleotidase


Mass: 60464.340 Da / Num. of mol.: 2 / Mutation: N53D, K145S, K147S, N311D, N333D, N403D, K478S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NT5E, NT5, NTE / Production host: Escherichia coli (E. coli) / References: UniProt: P21589, 5'-nucleotidase

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Antibody , 2 types, 4 molecules HMLN

#2: Antibody heavy chain mAb19


Mass: 23945.037 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody light chain mAB19


Mass: 23647.275 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct / Production host: Cricetulus griseus (Chinese hamster)

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Non-polymers , 3 types, 224 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.09 Å3/Da / Density % sol: 60.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 12 % w/v PEG 8000, 0.1 M magnesium Acetate and 0.1 M MOPS, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99985 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99985 Å / Relative weight: 1
ReflectionResolution: 2.726→147.7 Å / Num. obs: 59881 / % possible obs: 88.3 % / Redundancy: 4.7 % / Biso Wilson estimate: 71.67 Å2 / CC1/2: 1 / Net I/σ(I): 5.6
Reflection shellResolution: 2.726→2.865 Å / Num. unique obs: 2994 / CC1/2: 0.6

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H2F

4h2f


Resolution: 2.72→39.83 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.907 / SU R Cruickshank DPI: 3.473 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.819 / SU Rfree Blow DPI: 0.327 / SU Rfree Cruickshank DPI: 0.336
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2990 4.99 %RANDOM
Rwork0.208 ---
obs0.21 59939 83.5 %-
Displacement parametersBiso mean: 74.85 Å2
Baniso -1Baniso -2Baniso -3
1-6.8934 Å20 Å2-1.4156 Å2
2---2.9871 Å20 Å2
3----3.9063 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: 1 / Resolution: 2.72→39.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14650 0 6 218 14874
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00814996HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0120367HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5097SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2515HARMONIC5
X-RAY DIFFRACTIONt_it14996HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.29
X-RAY DIFFRACTIONt_other_torsion18.38
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1953SEMIHARMONIC5
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_contact15925SEMIHARMONIC4
LS refinement shellResolution: 2.72→2.79 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2488 -5.09 %
Rwork0.2457 1138 -
all0.2458 1199 -
obs--21.18 %
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)
11.37140.6961.75741.58773.34484.92160.28820.2945-0.315-0.3544-0.28220.1010.2968-0.4994-0.0060.304-0.0065-0.11490.0426-0.3099-0.391347.002-24.835118.8503
22.20990.24610.7610.786-0.20160.7446-0.01040.2246-0.0536-0.05720.08940.0046-0.0022-0.0143-0.0790.04190.00690.0136-0.1801-0.0059-0.1189-4.0387-8.269464.2657
32.27720.2393-0.68190.9687-0.11930.7541-0.05880.26080.0567-0.07470.0546-0.005-0.0319-0.01940.00420.0679-0.0051-0.0951-0.1992-0.0273-0.157344.274610.236464.3699
41.10340.8698-0.55062.03-2.21717.48580.07960.3026-0.0379-0.43530.3131-0.10180.3956-0.2912-0.3927-0.08630.0761-0.1569-0.03750.3224-0.321-24.852116.244112.5039
5-0.00810.425-0.58551.5283-3.4386.80680.07740.21210.1028-0.25080.09470.0879-0.11480.0594-0.17210.0724-0.0090.00920.02460.3072-0.2176-8.853523.635515.3542
61.7310.11091.89821.60382.59725.72120.30740.8961-0.2603-0.32040.18910.01330.04140.7279-0.49650.07620.00980.09960.2785-0.307-0.421564.0378-17.583214.7534
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ N|* }
2X-RAY DIFFRACTION2{ A|* }
3X-RAY DIFFRACTION3{ B|* }
4X-RAY DIFFRACTION4{ H|* }
5X-RAY DIFFRACTION5{ L|* }
6X-RAY DIFFRACTION6{ M|* }

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