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- PDB-6hxw: structure of human CD73 in complex with antibody IPH53 -

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Basic information

Entry
Database: PDB / ID: 6hxw
Titlestructure of human CD73 in complex with antibody IPH53
Components
  • 5'-nucleotidase
  • IPH53 heavy chain
  • IPH53 light chain
KeywordsIMMUNE SYSTEM / Inhibitor antibody
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; domain 2 / 5'-Nucleotidase, C-terminal domain / 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 / Metallo-dependent phosphatases ...5'-nucleotidase; domain 2 / 5'-Nucleotidase, C-terminal domain / 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 / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.78 Å
AuthorsRoussel, A. / Amigues, B.
CitationJournal: Cell Rep / Year: 2019
Title: Blocking Antibodies Targeting the CD39/CD73 Immunosuppressive Pathway Unleash Immune Responses in Combination Cancer Therapies.
Authors: Perrot, I. / Michaud, H.A. / Giraudon-Paoli, M. / Augier, S. / Docquier, A. / Gros, L. / Courtois, R. / Dejou, C. / Jecko, D. / Becquart, O. / Rispaud-Blanc, H. / Gauthier, L. / Rossi, B. / ...Authors: Perrot, I. / Michaud, H.A. / Giraudon-Paoli, M. / Augier, S. / Docquier, A. / Gros, L. / Courtois, R. / Dejou, C. / Jecko, D. / Becquart, O. / Rispaud-Blanc, H. / Gauthier, L. / Rossi, B. / Chanteux, S. / Gourdin, N. / Amigues, B. / Roussel, A. / Bensussan, A. / Eliaou, J.F. / Bastid, J. / Romagne, F. / Morel, Y. / Narni-Mancinelli, E. / Vivier, E. / Paturel, C. / Bonnefoy, N.
History
DepositionOct 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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
C: IPH53 heavy chain
D: IPH53 light chain
H: IPH53 heavy chain
L: IPH53 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,36712
Polymers213,6636
Non-polymers7046
Water14,592810
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14860 Å2
ΔGint-229 kcal/mol
Surface area74510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.347, 209.429, 65.065
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Antibody , 2 types, 4 molecules CHDL

#2: Antibody IPH53 heavy chain


Mass: 25144.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody IPH53 light chain


Mass: 23008.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Cricetulus griseus (Chinese hamster)

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Protein / Sugars , 2 types, 4 molecules AB

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


Mass: 58678.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NT5E, NT5, NTE / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P21589, 5'-nucleotidase
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 814 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 810 / 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: 3.19 Å3/Da / Density % sol: 61.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1M succinic acid pH7.0 15% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98004 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98004 Å / Relative weight: 1
ReflectionResolution: 2.78→48.84 Å / Num. obs: 68010 / % possible obs: 99.5 % / Redundancy: 9.3 % / Biso Wilson estimate: 67.89 Å2 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.041 / Rrim(I) all: 0.129 / Net I/σ(I): 5.5
Reflection shellResolution: 2.78→2.93 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 1 / Num. unique obs: 9400 / Rpim(I) all: 0.265 / % possible all: 95.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.78→48.84 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.882 / SU R Cruickshank DPI: 0.865 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.345 / SU Rfree Blow DPI: 0.311 / SU Rfree Cruickshank DPI: 0.308
RfactorNum. reflection% reflectionSelection details
Rfree0.232 3436 5.06 %RANDOM
Rwork0.192 ---
obs0.194 67937 99.3 %-
Displacement parametersBiso max: 183.96 Å2 / Biso mean: 79.35 Å2 / Biso min: 5.88 Å2
Baniso -1Baniso -2Baniso -3
1-13.4918 Å20 Å20 Å2
2--13.7957 Å20 Å2
3----27.2874 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: final / Resolution: 2.78→48.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14665 0 32 810 15507
Biso mean--83.5 58.07 -
Num. residues----1693
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5106SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2534HARMONIC5
X-RAY DIFFRACTIONt_it15041HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1961SEMIHARMONIC5
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_contact17012SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d15041HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg20430HARMONIC21.21
X-RAY DIFFRACTIONt_omega_torsion3.35
X-RAY DIFFRACTIONt_other_torsion18.89
LS refinement shellResolution: 2.78→2.8 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3371 68 5 %
Rwork0.2492 1291 -
all0.2536 1359 -
obs--74.89 %
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)
10.4166-0.5902-0.07431.940.020.172-0.0839-0.1304-0.04740.09690.12010.1962-0.01550.0185-0.0361-0.1262-0.0013-0.029-0.06310.00790.171725.66758.334313.7371
21.1056-0.6659-0.02641.3969-0.17780.3119-0.0374-0.0485-0.09710.10460.05770.1524-0.00950.0198-0.0203-0.08970.0189-0.0084-0.06050.02570.08740.7815-47.767717.0275
30.953.50670.12261.3444-0.53820.54650.0554-0.04360.0656-0.2765-0.09720.05820.3555-0.24490.04170.0407-0.0554-0.1846-0.2942-0.11920.613722.9809-97.01866.3531
404.23410.12556.1174-1.00790.0969-0.0671-0.36010.07370.15430.1784-0.02760.3732-0.0945-0.1113-0.0074-0.07920.1114-0.29290.22850.547828.1577-106.93222.0298
50.65640.55860.1891.6235-1.50431.557-0.06120.307-0.1176-0.11560.1877-0.11220.2022-0.1489-0.1265-0.1904-0.0030.04150.0337-0.0140.1162-3.091142.0805-14.6852
60.70030.1471-0.20080.67-0.36750.6819-0.03160.23190.34620.01030.11930.2017-0.1577-0.2344-0.0877-0.1692-0.0003-0.0396-0.02740.11270.23678.661557.0506-16.8968
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A27 - 549
2X-RAY DIFFRACTION2{ B|* }B27 - 549
3X-RAY DIFFRACTION3{ C|* }C1 - 221
4X-RAY DIFFRACTION4{ D|* }D2 - 210
5X-RAY DIFFRACTION5{ H|* }H1 - 221
6X-RAY DIFFRACTION6{ L|* }L2 - 210

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