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- PDB-6vc9: TB19 complex -

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Basic information

Entry
Database: PDB / ID: 6vc9
TitleTB19 complex
Components
  • 5'-nucleotidase, ecto (CD73), isoform CRA_a
  • TB19 heavy chain
  • TB19 light chain
KeywordsIMMUNE SYSTEM / Fab / Enzyme
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 / nucleotide catabolic process / 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 / side of membrane / 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 / metal ion 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
PHOSPHATE ION / 5'-nucleotidase / 5'-nucleotidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsZhou, Y.F. / Lord, D.M.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: A highly potent CD73 biparatopic antibody blocks organization of the enzyme active site through dual mechanisms.
Authors: Stefano, J.E. / Lord, D.M. / Zhou, Y. / Jaworski, J. / Hopke, J. / Travaline, T. / Zhang, N. / Wong, K. / Lennon, A. / He, T. / Bric-Furlong, E. / Cherrie, C. / Magnay, T. / Remy, E. / ...Authors: Stefano, J.E. / Lord, D.M. / Zhou, Y. / Jaworski, J. / Hopke, J. / Travaline, T. / Zhang, N. / Wong, K. / Lennon, A. / He, T. / Bric-Furlong, E. / Cherrie, C. / Magnay, T. / Remy, E. / Brondyk, W. / Qiu, H. / Radosevic, K.
History
DepositionDec 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 6, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: TB19 heavy chain
L: TB19 light chain
A: 5'-nucleotidase, ecto (CD73), isoform CRA_a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,09311
Polymers107,5103
Non-polymers1,5838
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-87 kcal/mol
Surface area31610 Å2
Unit cell
Length a, b, c (Å)118.310, 74.220, 148.326
Angle α, β, γ (deg.)90.000, 93.610, 90.000
Int Tables number5
Space group name H-MI121

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody TB19 heavy chain


Mass: 24919.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody TB19 light chain


Mass: 23707.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 2 molecules A

#3: Protein 5'-nucleotidase, ecto (CD73), isoform CRA_a / / Ecto-5'-nucleotidase


Mass: 58882.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NT5E, hCG_401111 / Production host: Homo sapiens (human)
References: UniProt: Q53Z63, UniProt: P21589*PLUS, 5'-nucleotidase
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 133 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 3.02 Å3/Da / Density % sol: 59.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium potassium phosphate pH 6.2, 35% 5-methyl-2,4-pentanediol, and 2.5% pentaerythritol ethoxylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.25→59.038 Å / Num. obs: 60808 / % possible obs: 99.2 % / Redundancy: 3.851 % / Biso Wilson estimate: 53.014 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.082 / Χ2: 1 / Net I/σ(I): 11.15 / Num. measured all: 234177 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.25-2.313.9020.7292.1317366447244510.8260.84599.5
2.31-2.373.9180.6492.4917102438243650.8490.75399.6
2.37-2.443.9070.5572.8916600427342490.8690.64699.4
2.44-2.523.8940.4593.4416008413641110.9060.53299.4
2.52-2.63.8890.3564.2915589402940090.9460.41299.5
2.6-2.693.8580.2965.0615023391738940.9580.34499.4
2.69-2.793.8480.2236.3114296373837150.9740.25999.4
2.79-2.93.8390.187.4313872364936130.9820.20999
2.9-3.033.8130.1438.8412986345934060.9870.16798.5
3.03-3.183.7650.11110.9812414332432970.9910.12999.2
3.18-3.353.7010.08513.5711559315731230.9930.198.9
3.35-3.563.9280.06616.911716301029830.9960.07799.1
3.56-3.83.9120.05519.8310949281927990.9960.06499.3
3.8-4.113.8730.04922.7510183265026290.9970.05799.2
4.11-4.53.8140.04424.79142242123970.9970.05199
4.5-5.033.7940.04226.088229218721690.9960.04999.2
5.03-5.813.7450.0425.547284196219450.9970.04699.1
5.81-7.123.8760.03926.426356165516400.9980.04599.1
7.12-10.063.8490.03230.214954130012870.9980.03799
10.06-59.0383.5110.02830.7125497497260.9980.03396.9

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H2I

4h2i


Resolution: 2.25→30 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.912 / SU B: 17.457 / SU ML: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.225 / ESU R Free: 0.203
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2785 2017 3.3 %RANDOM
Rwork0.2366 ---
obs0.238 58763 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 156.87 Å2 / Biso mean: 60.829 Å2 / Biso min: 31.1 Å2
Baniso -1Baniso -2Baniso -3
1-5.37 Å20 Å22.87 Å2
2---3.4 Å2-0 Å2
3----2.32 Å2
Refinement stepCycle: final / Resolution: 2.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5814 0 95 126 6035
Biso mean--89.97 56.09 -
Num. residues----749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0136037
X-RAY DIFFRACTIONr_bond_other_d0.0050.0175513
X-RAY DIFFRACTIONr_angle_refined_deg1.7571.6568187
X-RAY DIFFRACTIONr_angle_other_deg1.2511.58612836
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0015746
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.86122.887291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.523151001
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4081531
X-RAY DIFFRACTIONr_chiral_restr0.0770.2799
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026673
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021219
LS refinement shellResolution: 2.25→2.308 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 147 -
Rwork0.323 4273 -
all-4420 -
obs--99.75 %
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)
13.3916-0.7137-0.5265.5079-0.38162.999-0.12630.62620.3908-1.34640.12430.5517-0.1718-0.68870.00190.96220.0894-0.45020.66040.02690.2434-44.941-8.7062-1.3026
21.832-0.17440.10752.3552-0.06416.0645-0.08150.7189-0.1236-1.46140.1209-0.23210.00750.4329-0.03941.2997-0.05710.07210.5387-0.08720.0637-27.0958-20.3115-7.5175
34.8454-0.3754-1.13483.10.17554.160.1696-0.40970.2260.2155-0.0484-0.5126-0.22240.4924-0.12120.1988-0.0143-0.08820.1546-0.0220.1141-20.0566-7.122339.6417
42.30960.02960.18132.58810.39051.47670.07290.1225-0.2894-0.4475-0.0407-0.28530.31520.0103-0.03230.2747-0.00160.01970.16480.00070.0767-25.4836-17.091326.0764
51.0452-0.6902-0.31023.02781.07662.34430.02260.0582-0.0038-0.0997-0.10370.36580.0349-0.26980.08120.1742-0.0065-0.06210.1780.00720.0671-37.0153-5.83331.6475
612.12866.4332-2.9147.5679-0.08421.89260.0376-0.23120.18460.31720.05550.3030.0239-0.1104-0.09310.23230.01250.01510.18790.00140.1563-42.1131-3.187848.5759
71.19220.6454-1.6271.0137-1.3522.5755-0.114-0.0095-0.2181-0.2948-0.2367-0.26030.36460.2190.35070.31260.0237-0.04220.3861-0.02730.1681-7.353-3.116720.5241
82.4353-0.2237-0.96832.6415-0.12753.10620.0240.1932-0.13850.0418-0.15030.37390.0014-0.26290.12630.1848-0.01790.03380.3492-0.04070.0729-12.21910.60737.8531
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H2 - 119
2X-RAY DIFFRACTION2L1 - 108
3X-RAY DIFFRACTION3A27 - 83
4X-RAY DIFFRACTION4A84 - 148
5X-RAY DIFFRACTION5A149 - 290
6X-RAY DIFFRACTION6A291 - 304
7X-RAY DIFFRACTION7A305 - 379
8X-RAY DIFFRACTION8A380 - 549

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