[English] 日本語
Yorodumi
- PDB-6vc9: TB19 complex -

+
Open data


ID or keywords:

Loading...

-
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 / : / ADP catabolic process / 5'-deoxynucleotidase / 5'-deoxynucleotidase activity / 7-methylguanosine nucleotidase / adenosine biosynthetic process / inhibition of non-skeletal tissue mineralization / Pyrimidine catabolism / AMP catabolic process ...thymidylate 5'-phosphatase / : / ADP catabolic process / 5'-deoxynucleotidase / 5'-deoxynucleotidase activity / 7-methylguanosine nucleotidase / adenosine biosynthetic process / inhibition of non-skeletal tissue mineralization / Pyrimidine catabolism / AMP catabolic process / : / nucleotide catabolic process / IMP-specific 5'-nucleotidase / : / Nicotinate metabolism / Purine catabolism / 5'-nucleotidase / 5'-nucleotidase activity / leukocyte cell-cell adhesion / DNA metabolic process / response to ATP / Purinergic signaling in leishmaniasis infection / ATP metabolic process / calcium ion homeostasis / negative regulation of inflammatory response / external side of plasma membrane / nucleotide binding / cell surface / extracellular exosome / zinc ion binding / nucleoplasm / metal ion binding / identical protein binding / membrane / 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 / Alpha-Beta Complex / Alpha Beta
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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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)

-
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

-
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


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


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


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more