[English] 日本語
Yorodumi
- PDB-6vca: TB38 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vca
TitleTB38 complex
Components
  • 5'-nucleotidase, ecto (CD73), isoform CRA_a
  • TB38 heavy chain
  • TB38 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 / : / IMP-specific 5'-nucleotidase / nucleotide catabolic process / : / 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 / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
5'-nucleotidase / 5'-nucleotidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.73 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 30, 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
A: 5'-nucleotidase, ecto (CD73), isoform CRA_a
B: 5'-nucleotidase, ecto (CD73), isoform CRA_a
C: 5'-nucleotidase, ecto (CD73), isoform CRA_a
D: 5'-nucleotidase, ecto (CD73), isoform CRA_a
H: TB38 heavy chain
L: TB38 light chain
E: TB38 heavy chain
F: TB38 light chain
P: TB38 heavy chain
O: TB38 light chain
K: TB38 heavy chain
J: TB38 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)428,80615
Polymers427,57312
Non-polymers1,2323
Water00
1
A: 5'-nucleotidase, ecto (CD73), isoform CRA_a
B: 5'-nucleotidase, ecto (CD73), isoform CRA_a
H: TB38 heavy chain
L: TB38 light chain
E: TB38 heavy chain
F: TB38 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,7988
Polymers213,7876
Non-polymers1,0112
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-nucleotidase, ecto (CD73), isoform CRA_a
D: 5'-nucleotidase, ecto (CD73), isoform CRA_a
P: TB38 heavy chain
O: TB38 light chain
K: TB38 heavy chain
J: TB38 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,0087
Polymers213,7876
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)236.910, 336.200, 222.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222

-
Components

-
Protein , 1 types, 4 molecules ABCD

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


Mass: 58882.996 Da / Num. of mol.: 4
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

-
Antibody , 2 types, 8 molecules HEPKLFOJ

#2: Antibody
TB38 heavy chain


Mass: 25160.055 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody
TB38 light chain


Mass: 22850.287 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

-
Sugars , 3 types, 3 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.17 Å3/Da / Density % sol: 76.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 1.6M sodium phosphate monobasic monohydrate, 0.4M potassium phosphate dibasic, and 0.1M sodium phosphate citrate pH 5.3

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.73→78.612 Å / Num. obs: 92120 / % possible obs: 99.9 % / Redundancy: 6.586 % / Biso Wilson estimate: 135.164 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.255 / Rrim(I) all: 0.277 / Χ2: 0.939 / Net I/σ(I): 6.12 / Num. measured all: 606702 / Scaling rejects: 75
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
3.73-3.836.6843.5850.5945232676867670.1943.889100
3.83-3.936.7962.8930.7844583656565600.283.13499.9
3.93-4.056.642.1641.0642447639763930.4172.3599.9
4.05-4.176.9181.6861.4943003621962160.5641.824100
4.17-4.316.8111.311.9341155604860420.6971.41999.9
4.31-4.466.6740.9292.7739019584658460.8191.008100
4.46-4.636.320.6833.5535647564556400.8770.74599.9
4.63-4.826.6740.5764.1736271544054350.9240.62599.9
4.82-5.036.4960.4545.0234066524452440.9420.494100
5.03-5.286.8520.4185.5334128498149810.9460.453100
5.28-5.566.770.3695.9532230476147610.9540.4100
5.56-5.96.6060.3356.2929788451045090.960.364100
5.9-6.36.4160.2697.1927221424342430.9680.293100
6.3-6.816.4650.2118.6425602396239600.980.2399.9
6.81-7.466.7260.14711.7124558365236510.9890.16100
7.46-8.346.410.09715.8521282332433200.9950.10699.9
8.34-9.636.0460.06920.1217823294929480.9960.076100
9.63-11.86.1670.05624.4715466251125080.9970.06199.9
11.8-16.685.7390.05224.7211323197619730.9970.05899.8
16.68-78.6125.2160.05425.035858115311230.9960.0697.4

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H2F

4h2f


Resolution: 3.73→40 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.921 / SU B: 46.313 / SU ML: 0.584 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.566
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.264 4586 5 %RANDOM
Rwork0.2238 ---
obs0.2258 87359 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 548.42 Å2 / Biso mean: 180.637 Å2 / Biso min: 59.64 Å2
Baniso -1Baniso -2Baniso -3
1--2.45 Å2-0 Å20 Å2
2---6.17 Å2-0 Å2
3---8.62 Å2
Refinement stepCycle: final / Resolution: 3.73→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27730 0 81 0 27811
Biso mean--228.12 --
Num. residues----3616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01328519
X-RAY DIFFRACTIONr_bond_other_d0.0020.01725937
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.64238782
X-RAY DIFFRACTIONr_angle_other_deg1.1741.57660402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.30453613
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19223.1421308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.926154630
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2515122
X-RAY DIFFRACTIONr_chiral_restr0.0650.23718
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0231967
X-RAY DIFFRACTIONr_gen_planes_other0.0020.025792
LS refinement shellResolution: 3.73→3.826 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 365 -
Rwork0.392 6279 -
all-6644 -
obs--99.18 %

+
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